This specification describes CODO, an integrated ontological data model, a formal Ontology for collection and analysis of COVID-19 and related data. The Introduction section further provides the overall scope of the ontology and its usage. It is designed using W3C's RDF technology. 2020-04-27 Biswanath Dutta Debanjali Bain https://creativecommons.org/licenses/by/4.0/ 2022-04-16 2023-03-31 2023-07-11 Indian Statistical Institute CODO: an Ontology for collection and analysis of COviD-19 data https://w3id.org/codo codo https://w3id.org/codo CQ 1: What mutations were discovered in patient p1's genomic testing results? CQ 2: Which patient's test result revealed the N501Y mutation? CQ 3: Which SARS-CoV-2 variant has patient p1 been diagnosed with? CQ 4: Which sequencing method was used in the genome sequencing test for patient p1? CQ 5: Who has been diagnosed as an Omicron patient? CQ 6: Which patients' nasopharyngeal swabs have been collected? CQ 7: A person's genomic sequence report reveals that the spike protein has a del69-70 mutation. Which variants might there be? CQ 8: What are the characteristic mutations found in the test result of a person (p2) diagnosed with the B.1.1.529 variant? CQ 9: What are all the substitution mutations that occurred in B.1.1.7? CQ 10: What mutations are detected in Delta? CQ 11: Where and when was the initial B.1.351 variant discovered? CQ 12: What structural proteins are present in SARS-CoV-2? CQ 13. Which therapeutics are recommended for COVID-19 patients with specific underlying health conditions? CQ 14. What are the potential adverse effects of specific COVID-19 drugs? CQ 15. Identify the drug interactions that may occur with a particular COVID-19 therapeutic. CQ 16. What are the risk factors associated with severe COVID-19 infection? CQ 17. How does the choice of COVID-19 therapeutics vary based on patient characteristics? CQ 18. Which drugs should be avoided due to known interactions with commonly prescribed COVID-19 medications? The spatial or temporal topic of the resource, spatial applicability of the resource, or jurisdiction under which the resource is relevant. coverage Spatial characteristics of the resource, e.g., the geographic coverage of a disease. spatial coverage Temporal characteristics of the resource. temporal coverage has occupation Indicates a unit which is part of this Organization, e.g. a Department within a larger Organization. has unit has department Indicates an Organization of which this Unit is a part, e.g. a Department within a larger Organization. unit of Gender of a person. has gender The Person's occupation. For past professions, use Role for expressing dates. has occupation Nationality of the person. nationality approved by authorized under approves has adverse effect has concommitant has participant has immunocompromised state has present medical history has social history has treatment procedure has underlying health condition is adverse effect of is immunocompromised state of is social history of is underlying health condition of may interacts with may not interacts with not approved by ongoing medication belongs to collected specimen collected test sample "FirstDetectedIn" is a notation used to indicate the country or region where a specific variant of SARS-CoV-2 was first detected or identified. For example, the B.1.1.7 variant of SARS-CoV-2, also known as the UK variant, was first detected in the United Kingdom. The P.1 variant, also known as the Brazilian variant, was first detected in Brazil. This notation is often used in scientific and public health literature to describe and track the spread of different variants of SARS-CoV-2. first detectedIn Origin gene of genome seqeunce test result of genome sequence test result 'hasAssemblyMethod' refers to the method or technique used to assemble a genome sequence. It is typically used in the context of genomic sequencing data, where multiple sequencing reads are assembled together to form a complete genome sequence. The 'hasAssemblyMethod' property can be used to provide information about the specific method used to generate the genome sequence data, such as the software tools, parameters, and quality control measures used in the assembly process. has assembly method Variant has characteristic mutation refers to a specific mutation or set of mutations that is characteristic or unique to a particular variant of a virus, such as SARS-CoV-2. Characteristic mutations can help in identifying and tracking the spread of a variant and assessing its potential impact on disease transmission and severity. For example, the Delta variant of SARS-CoV-2 is characterized by a set of mutations including L452R and P681R, which have been associated with increased transmissibility and vaccine resistance. has characteristic mutation 'hasDescendant' refers to the fact that a SARS-CoV-2 variant may have descendant variants that share similar genetic mutations but with additional differences. This relationship between variants can be represented as a hierarchical tree structure. has descendant 'hasGene' refers to the fact that SARS-CoV-2 is a virus that has a genetic material consisting of RNA, which codes for various proteins, including the spike (S) protein that enables the virus to enter human cells. The genetic material of the virus is organized into multiple genes that perform various functions during the viral life cycle, such as replication, transcription, and translation. has gene hasMutation is a relationship indicating that a particular SARS-CoV-2 variant has a specific mutation(s) in its genome. For example, the Delta variant of SARS-CoV-2 has several mutations in the spike protein, including L452R and T478K. has mutation hasOriginatingLab is a relationship indicating that a specimen was tested for SARS-CoV-2 at a particular laboratory. This relationship can be used to track the testing and diagnostic process for individuals who have been tested for the virus. has originating lab has protein has sample has sampling strategy 'hasSequencingTechnology' refers to the sequencing technology used to sequence the genetic material (RNA or DNA) of the SARS-CoV-2 virus in a specimen. has sequencing technology hasSubmittingLab' implies that a test result entity has a submitting laboratory entity. The submitting laboratory entity refers to the laboratory that submitted the sample for testing and produced the test result. This relationship can be used to track the source of the test result and to help with contact tracing and outbreak investigations. has submitting lab hasVariant is a relationship between a virus and a variant of that virus. It indicates which variant of the virus is present in a particular sample or individual. This relationship is important for tracking the spread and prevalence of different variants over time and across geographic locations. has variant host host of is assembly method of is characteristic mutation of is descendant of is genetically related is mutation of is originating lab of is sampling strategy of is sequencing technology of is submitting lab of is variant of The term "most recent genome sequence test result" is a relationship between a person and their most recent COVID-19 genome sequence test result. It indicates that the person has undergone a COVID-19 genome sequence test, and the result of that test is the most recent one available for that person. This information is important in tracking the spread of the virus and identifying individuals who may need to be isolated or treated to prevent further transmission. most recent genome sequence test result most recent genome sequence test result of mutation occurred in of gene protein of sample of test sample collected at specimen collected at A response component. has response component imposed preventive measure is part of response component is part of weather information a response component is response component of is response of is target of response to Covid-19 target weather condition administered on A property to link between a resource (e.g., vaccination statistics) to its target age group. age group a custodian who is hired to take care of something (property or a person). caretaker a variant causes a disease, like COVID-19. cause disease cleaners Two persons in co-worker relation. co-worker conducted test Indicates a place has a place part. contained in A place is part of another place. contains In case the patient contracted the virus from is known, this property mentions the case number of the "patinet" [source: https://www.isibang.ac.in/~athreya/incovid19/data.html] contracted virus from The Place (typically a City but could be a building, state, etc.) where a Person currently lives currentResident detected disinterred the driver of a flight/ train/ bus/ taxi/ auto rickshaw, etc. driver exposed environmental condition of facility type a person you know well and regard with affection and trust. friend gender gender of given treatment Antibody tests (aka serology tests) is a test that diagonise if you have had a past infection with the virus that causes COVID-19. Your body creates antibodies after getting infected with SARS-CoV-2 or after getting vaccinated against COVID-19. These tests are called “antibody” or “serology” tests. has antibody test The sister of your father or mother; the wife of your uncle. has aunt A male with the same parents as someone else. has brother has child has city has close relationship listed specific comorbidity per case. has comorbid chronic disease has country has cousin The medical clinic where testing/ diagnosis for COVID-19 disease is available. has covid-19 clinical facility has daughter The diagnosis details of a patient. has diagnosis Type of test done (e.g., RT PCR, Anitigen, Antybody) has diagnostic procedure has diagnostic technique has district A person is a domestic help to anothe person. domestic help has exposure to has family member has father has husband has member has mother has neighbor A son of your brother or sister. has nephew A daughter of your brother or sister. has niece has parent something determined in relation to something that includes it (source: WordNet) has part has component has past illness has present illness A generic property to store the relationships between persons. has relationships An associate who shares a room with you. roommate has sibling A female person who has the same parents as another person. has sister has social history has son Two persons in married relationship. spouse has state has province A generic property to connect to the metrics related to the casualities, vaccination, resources, tests, etc. of the disease. has statistics Any sensation or change in bodily function that is experienced by a patient and is associated with a particular disease. has symptom has symptom has test result has travel companion has treatment The brother of your father or mother; the husband of your aunt. has uncle has union territory Viral tests for SARS-CoV-2 tell you if you have an infection at the time of the test. This type of test is called a “viral” test because it looks for viral infection. has viral test A patient has clinical test result. has vital sign has vital sign has wife is age group for is antibody test for is brother of is caretaker of is caused by is comorbid chronic disease of is coverage of is covid-19 clinical facility for is current resident of is diagnosed during is diagnosis for is diagnosis of isDiagnosisFor is diagnostic procedure of is diagnostic technique of is domestic help for is facility type of is given to is location of is member of is nationality of is occupation of is organization type of is origin of a thing part in relation to something. is part of is component of is past illness of is permanent resident of is place of death of is present illness of is sister of is social history of is spatial coverage of is statistics of is status of patient is suspected reason of catching covid-19 for patient is symptom of patient is symptom of patient is temporal coverage of is test result of is travel history of is treatment of is vaccinated with vaccine administered is viral test for is vital sign of A male relative. kinsman A female relative. kins women lift man milk vendor The most recent covid-19 clinical findings of viral signs. most recent vital sign most recent vital sign most recent vital sign of next of The next clinical vital sign of a patient. next vital sign organization type passed virus to patient status The Place (typically a City but could be a building, State, etc.) that a Person has as their permanent home. permanent resident Place of death, e.g., hospital, house, or any other facility place of death previous of The previous clinical vital sign of a patient. previous vital sign A security guard of a person. security guard The suspected reasons of catching covid-19 disease, for example, travel, attending a marriage anniversary, while treating a patient, infected famility member. suspected reasons of catching covid-19 test conducted in A covid-19 patient, or a suspected object who is the cause for sperading the virus to others transit through a place. transit travel history A covid-19 patient, or a suspected object who is the cause for sperading the virus to others travelled from a place. travelled from A covid-19 patient, or a suspected object who is the cause for sperading the virus to others travelled to a place. travelled to vaccination status vaccination status of vegetable vendor description A name for some thing. name Physical address of the item. address The locality in which the street address is, and which is in the region. For example, BHEL Layout. address locality The latitude of a location. For example 37.42242 latitude The longitude of a location. For example -122.08585. longitude The postal code. For example, 560060 postal code The street address. For example, 1st Main, Muthurainagara. street address measures in kg/m2. BMI dose drug code frequency is pregnant medication company name medication name route strenght Cumulative total number of first dose vaccinated till date. cumulative first dose vaccine administered Cumulative total number of second dose vaccinated till date. cumulative second dose vaccine administered DBP Distolic Blood Pressure Blood Pressure (Distolic) Distolic blood pressure SBP Systolic Blood Pressure Blood Pressure (Systolic) Systolic blood pressure The peripheral capillary oxygen saturation, an estimate (in %) of the amount of oxygen in the blood. SpO2 peripheral capillary oxygen saturation(SpO2) The GISAID nomenclature There are many thousands of complete and high-coverage genomes available on the Global Initiative on Sharing Avian Influenza Data (GISAID). GISAID separates the clades of SARS-CoV-2 into S, O, L, V, G, GH, GR, GV, and GRY. The S and L clades were around at the beginning of the pandemic. S continued to be prevalent initially whilst L split into G and V. G further split into GR and GH, and then later GV. GR split into GRY after July 2020. The letters come from the mutations that caused them to branch. The G clade is equivalent to PANGO B.1 lineage, with GR representing PANGO B.1.1 lineage. The S clade is equivalent to PANGO A lineage (the original virus, sequence zero, used as the reference), and the V strand is PANGO B.2 lineage. L is another eaerly lineage. O stands for others that do not match the genetic criteria of the other clades. At the beginning of the pandemic, in January 2020, the L, S and O clades had the majority. These all decreased as the G clade and its descendants increased in proportion over the next year. As of March 2021, the L, S and O clades constitute almost nothing, with the new GRY clade taking up the biggest proportion of the G clades. The GRY clade represents the B.1.1.7 strain that originated in Britain and has since spread across the globe to over 90 countries. GISAIDclade name The International Committee on Taxonomy of Viruses (ICTV) is an organization that is responsible for establishing and maintaining a standardized system for the classification and nomenclature of viruses. The ICTV was established in 1966 and is made up of a group of virologists from around the world who work together to develop and refine the rules and guidelines for virus taxonomy. The organization is affiliated with the International Union of Microbiological Societies (IUMS) and is recognized as the official taxonomic authority for viruses by the World Health Organization (WHO). The ICTV's main role is to develop and maintain a hierarchical classification system for viruses that is based on their genetic and biological characteristics. This system includes several levels of classification, such as family, genus, and species, which are used to group viruses together based on their similarities and differences. The ICTV also establishes the rules and guidelines for the naming of viruses and their variants, which helps to ensure that viruses are identified and classified consistently across different research groups and organizations. Overall, the ICTV plays a critical role in advancing our understanding of viruses and their impact on human health and the environment, by providing a standardized framework for virus taxonomy and nomenclature that is recognized and used by scientists around the world. ICTV name Nextstrain nomenclature Alternatively, Nextstrain divides the SARS-CoV-2 strains into 19A, 19B, 20A, 20B, 20C, 20D, 20E, 20F, 20G, 20H, 20I, 20 J. Phylogenetic trees and geographical/ temporal maps can be viewed for these classifications here. Within these clades, 19B is the original reference strain. 20I/501Y.V1 refers to the B.1.1.7 variant that originated in Britain; 20H/501Y.V2 refers to the B.1.351 strain that originated in South Africa; and 20J/501Y.V3 refers to the P.1 strain that originated and spread from Brazil. NEXTSTRAINclade name PANGOLIN nomenclature The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software team proposed nomenclature for the SARS-CoV-2 clades in a Rambaut et al. (2020) article. This contains the main lineages of A, B, B.1, B.1.1, B.1.177 and B.1.1.7. These lineages divide up further. The generally used names of strains e.g. the B.1.1.7 (British originating) and B.1.351 (South African originating) strain derive from this. A is the original strain used as a reference sequence. PANGO name The SIG Variant classification scheme defines four classes of SARS-CoV-2 variants: Variant Being Monitored (VBM), Alpha (B.1.1.7 and Q lineages) Beta (B.1.351 and descendent lineages) Gamma (P.1 and descendent lineages) Delta (B.1.617.2 and AY lineages) Epsilon (B.1.427 and B.1.429) Eta (B.1.525) Iota (B.1.526) Kappa (B.1.617.1) 1.617.3 Mu (B.1.621, B.1.621.1) Zeta (P.2) Variant of Interest (VOI) Variant of Concern (VOC) Omicron (B.1.1.529, BA.1, BA.1.1, BA.2, BA.3, BA.4 and BA.5 lineages) Variant of High Consequence (VOHC) SIG name WHO has assigned simple, easy to say and remember labels for key variants of SARS-CoV-2, the virus that causes COVID-19, using letters of the Greek alphabet. These labels were chosen after wide consultation and a review of many potential naming systems. WHO convened an expert group of partners from around the world to do so, including experts who are part of existing naming systems, nomenclature and virus taxonomic experts, researchers and national authorities. These labels do not replace existing scientific names (e.g. those assigned by GISAID, Nextstrain and Pango), which convey important scientific information and will continue to be used in research. (https://www.who.int/activities/tracking-SARS-CoV-2-variants) WHO name additional host information additional location information comment e.g. 70x, 1,000x, 10,000x (average) coverage GISAID sample accession id "Date, Location e.g. type of gathering, Family cluster, etc." outbreak detail patient age It refers to a patient's sample/speciman collection accession id. sample accession id sample collection date cloud cover The 'Heat Index' is a measure of how hot weather "feels" to the body. The combination of temperature an humidity produce an "apparent temperature" or the temperature the body "feels". heat index humidity relative humidity Maximum weather temperature maximum temperature max. temperature Minimum weather temperature. minimum temperature min. temperature precipitation temperature (weather) weather temperature wind direction A gust or wind gust is a brief increase in the speed of the wind, usually less than 20 seconds. A sudden increase in wind speed above the average wind speed. wind gust wind speed An acronym. acronym Number of active covid cases. active cases address A patient admitted on a particular day and time. admitted on date of admission An age of a person. age Tthe extent of a 2-dimensional surface enclosed within a boundary (in sq. km.). area The number of beds that are required to accommodate the patients (whether suspected or confirmed COVID-19). bed needed Total number of beds that are occupied. bed occupied number of bed shortage. bed shortage booster dose vaccine administered on The proportion of people diagnosed with a certain disease e.g., (COVID-19), who end up dying of it. A CFR is generally expressed as a percentage case fatality rate case-fatality risk covid-19 cases on a day case on Number of covid cases. cases The country code. Example, "IND" for India. country code Number of cumulative decease patients cumulative decease Number of cumulative discharge cumulative discharge Number of cumulative positive cases cumulative positive cases The cumulative total number of RT-PCR test. cumulative total RT-PCR test The cumulative total number of rapid antigen detection test. cumulative total rapid antigen detection test The total cumulative number of tests. cumulative total tests Cumulative total number of vaccine. cumulative total vaccine administered daily case Daily number of deceased covid-19 patients. daily decease daily death Number of daily discharge patient daily discharge First dose of vaccination administered daily. daily first dose vaccine administered daily 1st dose vaccine administered Total no,. of active cases in Date 2 - total no. of active cases in Date 1 daily increased cases The number of daily RT-PCR test. daily RT-PCR test The number of daily rapid antigen detection test. daily rapid antigen detection test Second dose of vaccination administered daily. daily second dose vaccine administered daily 2nd dose vaccine administered The number of daily total tests. daily total test The daily total vaccine administered. daily total vaccine administered A particular day specified as the time something happens. Value format: 2021-08-11T00:00:00 date date date of designation date when the case began exhibiting symptoms. The initial date of reported symptoms. date of onset of symptom The diagnosis took place on a day. diagnosed on date of confirmation tested positive on The patient ID assigned at the district level (usually a first level of administrative division within a state/ province). district wise patient ID end date event date first dose vaccine administered on geo name had covid test This indiicates the the secondary infections caused, if any. The values are either "yes", "no" and indicate if the patient has caused any [known] secondary infections [source: https://www.isibang.ac.in/~athreya/incovid19/data.html]. has caused any secondary infections has travelled to covid-19 area The rate at which the heart beats; usually measured to obtain a quick evaluation of a person's health. Heart rate height no. of invasive ventilators needed. icu bed needed no. of icu bed shortage. icu bed shortage no. of invasive ventilators needed. invasive ventilator needed last vaccinated on length of hospital stay A generic property to provide the result related to the covid-19 disease casualties, resources, tests, and vaccinations. metrics patient id Number of people migrated after recovery from the covid. people migrated population For humans, population density is the number of people per unit of area, usually quoted per square kilometre or square mile, and which may include or exclude for example areas of water or glaciers. population density The percentage of people who test positive for the virus of those overall who have been tested. positivity rate Number of people recovered from covid. recovered The rate of recovery of COVID-19 patients in percentage. recovery rate The patient released on a day from a covid dedicated facility. date of discharge out date released on Available/ required resource for covid treatment. resource Is the number of breaths a person take per minute. respiratory rate respiratory rate second dose vaccine administered on start date State (province) code. Example, "KL" of Kerala. state code The patient ID assigned at the state/province level. state wise patient ID The body temperature. body temperature The test result date. test result on vaccination The number of people refused to take vacine. vaccine refused The date of vital sign observed. vital sign result on The weight. weight working in healthcare setting working in high risk transmission area A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease. Source: https://www.mohfw.gov.in/pdf/FinalGuidanceonMangaementofCovidcasesversion2.pdf https://www.who.int/news-room/q-a-detail/q-a-coronaviruses Symptom Symptom schema:CovidTestingFacility A Medical clinic where testing for the COVID-19 Coronavirus disease is available. Covid testing facility schema:MedicalClinic A facility, often associated with a hospital or medical school, that is devoted to the specific diagnosis and/or healthcare. Medical clinic schema:MedicalOrganization A medical organization (physical or not), such as hospital, institution or clinic. Medical Organization Vaccine product against severe acute respiratory syndrome coronavirus 2 (medicinal product). COVID-19 vaccine SARS-CoV-2 vaccine owl:Thing An Organization which is recognized in the world at large, in particular in legal jurisdictions, with associated rights and responsibilities. Examples include a corporation, charity, government or church. Formal Organization A group of people who work together. Represents a collection of people organized together into a community or other social, commercial or political structure. The group has some common purpose or reason for existence which goes beyond the set of people belonging to it and can act as an Agent. Organizations are often decomposable into hierarchical structures. Organization An Organization such as a department or support unit which is part of some larger Organization and only has full recognition within the context of that Organization. In particular the unit would not be regarded as a legal entity in its own right. Organizational unit Department foaf:Agent An agent (eg. person, group, software or physical artifact). Agent foaf:Group Group foaf:Person A human being. Person A medical laboratory that offers on-site or off-site diagnostic services. Diagnostic Lab An enumeration of genders. Gender type A profession, may involve prolonged training and/or a formal qualification. Occupation refers to a person's job or profession. It plays a role in determining the level of exposure to various hazards, including infectious diseases, chemicals, physical risks, and other occupational health and safety concerns. Source: Occupational Safety and Health Administration (OSHA). (n.d.). Occupational Safety and Health Administration. Retrieved from: https://www.osha.gov/ Occupation A patient is any person recipient of health care services. Patient Place codo:AdministrativeArea Administrative area codo:AgeFactor Age is a significant factor when considering the risk of developing certain health conditions or experiencing certain health-related events. As individuals age, the likelihood of developing certain diseases or experiencing age-related changes increases. Source: World Health Organization (WHO). (2021). Ageing and Health. Retrieved from: https://www.who.int/news-room/fact-sheets/detail/ageing-and-health Age more than 60 years Age factor Age factor codo:AgeGroup A group people having approximately the same age. The people in a place or organization who were born during a particular period of time, for example all the people aged between 18 and 25. Age Group codo:Anniversary Anniversary codo:BusinessOrganization A business organization. Business organization codo:COVID-19CareFacility Any facility for providing care to COVID-19 patients. source: https://www.mohfw.gov.in/pdf/FinalGuidanceonMangaementofCovidcasesversion2.pdf https://covid19.karnataka.gov.in/new-page/Isolation%20Centers/en COVID-19 care facility codo:COVID-19Diagnosis COVID-19 diagnosis algorithm source: https://covid19.karnataka.gov.in/new-page/GENERAL%20INFORMATION/en The diagnosis as COVID-19 patient. The diagnosied COVID-19 patients are categorised to three different categories/cases based on various clinical test and vital signs. COVID-19 diagnosis COVID-19 diagnosis codo:COVID-19NucleicAcidTesting A Nucleic Acid Amplification Test, or NAAT, is a type of viral diagnostic test for SARS-CoV-2, the virus that causes COVID-19. NAATs detect genetic material (nucleic acids). NAATs for SARS-CoV-2 specifically identify the RNA (ribonucleic acid) sequences that comprise the genetic material of the virus. (Source: https://www.cdc.gov/coronavirus/2019-ncov/lab/naats.html) A nucleic acid test, often called a "NAT", (or nucleic acid amplification test - "NAAT") is a molecular technique used to detect a virus or a bacterium. (Source: https://www.wikidoc.org/index.php/Nucleic_acid_test) Tests for SARS-CoV-2 tell you if you have an infection at the time of the test. This type of test is called a “viral” test because it looks for viral infection. (source: https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/testing.html) https://www.ncbi.nlm.nih.gov/mesh/2052218 COVID-19 nucleic acid testing Nucleic Acid Amplification Test (NAAT) codo:COVID-19SerologicalTesting COVID-19 serology test or Antibody tests is a test that diagonise if you have had a past infection with the virus that causes COVID-19. Your body creates antibodies after getting infected with SARS-CoV-2 or after getting vaccinated against COVID-19. These tests are called “antibody” or “serology” tests. https://www.ncbi.nlm.nih.gov/mesh/2052219 COVID-19 serological testing COVID-19 Antibody Test codo:COVID-19SymtomClassificationByWHO COVID-19 symtom classification by WHO codo:COVID-19Testing COVID-19 (coronavirus disease 2019) is an illness caused by a virus. This virus is a new coronavirus that has spread throughout the world. It is called SARS-CoV-2. There are two types of tests for this virus: (1) A viral test tells you if you have a current infection; (2) An antibody (serology) test might tell you if you had a past infection. Centers for Disease Control and Prevention (MEDLINEPLUS) Diagnosis of COVID-19 by assaying bodily fluids or tissues for the presence of COVID-19 antibodies, SARS-COV-2 antigens or the VIRAL RNA of SARS-COV-2. (MSH) https://www.ncbi.nlm.nih.gov/mesh/2052196 COVID-19 testing codo:COVID-19TestingFacility COVID-19 testing facility codo:COVID-19Treatment A treatment for the COVID-19 disease. COVID-19 treatment codo:COVIDRO_AcidReducer medication or acid-reducing drug, refers to a type of medication that helps decrease the production of stomach acid or neutralize existing acid in the stomach. Acid reducers are commonly used to treat conditions such as gastroesophageal reflux disease (GERD), peptic ulcers, and acid-related indigestion. Source: Mayo Clinic. (2021). Acid Reflux (GER & GERD) in Adults. Retrieved from: https://www.mayoclinic.org/diseases-conditions/gerd/diagnosis-treatment/drc-20361959 Acid reducers work by either blocking the production of acid in the stomach or by directly neutralizing the acid. Common types of acid reducers include proton pump inhibitors (PPIs) and histamine-2 receptor blockers (H2 blockers). PPIs inhibit the enzyme responsible for acid production, while H2 blockers reduce acid production by blocking certain receptors in the stomach. These medications are available both over-the-counter (OTC) and by prescription, depending on the specific drug and dosage. It is important to follow the instructions provided by healthcare professionals or the product label and consult a healthcare provider if symptoms persist or worsen. Acid reducer Antacid codo:COVIDRO_AdverseEffect Adverse effect refers to an undesirable or harmful outcome that occurs as a result of medical treatment, intervention, medication, or exposure to a substance. Adverse effects can range from mild discomfort or inconvenience to severe complications or harm. These effects can include side effects, allergic reactions, complications, or unintended consequences. Sources: U.S. Food and Drug Administration (FDA): Understanding Unapproved Use of Approved Drugs "Off Label" World Health Organization (WHO): Safety Monitoring of Medicinal Products National Institutes of Health (NIH): MedlinePlus - Drug Reactions Adverse effect 18 65 codo:COVIDRO_AgeBetween18To64 AgeBetween18To64 refers to individuals whose age falls within the range of 18 to 64 years. It represents an age group commonly used in demographic categorization, research studies, and various contexts that require age-based criteria. Age between 18 to 64 Adult codo:COVIDRO_AllergyMedication Allergy medication refers to medications that are specifically designed to alleviate the symptoms associated with allergies. These medications aim to reduce or block the body's immune response to allergens, thus providing relief from symptoms such as sneezing, itching, runny nose, congestion, and watery eyes. There are several types of allergy medications available, including: Antihistamines: Antihistamines work by blocking the effects of histamine, a chemical released by the body during an allergic reaction. They help reduce itching, sneezing, and runny nose. Antihistamines can be classified as first-generation (e.g., diphenhydramine) or second-generation (e.g., cetirizine, loratadine) based on their sedative effects. Decongestants: Decongestants help relieve nasal congestion by narrowing blood vessels in the nasal passages. They can be found in both oral and nasal spray forms. However, nasal spray decongestants should be used for a limited duration to avoid rebound congestion. Nasal Corticosteroids: Nasal corticosteroids are available as nasal sprays and work by reducing inflammation in the nasal passages. They provide long-term relief from nasal congestion, runny nose, and sneezing. Mast Cell Stabilizers: Mast cell stabilizers, available as nasal sprays or eye drops, prevent the release of histamine and other inflammatory substances. They are used to prevent allergic reactions and provide relief from symptoms. Combination Medications: Some allergy medications combine antihistamines with decongestants to provide both symptom relief and nasal congestion relief. It's important to note that the choice of allergy medication depends on the specific symptoms, the individual's age, medical history, and the guidance of a healthcare professional. It's recommended to consult with a healthcare provider or allergist for proper diagnosis and treatment of allergies. Sources: American Academy of Allergy, Asthma & Immunology (AAAAI). Allergy Medications Guide. Retrieved from: https://www.aaaai.org/conditions-and-treatments/allergies/allergy-medications Mayo Clinic. Allergy medications: Know your options. Retrieved from: https://www.mayoclinic.org/diseases-conditions/allergies/in-depth/allergy-medications/art-20047403 Allergy medication codo:COVIDRO_Anti-Infective Anti-infectives, also known as antimicrobial agents or antibiotics, are medications used to treat infections caused by bacteria, viruses, fungi, or parasites. These medications work by inhibiting the growth or killing the microorganisms responsible for the infection. Anti-infectives are a vital tool in healthcare for combating infectious diseases and preventing their spread. There are different classes of anti-infective medications, including: Antibiotics: Antibiotics are primarily used to treat bacterial infections. They can target and kill bacteria or inhibit their growth. Examples include penicillins, cephalosporins, macrolides, tetracyclines, and fluoroquinolones. Antivirals: Antiviral medications are used to treat viral infections by targeting specific steps in the viral replication cycle. They can help reduce the severity and duration of viral illnesses such as influenza, herpes, HIV, and hepatitis. Antifungals: Antifungal medications are used to treat fungal infections, such as candidiasis (yeast infections) or dermatophytosis (ringworm). They can be used topically or systemically, depending on the severity and location of the infection. Antiparasitic agents: Antiparasitic medications are used to treat infections caused by parasites, such as malaria, helminth infections, or protozoal infections. These medications can kill or inhibit the growth of parasites. It's important to note that the choice of anti-infective medication depends on the type of infection, the causative microorganism, its susceptibility, and other patient-specific factors. It's crucial to use these medications appropriately, following the prescribed dosage and duration, to ensure effective treatment and minimize the risk of antibiotic resistance. Sources: World Health Organization (WHO). Antimicrobial Resistance. Retrieved from: https://www.who.int/health-topics/antimicrobial-resistance Mayo Clinic. Antibiotics: Uses and resistance. Retrieved from: https://www.mayoclinic.org/healthy-lifestyle/consumer-health/in-depth/antibiotics/art-20045720 Anti-Infective codo:COVIDRO_Anti-SARS-CoV-2AntiviralDrug Antiviral drugs, such as remdesivir, are designed to directly target the replication and spread of the SARS-CoV-2 virus within the body. Anti-SARS-CoV-2 antiviral drug codo:COVIDRO_AntiDiabeticMedication Anti-diabetic medications are a group of medications used to manage and treat diabetes, a chronic metabolic disorder characterized by high blood glucose levels. These medications aim to regulate blood sugar levels and improve insulin sensitivity, either by increasing insulin production or enhancing its effectiveness in the body. Source: American Diabetes Association. (2021). Standards of Medical Care in Diabetes. Diabetes Care, 44(Supplement 1), S111-S124. Retrieved from: https://care.diabetesjournals.org/content/44/Supplement_1/S111 Anti diabetic medication codo:COVIDRO_Antiarrhythmic Antiarrhythmics are medications used to prevent or control abnormal heart rhythms, helping to maintain a regular heartbeat. Antiarrhythmic codo:COVIDRO_Antibiotic Antibiotics are a class of drugs used to treat bacterial infections by inhibiting the growth or killing bacteria. They are not effective against viral infections. Antibiotic codo:COVIDRO_Anticoagulant Anticoagulants are drugs that prevent the formation of blood clots, reducing the risk of thrombosis or embolism. Anticoagulant codo:COVIDRO_Anticonvulsant Anticonvulsants, also known as antiepileptic drugs (AEDs), are medications used to treat and prevent seizures or convulsions. They are commonly prescribed for individuals with epilepsy or other seizure disorders. Anticonvulsants work by stabilizing electrical activity in the brain, preventing abnormal firing of neurons that can lead to seizures. Source: Mayo Clinic. (2021). Anticonvulsants. Retrieved from: https://www.mayoclinic.org/diseases-conditions/epilepsy/in-depth/antiseizure-medications/art-20045022 Anticonvulsants can be used to control various types of seizures, including generalized seizures (affecting both sides of the brain) and focal seizures (originating in a specific area of the brain). These medications may also have mood-stabilizing effects and are sometimes used to manage other conditions such as bipolar disorder and neuropathic pain. The choice of anticonvulsant medication depends on factors such as the type of seizures, the individual's age, overall health, and any potential drug interactions. It is important for individuals taking anticonvulsants to adhere to the prescribed dosage, as abrupt changes in medication or dosing can trigger seizures. Anticonvulsant codo:COVIDRO_Antidepressant An antidepressant is a medication used to treat depression and related mood disorders. It works by balancing neurotransmitters in the brain, such as serotonin, norepinephrine, and dopamine, which are thought to play a role in regulating mood and emotions. Antidepressants are commonly prescribed to improve mood, alleviate symptoms of depression, and promote a sense of well-being. They are available in various classes, including selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), tricyclic antidepressants (TCAs), and others. Antidepressant codo:COVIDRO_Antifungal Antifungals are drugs that are effective in treating fungal infections, preventing the growth and spread of fungi. Antifungal codo:COVIDRO_Antihypertensive Antihypertensives are drugs used to lower high blood pressure and manage hypertension, reducing the risk of related complications. Antihypertensive codo:COVIDRO_Antiparasitic Antiparasitics are medications used to treat parasitic infections by eliminating or controlling parasites in the body. Antiparasitic codo:COVIDRO_Antipsychotic An antipsychotic, also known as a neuroleptic, is a medication primarily used to manage psychosis and psychotic disorders, including schizophrenia and bipolar disorder. Antipsychotics help reduce the intensity of delusions, hallucinations, disorganized thoughts, and other symptoms associated with these conditions. They work by blocking dopamine receptors in the brain, which helps stabilize brain activity and mitigate symptoms. Antipsychotics are classified into first-generation (typical) and second-generation (atypical) based on their specific mechanism of action. Antipsychotic codo:COVIDRO_Antiviral Antivirals are medications used to inhibit the replication and spread of viruses in the body, helping to treat viral infections. Antiviral codo:COVIDRO_Anxiolytic An anxiolytic is a medication prescribed to alleviate anxiety and anxiety-related disorders. Also known as anti-anxiety drugs, anxiolytics work by modulating the activity of neurotransmitters in the brain, such as gamma-aminobutyric acid (GABA), to produce a calming effect and reduce excessive worry or fear. These medications are commonly used to manage generalized anxiety disorder (GAD), panic disorder, social anxiety disorder, and specific phobias. Anxiolytic codo:COVIDRO_Bronchodilator Bronchodilators are medications that relax and widen the airways in the lungs, making it easier to breathe. Bronchodilator codo:COVIDRO_CGRPAntagonist CGRP (Calcitonin Gene-Related Peptide) antagonists are a novel class of medications used to prevent migraines. They work by blocking the activity of CGRP, a neuropeptide believed to play a role in the development of migraines. By inhibiting CGRP, these drugs help reduce the frequency and severity of migraines in individuals prone to recurrent attacks. CGRP antagonist codo:COVIDRO_COVID-19ConvalescentPlasma COVID-19 convalescent plasma refers to a potential treatment option for COVID-19 that involves using plasma obtained from individuals who have recovered from the disease. Convalescent plasma contains antibodies that the recovered individuals developed in response to the SARS-CoV-2 virus. Source: U.S. Food and Drug Administration (FDA). (2021). Recommendations for Investigational COVID-19 Convalescent Plasma. Retrieved from: https://www.fda.gov/vaccines-blood-biologics/investigational-new-drug-ind-or-device-exemption-ide-process-cber/recommendations-investigational-covid-19-convalescent-plasma COVID-19 convalescent plasma codo:COVIDRO_COVID-19Therapeutics COVID-19 therapeutics refer to the medications and treatments used in the management and treatment of COVID-19, the respiratory illness caused by the novel coronavirus (SARS-CoV-2). These therapeutics aim to alleviate symptoms, reduce the severity of the disease, prevent complications, and improve patient outcomes. Source: World Health Organization (WHO). (2021). Therapeutics and COVID-19: living guideline. Retrieved from: https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2022.1 COVID-19 therapeutics codo:COVIDRO_COVID-19TherapeuticsDDI Alteration of the disposition and/or effect of a COVID-19 therapeutic A, owing to the presence of another COVID-19 therapeutic B. COVID-19 therapeutics DDI COVID-19 therapeutics Drug-drug interaction codo:COVIDRO_CalcineurinInhibitor Calcineurin inhibitors are a group of immunosuppressant medications used to prevent organ rejection in transplant recipients. They work by inhibiting calcineurin, an enzyme that activates immune cells responsible for transplant rejection. By suppressing the immune response, calcineurin inhibitors help prevent the body from attacking and rejecting the transplanted organ. Calcineurin inhibitor codo:COVIDRO_CardiovascularMedication Cardiovascular medications are a group of medications used to manage and treat various cardiovascular conditions and diseases. These medications aim to improve heart function, regulate blood pressure, control lipid levels, prevent blood clot formation, and manage other cardiovascular-related conditions. Source: American Heart Association. (2021). Medications Used to Treat Heart Disease. Retrieved from: https://www.heart.org/en/health-topics/heart-attack/treatment-of-a-heart-attack/medications-used-to-treat-heart-disease Cardiovascular medication codo:COVIDRO_CardiovascularSystemDisease Cardiovascular system diseases, also known as heart diseases, refer to a group of conditions that affect the heart and blood vessels. These can include conditions like coronary artery disease, heart failure, arrhythmias, valvular diseases, and congenital heart defects. Cardiovascular system disease codo:COVIDRO_CerebrovascularDisease Cerebrovascular disease refers to a group of conditions that affect the blood vessels supplying the brain. These conditions can include stroke, transient ischemic attack (TIA), and other disorders that disrupt blood flow to the brain, leading to neurological deficits. Cerebrovascular disease codo:COVIDRO_CholesterolAbsorptionInhibitor Cholesterol absorption inhibitors are medications that reduce the absorption of cholesterol from the diet, lowering cholesterol levels. Cholesterol absorption inhibitor 2 codo:COVIDRO_DDI Alteration of the disposition and/or effect of a drug A, owing to the presence of another drug B. DDI Drug-drug interaction codo:COVIDRO_Disability Disability refers to a physical, cognitive, sensory, or mental impairment that substantially limits one or more major life activities of an individual. Disabilities can affect mobility, communication, cognition, and other aspects of a person's life, requiring accommodations and support to facilitate equal participation in society. Disability codo:COVIDRO_DrugInteraction Alteration of the disposition and/or effect of a drug, owing to the presence of another factor such as a second drug, or food. Drug interaction refers to the alteration or modification of the effects of a drug when it is taken in combination with another drug, food, beverage, or substance. It can result in changes in the pharmacokinetics (absorption, distribution, metabolism, and excretion) or pharmacodynamics (interaction at the target site) of the drugs involved, leading to potential therapeutic or adverse effects. Source: U.S. Food and Drug Administration (FDA): Drug Interactions: What You Should Know Drug interaction codo:COVIDRO_EndothelinReceptorAntagonist Endothelin receptor antagonists are medications that block the action of endothelin, used to treat pulmonary arterial hypertension. Endothelin receptor antagonist 65 codo:COVIDRO_GreaterThan64 GreaterThan64 refers to individuals whose age is greater than 64 years. It represents an age group that includes individuals who are 65 years old or older. This age cutoff is commonly used in demographic categorization, healthcare guidelines, and various contexts where age-based criteria are relevant. greater than 64 OlderAdult codo:COVIDRO_HighExposureRiskOccupation High exposure risk occupations are those in which workers are at an increased risk of exposure to infectious diseases, including respiratory illnesses like COVID-19. These occupations involve close contact with the public, working in crowded environments, or providing healthcare or other essential services. Examples of high exposure risk occupations include: Healthcare Workers: Doctors, nurses, paramedics, and other healthcare personnel who directly care for patients in healthcare settings. First Responders: Emergency medical technicians (EMTs), paramedics, firefighters, and police officers who provide immediate emergency assistance. Public Transportation Workers: Bus drivers, subway/train operators, and other transportation employees who interact closely with the public. Essential Retail Workers: Grocery store employees, pharmacy staff, and workers in retail settings providing essential goods and services. Personal Care Workers: Home health aides, nursing home staff, and caregivers who assist individuals with personal care and daily activities. Food Service Workers: Restaurant staff, food delivery personnel, and workers in food processing facilities. High exposure risk occupation true 65 codo:COVIDRO_HighRiskPatient High Risk - Age 65 or older - Underlying health conditions (e.g., chronic respiratory diseases, cardiovascular diseases, diabetes, obesity, immunosuppression) - Immunocompromised state (e.g., organ transplant recipients, individuals undergoing cancer treatment) - Pregnancy - Occupation with high exposure risk (e.g., healthcare workers, essential workers in close contact with the public) - Social history (e.g., alcohol use, smoking habits, inactive etc.) High risk patient codo:COVIDRO_ImmuneModulator Immune modulators are a category of drugs that help activate, boost, or suppress the immune function. In the case of COVID-19 infection, the immune system can become hyperactive which may result in worsening of disease. Immune modulators can help suppress this hyperinflammation.   Immune modulators, such as tocilizumab and baricitinib, target specific components of the immune system to regulate the immune response and mitigate the cytokine storm that can occur in severe COVID-19 cases. Immune modulator codo:COVIDRO_ImmunocompromisedState Immunocompromised condition or weakened immune system Some people are immunocompromised or have a weakened immune system because of a medical condition or a treatment for a condition. This includes people who have cancer and are on chemotherapy, or who have had a solid organ transplant, like a kidney transplant or heart transplant, and are taking medication to keep their transplant. Other people have to use certain types of medicines for a long time, like corticosteroids, that weaken their immune system. One example is called primary immunodeficiency. Being immunocompromised can make you more likely to get very sick from COVID-19 or be sick for a longer period of time. Immunocompromised state codo:COVIDRO_Immunosuppressant Immunosuppressants are a group of medications that suppress or reduce the activity of the immune system. They are used to modulate the body's immune response in certain conditions where an overactive or misguided immune system can lead to harmful effects. Source: National Institute of Allergy and Infectious Diseases (NIAID). (2021). Immunosuppressants. Retrieved from: https://www.niaid.nih.gov/research/immunosuppressants Immunosuppressant codo:COVIDRO_Interferon Interferons are a group of proteins that play a crucial role in the body's immune response to viral infections, including COVID-19. They are part of the innate immune system and act as signaling molecules to stimulate antiviral defenses. Source: World Health Organization (WHO). (2021). Therapeutics and COVID-19: living guideline. Retrieved from: https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2022.1 Interferon 18 codo:COVIDRO_LessThan18 LessThan18 refers to individuals whose age is less than 18 years. It represents an age group that includes children and adolescents who have not yet reached the age of 18. This age cutoff is commonly used in various contexts such as legal frameworks, education systems, and healthcare guidelines that involve age-based distinctions. less than 18 Pediatric codo:COVIDRO_LeukotrieneReceptorAntagonist Leukotriene receptor antagonists are drugs that block the action of leukotrienes, used to manage asthma and allergies. Leukotriene receptor antagonist codo:COVIDRO_Lipid-Modifier Lipid-modifiers, also known as lipid-lowering medications or lipid-lowering agents, are a group of medications used to manage and regulate lipid levels in the body. These medications are primarily used to lower cholesterol and triglyceride levels, which are important factors in cardiovascular health. Source: American Heart Association. (2021). Cholesterol-Lowering Medications. Retrieved from: https://www.heart.org/en/health-topics/cholesterol/prevention-and-treatment-of-high-cholesterol-hyperlipidemia/cholesterol-medications Lipid-Modifier codo:COVIDRO_LowExposureRiskOccupation Low exposure risk occupations are those in which workers have minimal contact with the public or coworkers, reducing their risk of exposure to infectious diseases. These occupations may involve remote work or limited interaction with others. Examples of low exposure risk occupations include: Remote Office Workers: Professionals working from home or in isolated office settings with limited contact with others. Outdoor Workers: Construction workers, landscapers, and agricultural workers who work in open-air environments with minimal interaction with others. Manufacturing Workers: Employees in industrial settings where physical distancing and safety protocols can be implemented effectively. Research Scientists: Researchers working in laboratories or controlled environments with limited exposure to infectious agents. Delivery Drivers: Couriers or drivers who make contactless deliveries with minimal interaction with customers or coworkers. Low exposure risk occupation 18 codo:COVIDRO_LowRiskPatient Low Risk - Age below 18 years - No underlying health conditions - No immunocompromised state - Low exposure risk occupation Low risk patient codo:COVIDRO_MedicalTherapy Medical therapy refers to the use of medications, drugs, or other therapeutic agents to prevent, manage, or treat diseases or medical conditions. Medical therapy can involve the administration of drugs through various routes, including oral, intravenous, topical, or inhalation, among others, to achieve desired therapeutic effects. Medical therapy codo:COVIDRO_Medication Medication refers to a substance or drug that is prescribed or used to prevent, treat, or manage diseases, conditions, or symptoms in humans or animals. Medications are typically formulated in specific pharmaceutical preparations and are administered through various routes such as oral, topical, injection, or inhalation, depending on the medication and its intended use. Medications can be prescribed by healthcare professionals, such as doctors or veterinarians, and are regulated by health authorities to ensure their safety, efficacy, and quality. They play a crucial role in the field of healthcare and are used to alleviate symptoms, control diseases, cure infections, manage chronic conditions, or provide relief from pain or discomfort. It's important to follow the prescribed dosage and instructions for medication use to achieve the desired therapeutic effect and minimize the risk of adverse effects. Medication codo:COVIDRO_MentalHealthCondition A mental health condition refers to a broad range of conditions that affect an individual's emotional, psychological, and social well-being. These conditions can include mood disorders (such as depression or bipolar disorder), anxiety disorders, psychotic disorders, eating disorders, and other mental health-related conditions. Mental health condition codo:COVIDRO_MigraineReducer Migraine reducers are a class of medications specifically designed to alleviate or reduce the symptoms associated with migraines. Migraines are recurring headaches that can cause intense pulsing or throbbing pain, often accompanied by other symptoms such as nausea, vomiting, and sensitivity to light and sound. Source: American Migraine Foundation. (2021). Migraine Treatments. Retrieved from: https://americanmigrainefoundation.org/resource-library/migraine-treatments/ Migraine reducer 18 65 codo:COVIDRO_ModerateRiskPatient Moderate Risk - Age between 18 and 64 years - Some underlying health conditions (e.g., mild respiratory diseases, well-controlled chronic conditions) - No significant immunocompromised state - Social history (e.g., alcohol use, smoking habits, inactive etc.) Moderate risk patient codo:COVIDRO_NeurologicalCondition A neurological condition refers to a disorder or disease that affects the brain, spinal cord, and nerves. Neurological conditions can include neurodegenerative disorders (such as Alzheimer's disease or Parkinson's disease), epilepsy, multiple sclerosis, stroke, migraines, and other disorders that impact the nervous system. Neurological condition codo:COVIDRO_NeuropsychiatricMedication Neuropsychiatric medications are a group of medications used to treat various mental health conditions that affect brain function and behavior. These medications can help manage symptoms associated with conditions such as depression, anxiety disorders, bipolar disorder, schizophrenia, attention-deficit/hyperactivity disorder (ADHD), and other neuropsychiatric disorders. Examples of neuropsychiatric medications include antidepressants, antipsychotics, mood stabilizers, anxiolytics, and stimulants. The choice of medication depends on the specific condition and individual needs, and it is important to work closely with a healthcare professional to determine the most appropriate medication and dosage for effective management. Neuropsychiatric medication codo:COVIDRO_NonsteroidalAnti-inflammatoryDrug NSAIDs are a class of medications that provide pain relief, reduce inflammation, and lower fever, but they are not steroids. Nonsteroidal anti-inflammatory drug NSAID 30 40 codo:COVIDRO_Opioid Opioids are drugs used to relieve severe pain by interacting with opioid receptors in the body's nervous system. Opioid codo:COVIDRO_OrganTransplant Organ transplant is a surgical procedure where a healthy organ or tissue from a donor is surgically implanted into a recipient's body to replace a diseased or non-functioning organ. Organ transplantation is performed to improve the recipient's quality of life and increase their chances of survival. Organ transplant 25 30 codo:COVIDRO_Overweight Overweight (defined as a body mass index (BMI) is 25 kg/m2 or higher, but under 30 kg/m2), obesity (BMI is 30 kg/m2 or higher, but under 40 kg/m2), or severe obesity (BMI is 40 kg/m2 or higher), can make you more likely to get very sick from COVID-19. The risk of severe illness from COVID-19 increases sharply with higher BMI. Overweight codo:COVIDRO_PainReducer Pain reducers, also known as analgesics, are medications used to alleviate or reduce pain sensations. They can be classified into different categories, including nonsteroidal anti-inflammatory drugs (NSAIDs), opioids, and adjuvant analgesics. NSAIDs, such as ibuprofen or naproxen, work by reducing inflammation and relieving pain. Opioids, such as codeine or morphine, act on the central nervous system to block pain signals. Adjuvant analgesics, such as certain antidepressants or anticonvulsants, may be prescribed alongside other pain relievers to enhance their effects. The choice of pain reducer depends on the type and severity of pain, as well as individual factors such as medical history and potential interactions with other medications. Pain reducer codo:COVIDRO_PastMedicalHistory Past medical history codo:COVIDRO_PatientRiskLevel PatientRiskLevel refers to the categorization or classification of a patient based on their level of risk for a particular condition or situation. The risk level is determined by evaluating various factors such as age, underlying health conditions, immunocompromised state, occupation, and social determinants of health. The patient's risk level helps inform healthcare decisions and interventions to ensure appropriate care and management based on their specific risk profile. Patient risk level codo:COVIDRO_PharmaceuticalPreparation PharmaceuticalPreparation refers to a product or formulation created by pharmaceutical companies for medicinal use. It includes a wide range of medications, drugs, vaccines, and other healthcare products that are specifically developed, manufactured, and packaged for administration to patients for the prevention, treatment, or management of diseases, conditions, or symptoms. Pharmaceutical preparations undergo rigorous testing, quality control, and regulatory processes to ensure their safety, efficacy, and proper usage. They can be available in various forms such as tablets, capsules, injections, topical creams, inhalers, and more. Pharmaceutical preparation codo:COVIDRO_PresentMedicalHistory Present medical history codo:COVIDRO_ProstacyclinAnalogue Prostacyclin analogues are drugs that mimic the action of prostacyclin, a natural substance that dilates blood vessels and prevents clot formation. Prostacyclin analogue codo:COVIDRO_PulmonaryHypertensionMedication Pulmonary hypertension medications are used to manage and treat pulmonary hypertension, a condition characterized by high blood pressure in the arteries of the lungs. These medications aim to improve blood flow in the pulmonary arteries, reduce symptoms, and slow down the progression of the disease. Some examples of pulmonary hypertension medications include calcium channel blockers, endothelin receptor antagonists, phosphodiesterase-5 inhibitors, and prostacyclin analogs. The choice of medication depends on the specific type and severity of pulmonary hypertension, as well as individual patient factors, and requires close monitoring and management by a healthcare professional specializing in pulmonary hypertension. Pulmonary hypertension medication codo:COVIDRO_RecommendedTherapeutics Recommended therapeutics for specific medical conditions can vary based on various factors, including the individual's medical history, severity of the condition, and response to treatment. Recommended therapeutics codo:COVIDRO_RecommendedTherapeuticsAnakinra Kineret (anakinra) is authorized for the treatment of COVID-19 in hospitalized adults with pneumonia requiring supplemental oxygen (low- or high-flow oxygen) who are at risk of progressing to severe respiratory failure and likely to have an elevated plasma soluble urokinase plasminogen activator receptor (suPAR). Recommended therapeutics Anakinra codo:COVIDRO_RecommendedTherapeuticsBaricitinib Olumiant (baricitinib) is approved for the treatment of COVID-19 in hospitalized adults requiring supplemental oxygen, non-invasive or invasive mechanical ventilation, or extracorporeal membrane oxygenation (ECMO). Olumiant (baricitinib) is authorized for the treatment of COVID-19 in pediatric patients 2 to less than 18 years of age requiring supplemental oxygen, invasive mechanical ventilation, or extracorporeal membrane oxygen (ECMO). Recommended therapeutics Baricitinib codo:COVIDRO_RecommendedTherapeuticsForCOVID-19 Recommended therapeutics for COVID-19 refer to the medications and treatment approaches that have been suggested or authorized for the management and treatment of COVID-19, the respiratory illness caused by the SARS-CoV-2 virus. These therapeutics are based on scientific evidence, clinical trials, and expert guidelines from reputable health organizations. Source: World Health Organization (WHO). (2021). Therapeutics and COVID-19: living guideline. Retrieved from: https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2022.1 Recommended therapeutics for COVID-19 codo:COVIDRO_RecommendedTherapeuticsHigh-TiterCOVID-19ConvalescentPlasma High-Titer COVID-19 Convalescent Plasma Authorized under an FDA EUA for the treatment of COVID-19 in patients who are immunocompromised or who are receiving immunosuppressive treatment. Recommended therapeutics high-titer COVID-19 convalescent plasma 18 18 codo:COVIDRO_RecommendedTherapeuticsMolnupiravir Molnupiravir Authorized under an FDA EUA for the treatment of mild to moderate COVID-19 in high-risk individuals aged ≥18 years. Recommended therapeutics Molnupiravir 0.07 3 0.07 3 codo:COVIDRO_RecommendedTherapeuticsRemdisivir Remdesivir Approved by the FDA for the treatment of COVID-19 in individuals aged ≥28 days and weighing ≥3 kg. Veklury (Remdesivir) is approved for the treatment of COVID-19 in adults and pediatric patients (28 days of age and older and weighing at least 3 kilograms) who are: hospitalized, or not hospitalized and have mild-to-moderate COVID-19 and are at high risk for progression to severe COVID-19, including hospitalization or death. Veklury (remdesivir) is approved for the treatment of COVID-19 in adults and pediatric patients (28 days of age and older and weighing at least 3 kilograms) with positive results of direct SARS-CoV-2 viral testing, who are: hospitalized, or not hospitalized and have mild-to-moderate COVID-19 and are at high risk for progression to severe COVID-19, including hospitalization or death. Recommended therapeutics Remdisivir 12 40 12 40 codo:COVIDRO_RecommendedTherapeuticsRitonavir-BoostedNirmatrelvir Paxlovid (nirmatrelvir and ritonavir) is approved for the treatment of mild-to-moderate COVID-19 in adults who are at high risk for progression to severe COVID 19, including hospitalization or death. Paxlovid is not approved for use as pre-exposure or post-exposure prophylaxis for prevention of COVID-19. Ritonavir-Boosted Nirmatrelvir (Paxlovid) Authorized under an FDA EUA for the treatment of mild to moderate COVID-19 in high-risk individuals aged ≥12 years and weighing ≥40 kg. Recommended therapeutics Ritonavir-Boosted Nirmatrelvir codo:COVIDRO_RecommendedTherapeuticsTocilizumab Actemra (Tocilizumab) is approved for the treatment of COVID-19 in hospitalized adults who are receiving systemic corticosteroids and require supplemental oxygen, non-invasive or invasive mechanical ventilation, or extracorporeal membrane oxygenation (ECMO). Actemra (tocilizumab) is authorized for the treatment of COVID-19 in hospitalized pediatric patients 2 to less than 18 years of age who are receiving systemic corticosteroids and require supplemental oxygen, non-invasive or invasive mechanical ventilation, or extracorporeal membrane oxygenation (ECMO). Recommended therapeutics Tocilizumab codo:COVIDRO_RecommendedTherapeuticsVilobelimab Gohibic (vilobelimab) is authorized for the treatment of COVID-19 in hospitalized adults when initiated within 48 hours of receiving invasive mechanical ventilation (IMV) or extracorporeal membrane oxygenation (ECMO). Recommended therapeutics Vilobelimab codo:COVIDRO_RespiratoryMedication Respiratory medications are a group of medications used to manage various respiratory conditions, such as asthma, chronic obstructive pulmonary disease (COPD), and other respiratory disorders. These medications aim to improve lung function, reduce inflammation, open airways, and alleviate symptoms like coughing, wheezing, and shortness of breath. There are different types of respiratory medications, including bronchodilators (e.g., beta-agonists, anticholinergics), corticosteroids, leukotriene modifiers, and mucolytics. The choice of respiratory medication depends on the specific respiratory condition, severity of symptoms, and individual patient needs, and it is important to work closely with a healthcare professional to determine the most appropriate medication and treatment plan. Respiratory medication codo:COVIDRO_RespiratoryTherapy Care of patients with deficiencies and abnormalities associated with the cardiopulmonary system. It includes the therapeutic use of medical gases and their administrative apparatus, environmental control systems, humidification, aerosols, ventilatory support, bronchopulmonary drainage and exercise, respiratory rehabilitation, assistance with cardiopulmonary resuscitation, and maintenance of natural, artificial, and mechanical airways. (MSH) Respiratory therapy codo:COVIDRO_SARS-COV-2-targetingMonoclonalAntibody Monoclonal antibody therapies, such as casirivimab/imdevimab and bamlanivimab/etesevimab, are designed to neutralize the virus and help the immune system in fighting the infection. SARS-COV-2-targeting monoclonal antibody 40 codo:COVIDRO_SevereObesity Overweight (defined as a body mass index (BMI) is 25 kg/m2 or higher, but under 30 kg/m2), obesity (BMI is 30 kg/m2 or higher, but under 40 kg/m2), or severe obesity (BMI is 40 kg/m2 or higher), can make you more likely to get very sick from COVID-19. The risk of severe illness from COVID-19 increases sharply with higher BMI. Severe obesity codo:COVIDRO_SocialHistory SCTID: 160476009 Social history codo:COVIDRO_Statin Statins are a class of drugs used to lower cholesterol levels in the blood, reducing the risk of cardiovascular diseases. Statin codo:COVIDRO_SubstanceUseDisorder Substance use disorder (SUD) is a condition characterized by the compulsive and problematic use of substances, including drugs or alcohol, despite negative consequences. SUD can lead to physical and psychological dependence, as well as adverse health, social, and behavioral effects. Substance use disorder codo:COVIDRO_TreatmentProcedure A treatment procedure refers to a specific medical intervention or approach used to manage, cure, or alleviate a disease or medical condition. Treatment procedures can include surgical procedures, medical therapies, rehabilitation techniques, and other interventions tailored to the specific needs of the patient. Treatment procedure codo:COVIDRO_Triptan Triptans are a class of medications used to treat migraines and cluster headaches. They work by narrowing blood vessels in the brain and inhibiting the release of certain substances that trigger migraines, thereby providing relief from migraine symptoms, such as severe headaches, nausea, and sensitivity to light and sound. Triptans are available in various formulations, including oral tablets, nasal sprays, and injections. Triptan codo:COVIDRO_UnderlyingHealthCondition An underlying health condition refers to a pre-existing medical condition or disease that a person has before the onset of another illness or condition. Underlying health conditions can include chronic diseases like diabetes, hypertension, asthma, heart disease, autoimmune disorders, and other conditions that may affect the individual's overall health and increase the risk of complications. Underlying health condition Condition codo:COVIDRO_Vasodilator Vasodilators are medications that relax and widen blood vessels, increasing blood flow and reducing blood pressure. Vasodilator codo:COVIDRO_mTORInhibitor mTOR (mammalian target of rapamycin) inhibitors are a class of immunosuppressive drugs used in organ transplantation and the treatment of certain cancers. They act by inhibiting mTOR, a protein kinase that regulates cell growth, proliferation, and survival. In transplantation, mTOR inhibitors help prevent rejection of the transplanted organ by suppressing the immune response. In cancer treatment, they interfere with cancer cell growth and promote tumor regression. mTOR inhibitor codo:CanisLupusFamiliaris The dog (Canis familiaris or Canis lupus familiaris) is a domesticated descendant of the wolf. Canis Lupus Familiaris codo:CaseStatistics Case statistics refer to numerical data that provides information about the number of cases of a particular disease or health condition within a given population or geographic area. Case statistics are often used to monitor and track the spread of diseases, and can help public health officials identify trends, patterns, and areas of concern. Case statistics may include the total number of cases, the number of new cases reported each day or week, the number of deaths related to the disease, the age, gender, and geographic distribution of cases, and other relevant data points. In the context of infectious diseases, case statistics can be used to calculate important epidemiological indicators such as the incidence rate, prevalence rate, and mortality rate, which can help guide public health interventions and policies. Case statistics are typically collected and reported by public health agencies, healthcare providers, and other organizations involved in disease surveillance and monitoring. They are often published online or through other public channels to increase awareness and understanding of the disease among the general public and health professionals. Sources: Centers for Disease Control and Prevention. (2021). COVID-19 Data Tracker. https://covid.cdc.gov/covid-data-tracker/ World Health Organization. (2021). Epidemiology. https://www.who.int/teams/blueprint/what-we-do/epidemiology Case Statistics codo:City A city. Towns with population of 1,00,000 and above are called cities. City codo:CityWard A ward is a containedIn a city. Calling it CityWard to avoid confusion with a hospital ward. City ward codo:CivicStructure A public structure, such as a town hall or concert hall. Civic structure codo:ClinicalFinding SCTID: 404684003 A Clinical Finding is a CLINICAL INVESTIGATION RESULT ITEM. A Clinical Finding represents the PATIENT DIAGNOSIS and symptoms of the PATIENT. For example: Asthma (disorder) Headache (Finding) Clinical, laboratory or molecular evidence, or absence of evidence of disease. Clinical Finding ClinicalFinding codo:ClinicalLaboratoryTechniques Techniques used to carry out clinical investigative procedures in the diagnosis and therapy of disease. (MSH) Mesh Clinical laboratory techniques codo:CloseContact Close contact, a suspected cause for catching COVID-19. Close contact codo:Cluster A Cluster is a group of patients with the same disease who are grouped by one or more properties that are considered critical to an analysis of how the disease has spread. Note that clusters are NOT disjoint, so a cluster can be an instance of a TimeCluster and other clusters. Cluster codo:CommunicableDisease A communicable disease, also known as an infectious disease, is a disease caused by a pathogen (such as bacteria, viruses, fungi, or parasites) that can be transmitted from one person to another, either directly or indirectly. a disease that can be communicated from one person to another. Communicable disease codo:Condition A state of being, such as a state of health. (NCI) An observable finding or state that persists over time and tends to require intervention or management, and, therefore, distinguished from an Observation made at a point in time; may exist before an Observation of the Condition is made or after interventions to manage the Condition are undertaken. Examples: equipment repair status, device recall status, a health risk, a financial risk, public health risk, pregnancy, health maintenance, chronic illness (HL7V3.0) Condition codo:ConfirmedCase A. A person with a positive Nucleic Acid Amplification Test (NAAT) including RT-PCR or any other similar test approved by ICMR. B. A person with a positive SARS-CoV-2 Antigen-RDT AND meeting either the probable case definition or suspect criteria OR C. An asymptomatic person with a positive SARS-CoV-2 Antigen-RDT who is a contact of a probable or confirmed case. Confirmed case codo:ContactCluster A cluster defined by contact with certain individuals. Note that to some extent all clusters are contact clusters so this class is used only for those clusters that specifically mention contact with individuals (or lack of knowledge about such contact) rather than geographic, time, or disease data. Contact cluster codo:ContactWithHealthWorkers Contact with health workers, suspect cause of COVID-19 Contact with health workers codo:ContagiousDisease Contagious diseases are infectious diseases that can be easily transmitted from one person to another through direct contact, respiratory droplets, or other modes of transmission. an Infectious disease that is readily spread (that is, communicated) by transmission of a pathogen through contact (direct or indirect) with an infected person. any disease easily transmitted by contact. Contagious disease codo:Continent one of the large landmasses of the earth; "there are seven continents"; "pioneers had to cross the continent on foot" Continent codo:CoronavirusDisease A disease caused by coronavirus. [Source: WHO. Naming the coronavirus disease (COVID-19) and the virus that causes it. https://www.who.int/] Coronavirus disease, also known as COVID-19, is a respiratory illness caused by the SARS-CoV-2 virus. It emerged in late 2019 and has since become a global pandemic. COVID-19 can cause a range of symptoms, from mild to severe, and can lead to complications, particularly in individuals with underlying health conditions or older age groups. Coronavirus disease codo:Country A country. Country codo:CountryWiseCaseStatistics Country-wise case statistics refer to the numerical data that provides information about the number of cases of a particular disease or health condition within a specific country. These statistics are often used to monitor and track the spread of diseases, assess the disease burden, and identify trends, patterns, and areas of concern within a particular country. Country-wise case statistics typically include the total number of cases, the number of new cases reported each day or week, the number of deaths related to the disease, the age, gender, and geographic distribution of cases, and other relevant data points. These statistics can help public health officials and policymakers make informed decisions regarding disease control and prevention efforts. In the context of infectious diseases, country-wise case statistics can be used to calculate important epidemiological indicators such as the incidence rate, prevalence rate, and mortality rate. These indicators can help guide public health interventions and policies at the national and local levels. Country-wise case statistics are typically collected and reported by national health agencies and other organizations involved in disease surveillance and monitoring. They are often published online or through other public channels to increase awareness and understanding of the disease among the general public and health professionals. Sources: World Health Organization. (2021). COVID-19 Weekly Epidemiological Update. https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---14-december-2021 European Centre for Disease Prevention and Control. (2021). COVID-19 Situation Update Worldwide. https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases Country Wise Case Statistics codo:CountryWiseResourceStatistics Country-wise resource statistics refer to numerical data that provides information about the availability and use of natural and human resources within a specific country. These statistics can include data on natural resources such as land, water, minerals, and forests, as well as human resources such as the labor force and skilled workers. Country wise resource statistics codo:CountryWiseTestStatistics Country-wise COVID test statistics refer to numerical data that provides information about the number of COVID-19 tests conducted and the number of positive cases detected within a specific country. These statistics are used to monitor and track the spread of the virus, assess the effectiveness of testing programs and interventions, and inform public health policies and decision-making. Country-wise COVID test statistics typically include the total number of tests conducted, the number of new tests conducted each day or week, the number of positive cases detected, the positivity rate (percentage of positive cases among total tests conducted), and other relevant data points such as age, gender, and geographical location of the tested population. These statistics are usually collected and reported by government agencies and public health organizations, and they are often published online or through other public channels to increase awareness and understanding of the COVID-19 situation in a particular country. Country wise test statistics codo:CountryWiseVaccinationStatistics Country wise vaccination statistics true codo:DiagnosedWithCOVID-19 A person diagnosed With COVID-19. Diagnosed with COVID-19 codo:Diagnosis identification a disease from its symptoms. Diagnosis Diagnosis codo:DiagnosisType This models the manner in which a diagnosis was discovered. E.g., via a pregnancy test, screening for a suspected disease, tests done before surgery, etc. Disgnosis type codo:DiagnosticLab Diagnostic laboratory is an institution (or facility within an institution) which is equipped with apparatus and reagents for the performance of diagnostic tests for human infections. Diagnostic lab codo:DiagnosticTechniquesAndProcedures A type of method or test used to help diagnose a disease or condition. Imaging tests and tests to measure blood pressure, pulse, and temperature are examples of diagnostic techniques. Methods, procedures, and tests performed to diagnose disease, disordered function, or disability. (MSH) https://www.ncbi.nlm.nih.gov/mesh/68019937 Diagnostic techniques and procedures codo:Disease A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown. (MSH) Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function. (NCI) Conceptually broad term referring primarily to physical illness. Also used when particular disorders are not specified. Use a more specific term if possible. For general discussions of health impairment consider also the term HEALTH. (PSY) Disease refers to a disorder or abnormal condition of the body or mind that impairs normal functioning. Diseases can be caused by various factors, including pathogens (such as bacteria, viruses, or parasites), genetic mutations, environmental factors, lifestyle choices, or a combination of these factors. MESH:D004194 SCTID: 64572001 an impairment of health or a condition of abnormal functioning. Disease codo:DiseaseCluster Patients clustered by diseases that made them susceptible to the virus Disease cluster codo:Disorder A disorder refers to an abnormal condition or disruption in the regular functioning of an organ, system, or overall body. It can involve physical, mental, or physiological dysregulation that affects normal processes and may lead to symptoms or impairments. In medicine, a disturbance of normal functioning of the mind or body. Disorders may be caused by genetic factors, disease, or trauma a functional abnormality or disturbance Disorder codo:District An adminidtrative area spanning regions or counties, several municipalities, subdivisions of municipalities, school district, or political district. District codo:DistrictWiseCaseStatistics District-wise case statistics refer to numerical data that provides information about the number of cases of a particular disease or health condition within a specific district or administrative region. These statistics are often used to monitor and track the spread of diseases, assess the disease burden, and identify trends, patterns, and areas of concern within a particular district or region. District-wise case statistics typically include the total number of cases, the number of new cases reported each day or week, the number of deaths related to the disease, the age, gender, and geographic distribution of cases, and other relevant data points. These statistics can help public health officials and policymakers make informed decisions regarding disease control and prevention efforts at the local level. In the context of infectious diseases, district-wise case statistics can be used to calculate important epidemiological indicators such as the incidence rate, prevalence rate, and mortality rate. These indicators can help guide public health interventions and policies at the local level, such as targeted testing and contact tracing efforts. District-wise case statistics are typically collected and reported by local health authorities and other organizations involved in disease surveillance and monitoring. They are often published online or through other public channels to increase awareness and understanding of the disease among the general public and local health professionals. Sources: Centers for Disease Control and Prevention. (2021). COVID-19 Data Tracker: Cases in the U.S. https://covid.cdc.gov/covid-data-tracker/#cases_casesinlast7days Government of India. (2021). Ministry of Health and Family Welfare: District-Wise COVID-19 Cases. https://www.mohfw.gov.in/ District Wise Case Statistics codo:DistrictWiseResourceStatistics District-wise resource statistics refer to numerical data that provides information about the availability and use of resources within a specific district or administrative region. District wise resource statistics codo:DistrictWiseTestStatistics District-wise COVID test statistics refer to numerical data that provides information about the number of COVID-19 tests conducted and the number of positive cases detected within a specific district or administrative region. These statistics are used to monitor and track the spread of the virus, assess the effectiveness of testing programs and interventions, and inform public health policies and decision-making at the local level. District-wise COVID test statistics typically include the total number of tests conducted, the number of new tests conducted each day or week, the number of positive cases detected, the positivity rate (percentage of positive cases among total tests conducted), and other relevant data points such as age, gender, and geographical location of the tested population. These statistics are usually collected and reported by local health departments and other relevant authorities, and they are often published online or through other public channels to increase awareness and understanding of the COVID-19 situation in a particular district or administrative region. District wise test statistics codo:DistrictWiseVaccinationStatistics District wise vaccination statistics codo:Doctor A licensed medical doctor. SCTID: 158965000 Doctor codo:Edema swelling from excessive accumulation of serous fluid in tissue Edema Dropsy Hydrops Oedema codo:EdemaDueToInfection Edema due to infection Edema due to infection codo:Environment The external elements and conditions which surround, influence, and affect the life and development of an organism or population. Environment codo:EnvironmentalCondition Environmental conditions, or the quality and state of the environment, are an inescapable part of daily life that can impact health. Environmental condition codo:ExposureToCOVID-19 The suspected causes of catching COVID-19. The causes can be a close contact, co-passenger, from some gathering, like aniversary, congregation, infected family member, etc. This class is to indicate the suspected reasons for contacting the virus for a patient. For example, for person 1, the suspected reason of catching the disease is his coworker person 2. The individuals of this class and its subclasses not necessary to be an individual person always, like, reason can be a gathering, job place, etc. Exposure to COVID-19 codo:ExposureViaCongregation Exposure via congregation codo:Finding That which is discovered by direct observation or measurement of an organism attribute or condition, including the clinical history of the patient. The history of the presence of a disease is a 'Finding' and is distinguished from the disease itself. Finding codo:Gathering Mass gathering, a suspected cause for catching COVID-19. Gathering codo:GeneralBodyStateFinding SCTID: 82832008 SNOMED CT General body state finding codo:GeneralFindingOfObservationOfPatient SCTID: 118222006 SNOMED CT General finding of observation of patient General condition of patient General observation of patient codo:GeographicCluster Patients clustered by the geographic region where they contracted the infection Geographic cluster codo:GeographicRegion Geographic regions such as the Middle East, North America, etc. For the cluster class Geographic region codo:GovernmentOrganization A governmental organization. Government organization codo:HealthCareProfessional Healthcare Professional means any member of the medical, dental, pharmacy or nursing professions or any other person who in the course of his or her professional activities may prescribe, recommend, purchase, supply, or administer a pharmaceutical product. Healthcare Professional or “HCP” shall mean any person licensed to prescribe Company products, as well as anyone working for a person licensed to prescribe a Company Therapeutic Product and in a position to influence a purchasing decision, including without limitation physicians and other providers (e.g., nurses, pharmacists), dialysis providers, other office personnel. Health care professional codo:Hospital Institutions with an organized medical staff which provide medical care to patients. Hospital codo:Host An organism that nourishes and supports another but does not benefit by the association; recipient of transplanted tissue or organ from a donor. (NCI) Any cellular component of a host cell. The host is an organism in which another organism, for instance a parasite or symbiont, spends part or all of its life cycle and from which it obtains nourishment and/or protection. [ISBN:0198506732] (GO) Host Sample host codo:Human Members of the species Homo sapiens. Human codo:Immunization The act of making immune (especially by inoculation). Immunization Immunisation codo:Immunogen any substance or organism that provokes an immune response (produces immunity) when introduced into the body. Immunogen Immunizing agent codo:InfectedBrother Infected brother codo:InfectedCo-Passenger InfectedCo-Passenger codo:InfectedCo-worker Infected Co-worker codo:InfectedCousin Infected cousin codo:InfectedDaughter Infected daughter codo:InfectedDomesticHelp Infected domestic help codo:InfectedFamilyMember Infected family member codo:InfectedFather Infected father codo:InfectedMother Infected mother codo:InfectedNeighbor Infected neighbor codo:InfectedNephew Infected nephew codo:InfectedNiece Infected niece codo:InfectedRoomMate Infected room mate codo:InfectedSister Infected sister codo:InfectedSon Infected son codo:InfectedSpouse Infected spouse codo:InfectedViaHealthcareWork Infected via healthcare work codo:InfectedViaJob Infected via job codo:InfectedViaPoliceWork Infected via police work codo:InfectedViaSupportStaff Support staff such as lift man, cleaners, security personnel, peons etc. Infected via support staff codo:InfectiousDisease Infectious diseases are caused by pathogenic microorganisms (such as bacteria, viruses, fungi, or parasites) that can invade and multiply within the body. These diseases can range from mild to severe and can be transmitted through various means, including person-to-person contact, contaminated surfaces, vectors (such as mosquitoes), or airborne droplets. a disease transmitted only by a specific kind of contact. Infectious disease codo:LaboratoryTestFinding Results of fluid and tissue tests such as urine and blood analysis. (OMS) Laboratory test finding Laboratory test observation Laboratory test result The outcome of a laboratory test. (NCI) codo:Landform A landform or physical feature. Landform elements include mountains, plains, lakes, rivers, seascape and oceanic waterbody interface features such as bays, peninsulas, seas and so forth, including sub-aqueous terrain features such as submersed mountain ranges, volcanoes, and the great ocean basins. Landform codo:LessCommonSymptom Less common symptom codo:LocalBusiness A local business physically situated in a place, and can be a branch of an organization, e.g., a restaurant, a local branch of a chain of restaurant, a branch of a bank, a club, etc. Local business codo:Man A man. Man codo:ManisJavanica The Sunda pangolin (Manis javanica), also known as the Malayan or Javan pangolin, is a species of pangolin. Manis Javanica codo:MedicalClinic A medical establishment run by a group of medical specialists. Medical clinic Clinic codo:MedicalOrganization A medical organization, such as hospital, diagnostic lab, clinic, etc. Medical organization 94 94 codo:MildAndVeryMildCOVID-19 Cases presenting with fever and/or upper respiratory tract illness (Influenza Like Illness, ILI). Mild and very mild COVID-19 Mild and very mild COVID-19 90 93 30 90 93 30 codo:ModerateCOVID-19 Moderate COVID-19 Symptoms: in additon to symptoms in mild cases, check for pneumonia which may not be apparent. Respiratory Rate (RR): >=30 SpO2: 90-93% on room air Moderate COVID-19 Moderate COVID-19 codo:MostCommonSymptom Most common symptom codo:Nurse A health professional skilled in caring for young children or the sick (usually under the supervision of a physician). SCTID: 106292003 Nurse Professional nurse codo:ObservationalFinding The act of measuring, questioning, evaluating, or otherwise observing a patient or a specimen from a patient in healthcare; the act of making a clinical judgment. The result, answer, judgment, or knowledge gained from the act of observing a patient or a specimen from a patient in healthcare Observational finding ClinicalObservation FindingOfObservation codo:Occupation A profession, may involve prolonged training and/or a formal qualification. the principal activity in your life that you do to earn money; "he's not in my line of business" Occupation codo:OrganizationType Organization type in terms of Public or Private. Organization type codo:OtherLessCommonSymptom Other less common symptom codo:OtherSymptom Other symptom codo:PathologicalState A pathological state refers to an abnormal or diseased condition of the body. It can involve structural or functional changes that deviate from the normal physiological state and may be associated with symptoms or manifestations of illness. An abnormal or physiologically unbalanced state of the body. illness, malady, sickness, unwellness. impairment of normal physiological function affecting part or all of an organism. Pathological state codo:Patient A patient is any recipient of health care services that are performed by healthcare professionals. Patients are categorised into three groups based on the following guidelines. Source: https://www.mohfw.gov.in/pdf/FinalGuidanceonMangaementofCovidcasesversion2.pdf SCTID: 116154003 Patient codo:Place Entities that have a somewhat fixed, physical extension. Place codo:PolicePerson a person whose job is to enforce laws, investigate crimes, and make arrests a member of the police. Police person codo:Pregnancy Pregnancy refers to the period during which a woman carries a developing fetus in her uterus. It is a natural process that typically lasts around 40 weeks. Pregnancy involves significant physiological and hormonal changes in the woman's body to support the growth and development of the fetus. Pregnancy Pregnancy codo:ProbableCase A. A patient who meets clinical criteria above AND is a contact of a probable or confirmed case, or linked to a COVID-19 cluster B. A suspect case with chest imaging showing findings suggestive of COVID-19 disease C. A person with recent onset of anosmia(loss of smell) or ageusia(loss of taste) in the absence of any other identified cause. D. Death, not otherwise explained, in an adult with respiratory distress preceding death AND was a contact of a probable or confirmed case or linked to a COVID-19 cluster. Probable case codo:PublicTransport Public transport refers to a system of transportation that is available to the general public and is usually operated by government or private organizations. It includes various modes of transport such as buses, trains, trams, and subways that are designed to move large numbers of people efficiently and affordably. Public transport is often used as an alternative to private transport, such as cars or motorcycles, and can help reduce traffic congestion, air pollution, and greenhouse gas emissions. It also provides access to mobility for people who do not own their own vehicles, such as those who are too young or too old to drive or who cannot afford to own a car. Public transport systems vary widely in terms of their coverage, frequency, and quality. In some cities, public transport is widely used and well-developed, while in others it may be limited or unreliable. Factors that can influence the quality and accessibility of public transport include government funding, infrastructure, and population density. Sources: World Bank. (2022). Public Transport. https://urbantranscripts.org/glossary/public-transport/ United Nations. (2014). Sustainable Urban Transport. https://sustainabledevelopment.un.org/content/documents/3392Sustainable%20Urban%20Transport.pdf Public transport codo:RadiologincFinding Imaging results obtained through a radiology procedure. ... (NCI) Radiologic finding Radiologic test result codo:Recommendation TreatmentRecommendation refers to a healthcare provider's advice or suggestion on a specific course of treatment for a patient's medical condition. It is based on the patient's medical history, symptoms, test results, and other relevant factors. A TreatmentRecommendation may include the type of medication, dosage, duration of treatment, and any necessary lifestyle modifications or follow-up appointments. It may also take into consideration the patient's preferences and goals for treatment. TreatmentRecommendations can come from a variety of healthcare professionals, including primary care physicians, specialists, and therapists. They play an important role in helping patients make informed decisions about their health and guiding them towards the best possible outcomes. Sources: American Medical Association. (2022). Treatment recommendations. https://www.ama-assn.org/delivering-care/patient-support-advocacy/treatment-recommendations National Center for Advancing Translational Sciences. (2022). Clinical Recommendations. https://www.ncbi.nlm.nih.gov/books/NBK553051/ Recommendation codo:ResourceStatistics Resource statistics refer to the numerical data that provides information about the availability and use of resources in a particular area or sector. These statistics can include data on natural resources, such as water, minerals, and forests, as well as human resources, such as the labor force and skilled workers. Resource statistics are used to monitor and evaluate the availability and sustainability of resources, as well as to identify areas where additional resources may be needed. They are often used by policymakers, researchers, and business leaders to make informed decisions about resource allocation, development, and management. For example, in the context of natural resources, resource statistics can help identify areas where there is a high demand for resources and where resource depletion may be a concern. This information can then be used to guide conservation efforts and resource management policies. In the context of human resources, resource statistics can provide insight into the size and skill level of the workforce in a particular area or sector. This information can be used to identify areas where additional training or education may be needed to meet the demands of the job market. Resource statistics are typically collected and reported by government agencies, research institutions, and other organizations involved in resource management and development. They are often published online or through other public channels to increase awareness and understanding of resource availability and use. Sources: United Nations. (2021). Sustainable Development Goal 12: Ensure sustainable consumption and production patterns. https://www.un.org/sustainabledevelopment/sustainable-consumption-production/ U.S. Department of Energy. (2021). Energy Resource Statistics. https://www.energy.gov/data/energy-resource-statistics Resource statistics codo:RespiratorySymptom Respiratory symptoms are common symptoms of lung or heart conditions, emotions, or injury. The medical terms for respiratory symptoms include dyspnea (difficulty breathing), tachypnea (rapid breathing), hypopnea (shallow breathing), hyperpnea (deep breathing), and apnea (absence of breathing). https://www.ncbi.nlm.nih.gov/mesh/68012818 Respiratory symptom codo:RespiratoryTractDisease Respiratory tract diseases refer to a variety of conditions that affect the airways, lungs, and respiratory system. These can include infections like pneumonia, bronchitis, asthma, chronic obstructive pulmonary disease (COPD), and other disorders that impact breathing and respiratory function. Respiratory tract disease codo:RespiratoryTractDiseases Respiratory diseases include asthma, chronic obstructive pulmonary disease (COPD), pulmonary fibrosis, pneumonia, and lung cancer. Also called lung disorder and pulmonary disease. https://www.ncbi.nlm.nih.gov/mesh/68012140 Respiratory Tract Diseases codo:RhinolophusAffinis Rhinolophus Affinis codo:RiskFactor A risk factor is any attribute, characteristic, or exposure that increases the likelihood of developing a particular disease or experiencing a certain health condition. Risk factors can be divided into two main categories: modifiable and non-modifiable. Source: Centers for Disease Control and Prevention (CDC). (2021). Understand Your Risk for Heart Disease. Retrieved from: https://www.cdc.gov/heartdisease/risk_factors.htm An aspect of personal behavior or lifestyle, environmental exposure, inborn or inherited characteristic, which, based on epidemiological evidence, is known to be associated with a health-related condition considered important to prevent. (MSH) Any aspect of an individual's life, behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a disease, condition or injury. (NCI) Personal behaviors or lifestyles, environmental effects, or inborn characteristics which epidemiological evidence has shown to be associated with the increased rate of a behavior or health-related condition. (PSY) SCTID: 80943009 Risk factor RiskFactor codo:SecondaryContact Secondary contact codo:SecurityGuard A security guard (also known as a security inspector, security officer, or protective agent) is a person employed by a government or private party to protect the employing party's assets (property, people, equipment, money, etc.) from a variety of hazards (such as criminal activity, waste, damaged property, unsafe worker behavior, etc.) by enforcing preventative measures. Security guards do this by maintaining a high-visibility presence to deter illegal and inappropriate actions, looking (either directly, through patrols, or indirectly, by monitoring alarm systems or video surveillance cameras) for signs of crime or other hazards (such as a fire), taking action to minimize damage (such as warning and escorting trespassers off property), and reporting any incidents to their clients and emergency services (such as the police or paramedics), as appropriate. Security guard 60 90 90 60 90 90 codo:SevereCOVID-19 Severe COVID-19 symptoms: any of the following symptoms - signs of severe pneumonia, acute respiratory distress syndrome (ARDS), septic shock, multi-organ dysfunction syndrome, or pneumonia with cyanosis, severe retraction of chest, lethargy, SpO2: < 90% on room air Severe COVID-19 Severe COVID-19 codo:SevereCOVID-19Symptom Severe COVID-19 symptom codo:Sign In medicine, a sign is something found during a physical exam or from a laboratory test that shows that a person may have a condition or disease. Some examples of signs are fever, swelling, skin rash, high blood pressure, and high blood glucose. Sign codo:SkinManifestation Dermatologic disorders attendant upon non-dermatologic disease or injury. (MSH) https://www.ncbi.nlm.nih.gov/mesh/68012877 SkinManifestation codo:SocialHistory Past events that occurred between individuals and/or their communities. (NCI) The Social History Observations define the patient's occupational, personal (e.g. lifestyle), social, and environmental history and health risk factors, as well as administrative data such as marital status, race, ethnicity and religious affiliation. (HL7V3.0) Social history codo:State A state or province of a country. State Province codo:StateWiseCaseStatistics State-wise case statistics refer to numerical data that provides information about the number of cases of a particular disease or health condition within a specific state or province. These statistics are often used to monitor and track the spread of diseases, assess the disease burden, and identify trends, patterns, and areas of concern within a particular state or province. State-wise case statistics typically include the total number of cases, the number of new cases reported each day or week, the number of deaths related to the disease, the age, gender, and geographic distribution of cases, and other relevant data points. These statistics can help public health officials and policymakers make informed decisions regarding disease control and prevention efforts at the state or provincial level. In the context of infectious diseases, state-wise case statistics can be used to calculate important epidemiological indicators such as the incidence rate, prevalence rate, and mortality rate. These indicators can help guide public health interventions and policies at the state or provincial level, such as targeted testing and contact tracing efforts. State-wise case statistics are typically collected and reported by state health departments and other organizations involved in disease surveillance and monitoring. They are often published online or through other public channels to increase awareness and understanding of the disease among the general public and state health professionals. Sources: Centers for Disease Control and Prevention. (2021). COVID-19 Data Tracker: Cases in the U.S. https://covid.cdc.gov/covid-data-tracker/#cases_casesinlast7days Government of India. (2021). Ministry of Health and Family Welfare: State-Wise COVID-19 Cases. https://www.mohfw.gov.in/ State Wise Case Statistics codo:StateWiseResourceStatistics State-wise resource statistics refer to numerical data that provides information about the availability and use of resources within a specific state or province. State wise resource statistics codo:StateWiseTestStatistics State-wise COVID test statistics refer to numerical data that provides information about the number of COVID-19 tests conducted and the number of positive cases detected within a specific state or province. These statistics are used to monitor and track the spread of the virus, assess the effectiveness of testing programs and interventions, and inform public health policies and decision-making at the state level. State-wise COVID test statistics typically include the total number of tests conducted, the number of new tests conducted each day or week, the number of positive cases detected, the positivity rate (percentage of positive cases among total tests conducted), and other relevant data points such as age, gender, and geographical location of the tested population. These statistics are usually collected and reported by state health departments and other relevant authorities, and they are often published online or through other public channels to increase awareness and understanding of the COVID-19 situation in a particular state or province. State wise test statistics codo:StateWiseVaccinationStatistics State wise vaccination statistics codo:Statistics Statistics based on each day. Statistics of COVID-19 cases which includes the deatils of active, recovered, deaths, and also the resources (e.g., beds required, shortage of beds, ICUs) on daily basis. Statistics codo:Status The current status of a patient, for example: recovered, hospitalized, deceased. Status 3 codo:SuspectCase A. A person who meets the clinical AND epidemiological criteria: Clinical Criteria: • Acute onset of fever AND cough; OR • Acute onset of ANY THREE OR MORE of the following signs or symptoms: Fever, cough, general weakness/ fatigue, headache, myalgia, sore throat, coryza, dyspnoea, anorexia/nausea/vomiting, diarrhoea, altered mental status. AND Epidemiological Criteria: • Residing or working in an area with high risk of transmission of virus: closed residential settings, humanitarian settings such as camp and camp-like settings for displaced persons; any time within the 14 days prior to symptom onset; or • Residing or travel to an area with community transmission any time within the 14 days prior to symptom onset; or • Working in any healthcare setting, including with in health facilities or within the community; any time within the 14 days prior of symptom onset. B. A patient with severe acute respiratory illness: (SARI: acute respiratory infection with history of fever or measured fever of ≥38 C°; and cough; with onset within the last 10 days; and requires hospitalization). Suspect case codo:SymptomaticTreatment Symptomatic treatment, supportive care, or supportive therapy is any medical therapy of a disease that only affects its symptoms, not the underlying cause. Symptomatic treatment Supportive care Supportive therapy codo:TestResult A test result. The result of a laboratory, radiologic, or other clinical test performed to determine the presence, absence, or degree of a condition. (NCI) Test result codo:TestStatistics test statistics refer to numerical data that provides information about the number of COVID-19 tests conducted, the number of positive cases detected, and other relevant data points related to COVID-19 testing. These statistics are used to monitor and track the spread of the virus and to assess the effectiveness of testing programs and interventions. Test statistics codo:TimeCluster A cluster defined by some event (including lack of knowledge) at a certain date. Note that clusters are not disjoint, so a cluster can be an instance of a TimeCluster and other clusters. Time cluster codo:Town Places which satisfy the following criteria are called towns: (i) A minimum population of 5,000; (ii) At least 75 per cent of the male main working population engaged in non-agricultural pursuits; and (iii) A density of population of at least 400 persons per sq. km. (i.e. 1000 per sq. Mile). Town codo:Transport Transport refers to the movement of people, goods, or materials from one location to another. It is an essential aspect of modern society and plays a critical role in facilitating economic and social activity. There are various modes of transport available, including road, rail, air, water, and pipelines. Each mode has its advantages and disadvantages and is suitable for different types of transport needs. Sources: United Nations. (2022). Sustainable Development Goal 9: Industry, Innovation and Infrastructure. https://www.un.org/sustainabledevelopment/infrastructure-industrialization/ Transport codo:TravelHistory A record of the places that a person has been. (NCI) Travel history codo:Treatment care by procedures or applications that are intended to relieve illness or injury. Treatment Treatment codo:UnionTerritory A union territory ('Federally administered territory/province') is a type of administrative division in the Republic of India. Unlike the states of India, which have their own governments, union territories are federal territories governed directly by the Central Government of India. Union Territory false codo:UntestedForCOVID-19 Untested for COVID-19 Person who has not gone through COVID-19 Testing Untested for COVID-19 false codo:UrgentlyNeedsCOVID-19Test Urgently needs COVID-19 test Urgently needs COVID-19 test codo:VGO_AccessoryProteinOfSARS-CoV-2 Accessory protein of SARS-CoV-2 codo:VGO_ActiveSurveillance Active surveillance is a method of disease surveillance that involves actively seeking out cases of a particular disease or condition by conducting regular monitoring and testing of individuals or populations at risk. Active surveillance codo:VGO_AlveolarLavageFluidSwabSpecimen Alveolar lavage fluid swab specimen is another term for bronchoalveolar lavage fluid swab specimen. It is a sample of fluid collected from the alveoli, which are the small air sacs in the lungs where gas exchange occurs. Alveolar lavage fluid swab specimen codo:VGO_AnalSwabSpecimen An anal swab specimen is a specific type of swab specimen that is collected from the anus or rectum. It is commonly used to diagnose infections such as sexually transmitted infections and gastrointestinal infections. The collection of an anal swab specimen involves the insertion of a swab into the anus or rectum to collect a sample of cells or secretions, which is then sent to a laboratory for analysis. The procedure is typically quick and relatively painless, but may be uncomfortable for some individuals. Anal swab specimen codo:VGO_AnteriorNareSwabSpecimen An anterior nare swab specimen is a sample of secretions collected from the inside of the nostril, specifically the anterior nares, which are the openings of the nasal cavity. The collection of an anterior nare swab specimen involves the insertion of a swab into the nostril to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used for COVID-19 testing and other respiratory infections. Anterior nare swab specimen codo:VGO_AssemblyMethod Assembly can be performed using an assembly software of your preference. Some examples of de novo assembly tools include: SPAdes, Edena, ABySS. Similarly, reference based assembly (using one or more reference genomes) can be conducted using a tool such as SMALT or Bowtie AssemblyMethod codo:VGO_BaselineSurveillance Baseline surveillance involves collecting data on a particular disease or condition before an intervention or change occurs, in order to establish a baseline for future comparisons. Baseline surveillance codo:VGO_Betacoronavirus Betacoronavirus (β-CoVs or Beta-CoVs) is one of four genera (Alpha-, Beta-, Gamma-, and Delta-) of coronaviruses. Member viruses are enveloped, positive-strand RNA viruses that infect mammals (of which humans are part). The natural reservoir for betacoronaviruses are bats and rodents. Rodents are the reservoir for the subgenus Embecovirus, while bats are the reservoir for the other subgenera. The coronavirus genera are each composed of varying viral lineages with the betacoronavirus genus containing four such lineages: A, B, C, D. In older literature, this genus is also known as "group 2 coronaviruses". The genus is in the subfamily Orthocoronavirinae in the family Coronaviridae, of the order Nidovirales. Betacoronavirus codo:VGO_Biospecimen Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions. Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products. Biospecimen Bio-Specimen Biological Sample codo:VGO_BloodSpecimen Blood specimen collection is performed routinely to obtain blood for laboratory testing. Blood can be obtained from venous access devices and sometimes by fingerstick. Blood is most frequently obtained via a peripheral vein puncture (venipuncture). Blood specimen codo:VGO_BodilyFluidSpecimen Body fluids, defined as specimens other than plasma, serum, or urine, include cerebrospinal fluid (CSF), dialysate, postsurgical drain fluid, wound fluid, and other fluids often obtained using ultrasound-guided aspiration (such as pancreatic, pericardial, and pleural fluid). Bodily fluid specimen codo:VGO_BronchialLavageFluidSwabSpecimen Bronchial lavage fluid swab specimen is a sample of fluid collected from the bronchial tubes using a bronchoscope, a thin, flexible tube with a light and camera on the end. During a bronchial lavage procedure, a small amount of sterile saline is instilled into the bronchial tubes and then aspirated back out, collecting a sample of fluid and cells for diagnostic testing and analysis. Bronchial lavage fluid swab specimen codo:VGO_BronchoAlveolarLavageFluidSwabSpecimen Bronchoalveolar lavage (BAL) fluid swab specimen is a sample of fluid collected from the lungs using a bronchoscope, a thin, flexible tube with a light and camera on the end. During a BAL procedure, a small amount of sterile saline is instilled into the lungs and then aspirated back out, collecting a sample of fluid and cells from the lower respiratory tract. This fluid can then be used for diagnostic testing and analysis, such as to detect infections or evaluate lung function. Broncho alveolar lavage fluid swab specimen codo:VGO_CLCGenomicsWorkbench12 CLC Genomics Workbench provides advanced NGS workflows for de novo assembly of whole genomes and transcriptomes, resequencing analysis (WGS, WES and targeted panel support), variant calling, RNA-seq, ChIP-seq and DNA methylation (bisulfite sequencing analysis). CLC Genomics Workbench 12 codo:VGO_CellSpecimen A cell specimen is a sample of cells collected from an individual for medical testing or diagnosis. It is a non-invasive or minimally invasive diagnostic tool used to detect and diagnose various medical conditions such as cancer, infections, and autoimmune diseases. Cell specimens can be collected from different parts of the body, such as the skin, blood, urine, or respiratory tract, using various techniques, including swabs, aspirates, and washes. The collected specimen is then analyzed in a laboratory to detect any abnormalities or signs of disease in the cells. Cell specimens are an important tool for clinicians and researchers to better understand the nature of diseases and develop effective treatments. Cell specimen codo:VGO_ClinicalTrial A clinical trial is a research study that tests the safety and effectiveness of new medical treatments, interventions, or devices in humans. Clinical trial codo:VGO_Cornidovirineae Cornidovirineae is a subfamily of viruses within the family Coronaviridae, which includes the well-known severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the more recent coronavirus disease 2019 (COVID-19) causing virus, SARS-CoV-2. These viruses are enveloped, single-stranded RNA viruses that have a genome size ranging from 26 to 32 kilobases. They have a characteristic club-like spike protein on their surface that binds to host cells and enables the virus to enter and infect them. This subfamily was first proposed in 2020 based on genetic analysis and distinctive features of the virus. The name "Cornidovirineae" is derived from the Latin word "cornu" meaning horn, which refers to the spike-like projections on the virus's surface. Source: Gorbalenya, A. E., Baker, S. C., Baric, R. S., de Groot, R. J., Drosten, C., Gulyaeva, A. A., ... & Ziebuhr, J. (2020). Severe acute respiratory syndrome-related coronavirus: The species and its viruses–a statement of the Coronavirus Study Group. BioRxiv, 1-15. Cornidovirineae codo:VGO_Coronaviridae Coronaviridae is a family of enveloped, positive-strand RNA viruses which infect amphibians, birds, and mammals. The group includes the subfamilies Letovirinae and Orthocoronavirinae; the members of the latter are known as coronaviruses. Coronaviridae codo:VGO_DeepCoughSputumSwabSpecimen A deep cough sputum swab specimen is a sample of mucus or phlegm coughed up from the lower respiratory tract. It is collected by having the individual cough deeply and expectorate sputum into a sterile container or by inducing sputum using a nebulizer. This specimen can then be analyzed in a laboratory to diagnose respiratory infections such as bronchitis or pneumonia. Deep cough sputum swab specimen codo:VGO_DeletionMutation Deletion mutation is a type of genetic mutation caused by the loss of one or more nucleotides from a DNA sequence, which can result in the loss of genetic information or the production of a non-functional protein. Deletion mutation codo:VGO_DiagnosedWithSARS-CoV-2VariantAlpha Patient Diagnosed with SARS-CoV-2 variant Alpha: This variant was first identified in the United Kingdom in December 2020. It has multiple mutations in the spike protein, including the N501Y mutation, which is thought to increase the virus's infectivity Diagnosed with SARS-CoV-2 variant Alpha codo:VGO_DiagnosedWithSARS-CoV-2VariantBeta Patient Diagnosed with SARS-CoV-2 variant Beta: This is another variant of SARS-CoV-2 that was first identified in South Africa in December 2020. It has several mutations in the spike protein, including the E484K mutation, which is thought to affect the virus's ability to be neutralized by antibodies. . Diagnosed with SARS-CoV-2 variant Beta codo:VGO_DiagnosedWithSARS-CoV-2VariantDelta Patient Diagnosed with SARS-CoV-2 variant Delta: This is a highly transmissible variant of SARS-CoV-2 that was first identified in India in December 2020. It has multiple mutations in the spike protein of the virus, including the L452R and P681R mutations, which are believed to increase its infectivity and ability to evade the immune system. Diagnosed with SARS-CoV-2 variant Delta codo:VGO_DiagnosedWithSARS-CoV-2VariantDeltaPlus Patient Diagnosed with SARS-CoV-2 variant Delta plus: The Delta plus variant, also known as AY.1, is a sublineage of the Delta variant. It has been classified as a Variant of Concern (VOC) by the Indian government due to its potential for increased transmissibility and potential impacts on vaccine effectiveness. However, the WHO has not yet classified it as a VOC. Diagnosed with SARS-CoV-2 variant Delta plus codo:VGO_DiagnosedWithSARS-CoV-2VariantEpsilon Patient Diagnosed with SARS-CoV-2 variant Epsilon: The Epsilon variant, also known as B.1.429, is a SARS-CoV-2 variant that was first identified in California, USA in July 2020. It has been classified as a Variant of Interest (VOI) by the World Health Organization (WHO) due to its potential for increased transmissibility and potential impacts on vaccine effectiveness. Diagnosed with SARS-CoV-2 variant Epsilon codo:VGO_DiagnosedWithSARS-CoV-2VariantEta Patient Diagnosed with SARS-CoV-2 variant Eta: The Eta variant, also known as B.1.525, is a SARS-CoV-2 variant that was first identified in Nigeria in December 2020. It has been classified as a Variant of Concern (VOC) by the World Health Organization (WHO) due to its potential for increased transmissibility and potential impacts on vaccine effectiveness. Diagnosed with SARS-CoV-2 variant Eta codo:VGO_DiagnosedWithSARS-CoV-2VariantGamma Patient Diagnosed with SARS-CoV-2 variant Gamma: The Gamma variant, also known as P.1, is a SARS-CoV-2 variant that was first identified in Brazil in December 2020. It has been classified as a Variant of Concern (VOC) by the World Health Organization (WHO) due to its increased transmissibility and potential impacts on vaccine effectiveness. Diagnosed with SARS-CoV-2 variant Gamma codo:VGO_DiagnosedWithSARS-CoV-2VariantKappa Patient Diagnosed with SARS-CoV-2 variant Kappa: The Kappa variant, also known as B.1.617.1, is a SARS-CoV-2 variant that was first identified in India in December 2020. It has been classified as a Variant of Interest (VOI) by the World Health Organization (WHO) due to its potential for increased transmissibility and potential impacts on vaccine effectiveness. Diagnosed with SARS-CoV-2 variant Kappa codo:VGO_DiagnosedWithSARS-CoV-2VariantLambda Patient Diagnosed with SARS-CoV-2 variant Lambda: The Lambda variant, also known as C.37, is a SARS-CoV-2 variant that was first identified in Peru in December 2020. It has been classified as a Variant of Interest (VOI) by the World Health Organization (WHO) due to its potential for increased transmissibility, resistance to antibodies, and potential impacts on vaccine effectiveness. Diagnosed with SARS-CoV-2 variant Lambda codo:VGO_DiagnosedWithSARS-CoV-2VariantLota Patient Diagnosed with SARS-CoV-2 variant Lota: This refers to a patient who has been diagnosed with a variant of the SARS-CoV-2 virus that has been given the name Lota. This variant has mutations in the spike protein of the virus that could potentially affect its ability to be recognized by the immune system or to be neutralized by certain antibodies. Diagnosed with SARS-CoV-2 variant Lota codo:VGO_DiagnosedWithSARS-CoV-2VariantMu Patient Diagnosed with SARS-CoV-2 variant Mu: This refers to a patient who has been diagnosed with the Mu variant of the SARS-CoV-2 virus, which was first identified in Colombia in January 2021. The Mu variant has mutations in the spike protein of the virus that could potentially affect its ability to be recognized by the immune system or to be neutralized by certain antibodies. Diagnosed with SARS-CoV-2 variant Mu codo:VGO_DiagnosedWithSARS-CoV-2VariantOmicron Patient Diagnosed with SARS-CoV-2 variant Omicron: This refers to a patient who has been diagnosed with the Omicron variant of the SARS-CoV-2 virus, which was first identified in South Africa in November 2021. The Omicron variant has a large number of mutations in the spike protein of the virus, which could potentially affect its transmissibility, severity of illness, or ability to be recognized by the immune system. Diagnosed with SARS-CoV-2 variant Omicron codo:VGO_DiagnosedWithSARS-CoV-2VariantOmicronStealth Patient Diagnosed with SARS-CoV-2 variant OmicronStealth: This refers to a patient who has been diagnosed with a variant of the SARS-CoV-2 virus that has been given the name OmicronStealth. It is not a currently recognized variant of the virus, and therefore it is unclear what specific mutations or characteristics it may have. Diagnosed with SARS-CoV-2 variant OmicronStealth codo:VGO_DiagnosedWithSARS-CoV-2VariantTheta Patient Diagnosed with SARS-CoV-2 variant Theta: This refers to a patient who has been diagnosed with a variant of the SARS-CoV-2 virus that has been given the name Theta. This variant has mutations in the spike protein of the virus that could potentially affect its ability to be recognized by the immune system or to be neutralized by certain antibodies. Diagnosed with SARS-CoV-2 variant Theta codo:VGO_DiagnosedWithSARS-CoV-2VariantWHO Diagnosed with SARS-CoV-2 variant (WHO) codo:VGO_DiagnosedWithSARS-CoV-2VariantZeta When a patient is diagnosed with SARS-CoV-2 variant Zeta, it means that the viral strain of the patient has been identified as the Zeta variant of the SARS-CoV-2 virus. The Zeta variant is also known as the P.2 variant, and it was first identified in Brazil in April 2020. It has several mutations in the spike protein, which is the part of the virus that allows it to infect human cells. These mutations could potentially affect the transmissibility and severity of the disease, as well as the effectiveness of some treatments and vaccines. However, more research is needed to fully understand the implications of the Zeta variant. Diagnosed with SARS-CoV-2 variant Zeta codo:VGO_EnvironmentalSpecimen An environmental specimen refers to a sample taken from the non-living elements in the environment, such as air, water, or soil, to identify the presence of microorganisms, toxins, or other pollutants. Environmental specimen codo:VGO_FaecalSpecimen Faecal specimen is a sample of the client's feces. It can be analyzed for the presence of blood; mucus; fat; microbes, such as bacteria and parasites; or other abnormal findings. Faecal specimen codo:VGO_FrameshiftMutation Frameshift mutation is a type of genetic mutation caused by the insertion or deletion of one or more nucleotides in a DNA sequence, which alters the reading frame of the sequence and may result in the production of a non-functional protein. Frameshift mutation codo:VGO_Gene A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms. (MSH) A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. (NCI) Biological macromolecule which is a segment of a DNA molecule and which consists of sets of nucleotide pairs organized into regions of coding, noncoding and regulatory sequences. (FMA) Description:A DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology (HL7V3.0) Segment of the genome that codes for a functional product. (CSP) Gene codo:VGO_GeneOfCoronaVirus Gene of coronavirus codo:VGO_GeneOfSARS-CoV-2 Gene of SARS-CoV-2 codo:VGO_Geneious10.2.4 Geneious Prime is packed with essential tools for molecular cloning, genomics and sequence analysis. Industry-leading algorithms, powerful analyses and superior visualizations allow you to gain critical insights while exploring your data. Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly. Geneious 10.2.4 codo:VGO_GeneticFinding A laboratory test result that indicates the status of a molecular genetic or cytogenetic event in a pathologic process. (NCI) GeneticFinding Genetic observation Genome Sequencing result codo:VGO_GenomeSequencingLab Sequencing Laboratory offers research accredited, scalable sequencing and expert genomic analysis. Genome sequencing lab codo:VGO_Illumina Illumina: Illumina is a popular brand of DNA sequencing technology that uses fluorescent tags to identify the order of nucleotides in a DNA sample. Illumina codo:VGO_InsertionMutation Insertion mutation is a type of genetic mutation caused by the addition of one or more nucleotides to a DNA sequence, which can also result in the production of a non-functional protein. Insertion mutation codo:VGO_IonTorrent Ion Torrent: Ion Torrent is a brand of DNA sequencing technology that uses semiconductor-based technology to detect changes in pH during DNA synthesis, allowing for the identification of the order of nucleotides in a DNA sample. Ion Torrent codo:VGO_LowerRespiratoryTractSwabSpecimen A lower respiratory tract swab specimen is a sample of secretions collected from the lower respiratory tract, which includes the lungs and bronchial tubes. The collection of a lower respiratory tract swab specimen involves the insertion of a swab through the nose or mouth into the lower respiratory tract to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used to diagnose infections such as pneumonia, tuberculosis, and COVID-19. Lower respiratory tract swab specimen codo:VGO_MEGAHITv1.2.9 MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly MEGAHIT v1.2.9 codo:VGO_MERS-CoVVariant MERS-CoV (Middle East Respiratory Syndrome Coronavirus) variants are different strains or types of the MERS-CoV virus that have developed through mutations in the virus's genetic material. Like other viruses, MERS-CoV can undergo mutations when it replicates, which can result in the emergence of new variants. These variants may have differences in their genetic makeup that can affect how easily they spread, their severity, and how well vaccines or treatments work against them. There have been several MERS-CoV variants identified since the virus was first discovered in 2012. For example, a variant of the virus that emerged in South Korea in 2015 was found to have several genetic differences from earlier strains, and was associated with a large outbreak of MERS in that country. It's important to monitor and track MERS-CoV variants to understand how they might impact the spread and severity of the disease, and to inform public health efforts to control and prevent its transmission. There are several MERS-CoV variants that have been identified by researchers. Here are some examples of MERS-CoV variants: EMC/2012 strain: This was the first strain of MERS-CoV to be identified in 2012 in Saudi Arabia. HuNoV-EMC/2012 strain: This variant was identified in 2012 in the Netherlands, and was associated with a case of MERS in a Qatari patient who had traveled to the country. Jeddah/1 strain: This variant was identified in 2014 in Saudi Arabia, and was associated with a large outbreak of MERS in the country. Korea outbreak strain: This variant was identified in 2015 in South Korea, and was associated with a large outbreak of MERS in that country. Al-Hasa_4_2013 strain: This variant was identified in 2013 in Saudi Arabia, and was associated with a cluster of MERS cases in the Al-Hasa region. MERS-CoV variant codo:VGO_Mid-TurbinateSwabSpecimen A mid-turbinate swab specimen is a sample of secretions collected from the middle of the nasal cavity, specifically from the area of the turbinates, which are bony structures that help warm and humidify air as it enters the nose. The collection of a mid-turbinate swab specimen involves the insertion of a swab into the nostril and up to the mid-turbinate region to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used for COVID-19 testing. Mid-turbinate swab specimen codo:VGO_Mutation A mutation is a change in the genetic material of an organism, which can result in altered characteristics or traits. Mutations can occur spontaneously or be induced by various factors, such as exposure to radiation, chemicals, or viruses. Mutation codo:VGO_NasopharyngealAndOropharyngealSwabSpecimen A nasopharyngeal and oropharyngeal swab specimen is a sample of secretions collected from both the nasal cavity and the pharynx. The collection of a nasopharyngeal and oropharyngeal swab specimen involves the insertion of a swab into the nostril and down the back of the throat to collect a sample of secretions from both areas, which is then sent to a laboratory for analysis. It is commonly used for respiratory infection testing, including COVID-19. Is a nasopharyngeal and oropharyngeal swab Nasopharyngeal and oropharyngeal swab specimen codo:VGO_NasopharyngealSwabSpecimen A nasopharyngeal swab specimen is a sample of secretions collected from the nasal cavity, specifically the nasopharynx, which is the upper part of the pharynx behind the nasal cavity. The collection of a nasopharyngeal swab specimen involves the insertion of a swab into the nostril and up to the nasopharynx to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used for respiratory infection testing, including COVID-19. Nasopharyngeal swab specimen codo:VGO_Nidovirales Nidovirales is an order of enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, molluscs, and helminths. The order includes the families Coronaviridae, Arteriviridae, Roniviridae, and Mesoniviridae. Nidovirales codo:VGO_NonStructuralProteinOfSARS-CoV-2 Non-sructural protein of SARS-CoV-2 codo:VGO_OrganSpecimen An organ specimen is a sample of tissue or cells collected from a specific organ of the body for medical testing or diagnosis. The collection of an organ specimen is usually done during a surgical procedure, biopsy, or autopsy, and is commonly used to diagnose various medical conditions such as cancer, infections, or autoimmune diseases. Organ specimens can be analyzed using various techniques, such as histopathology, molecular testing, and imaging, to identify any abnormalities or signs of disease in the organ tissue. Organ specimens are an essential tool for clinicians and researchers to better understand the nature of diseases and develop effective treatments. Organ specimen codo:VGO_OropharyngealSwabSpecimen An oropharyngeal swab specimen is a sample of secretions collected from the pharynx, specifically the oropharynx, which is the middle part of the pharynx behind the mouth. The collection of an oropharyngeal swab specimen involves the insertion of a swab into the mouth and down the back of the throat to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used for respiratory infection testing, including COVID-19. Oropharyngeal swab specimen codo:VGO_Orthocoronavirinae Coronaviruses constitute the subfamily Orthocoronavirinae, in the family Coronaviridae, order Nidovirales and realm Riboviria. Orthocoronavirinae codo:VGO_OutbreakInvestigation An outbreak investigation is a systematic process of identifying the cause and scope of an outbreak of a particular disease or condition in a specific population or geographic area. Outbreak investigation codo:VGO_OxfordNanoporeTechnology Oxford Nanopore technology: Oxford Nanopore technology is a brand of DNA sequencing technology that uses nanopores to detect changes in electrical current as nucleotides pass through, allowing for the identification of the order of nucleotides in a DNA sample. Oxford Nanopore technology codo:VGO_PharyngealSwabSpecimen A pharyngeal swab specimen is a sample of secretions collected from the back of the throat, specifically from the pharynx. The collection of a pharyngeal swab specimen involves the insertion of a swab into the mouth and down the back of the throat to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used for respiratory infection testing, including COVID-19. Pharyngeal swab specimen codo:VGO_PlasmaSpecimen Plasma is obtained from blood that has been mixed with an anticoagulant in the collection tube and has, therefore, not clotted. This mixed blood may then be centrifuged, yielding plasma, which contains albumin, globulin, and fibrinogen. Plasma specimen codo:VGO_PointMutation Point mutation is a type of genetic mutation caused by the substitution of one nucleotide for another in a DNA sequence, which can alter the genetic code and may result in the production of a different protein or no protein at all. Point mutation codo:VGO_Protein Protein codo:VGO_ProteinOfSARS-CoV-2 A protein is a biomolecule composed of amino acid chains folded into a three-dimensional structure. Proteins play critical roles in biological processes, including catalyzing chemical reactions, regulating gene expression, and serving as structural components of cells and tissues. SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. It has multiple proteins, including the spike protein, envelope protein, membrane protein, and nucleocapsid protein, which are classified as structural proteins. The non-structural proteins include NSP1 to NSP16, and the accessory proteins include ORF1a, ORF1b, ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10. These proteins play a variety of roles in the virus's life cycle and pathogenicity. Protein of SARS-CoV-2 codo:VGO_ResearchSpecificPopulation A research specific population refers to a group of individuals who share certain characteristics and are being studied in a research project or study. Research specific population codo:VGO_Riboviria Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses (with either RNA or DNA genomes) that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA (ribonucleic acid) from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA (deoxyribonucleic acid) from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins. Riboviria codo:VGO_S-GeneDropout S-Gene dropout refers to the absence of a specific gene, the S gene, in some COVID-19 variants. This can impact the results of certain diagnostic tests, particularly those that target the S gene. S-Gene dropout codo:VGO_SARS-CoV-2Variant SARS-CoV-2 variant refers to a strain of the SARS-CoV-2 virus, which is the virus responsible for causing coronavirus disease 2019 (COVID-19). As the virus spreads from person to person, it undergoes mutations or changes in its genetic code, leading to the emergence of different strains or variants. Some SARS-CoV-2 variants are classified as variants of concern (VOCs) or variants of interest (VOIs) based on their potential impact on public health. For example, the Alpha variant (B.1.1.7) was first identified in the UK and has been associated with increased transmissibility and possibly increased severity of disease. The Delta variant (B.1.617.2) was first identified in India and has been associated with increased transmissibility and vaccine breakthrough infections. Public health officials closely monitor the emergence and spread of SARS-CoV-2 variants to determine their potential impact on global health and to make recommendations on public health measures such as vaccination, testing, and quarantine policies. Sources: Centers for Disease Control and Prevention. (2022). About Variants of the Virus that Causes COVID-19. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html World Health Organization. (2022). Tracking SARS-CoV-2 variants. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ SARS-CoV-2 variant codo:VGO_SPAdes SPAdes Genome Assembler is an open source tool for de novo sequencing. SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtain SPAdes is an assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software SPAdes codo:VGO_SalivaSpecimen Saliva sampling is a simple and reliable method for collecting DNA and is a great alternative to blood collection, particularly for those patients who are anxious about having blood collected. Saliva specimen codo:VGO_SamePatientSamplingStrategy Same patient sampling strategy involves collecting multiple samples from the same individual over time, in order to track changes in disease status or treatment response. Same patient sampling strategy codo:VGO_SamplingStrategy A sampling strategy refers to a plan for selecting individuals or groups from a larger population to obtain a representative sample for analysis or research purposes. It involves choosing the sample size, sample type, and sample selection method. Sampling strategy codo:VGO_SangerSequencing Sanger sequencing: Sanger sequencing is a method of DNA sequencing that uses fluorescently labeled dideoxynucleotides to terminate DNA synthesis, allowing for the identification of the order of nucleotides in a DNA sample Sanger sequencing codo:VGO_SentinelSurveillanceARI Sentinel surveillance for acute respiratory infections (ARI) involves monitoring a network of healthcare facilities or providers for a specific set of symptoms, in order to identify and track outbreaks of respiratory illnesses. Sentinel surveillance (ARI) codo:VGO_SentinelSurveillanceILI Sentinel surveillance for influenza-like illness (ILI) involves monitoring a network of healthcare facilities or providers for a specific set of symptoms, in order to identify and track outbreaks of influenza or other respiratory illnesses. Sentinel surveillance (ILI) codo:VGO_SentinelSurveillanceSARI Sentinel surveillance for severe acute respiratory infections (SARI) involves monitoring a network of healthcare facilities or providers for severe cases of respiratory illness, in order to identify and track outbreaks of severe respiratory illnesses. Sentinel surveillance (SARI) codo:VGO_SequencingTechnology Sequencing technology: Sequencing technology refers to the methods and tools used to determine the order of nucleotides in a DNA or RNA sample.. Sequencing technology codo:VGO_SerumSpecimen Specimen collected from Serum Serum specimen codo:VGO_Specimen A part of a thing, or of several things, taken to demonstrate or to determine the character of the whole, e.g. a substance, or portion of material obtained for use in testing, examination, or study; particularly, a preparation of tissue or bodily fluid taken for examination or diagnosis. Specimen Research Specimen Sample codo:VGO_StoolSpecimen A stool specimen is a sample of feces collected from an individual for medical testing or diagnosis. It is a non-invasive and commonly used diagnostic tool to detect and diagnose various medical conditions such as gastrointestinal infections, digestive disorders, and colon cancer. Stool specimens can be collected using different methods, including the use of a clean container or a stool collection kit. The collected specimen is then analyzed in a laboratory to detect any abnormalities or signs of infection or disease. Stool specimen is a sample of the client's feces. It can be analyzed for the presence of blood; mucus; fat; microbes, such as bacteria and parasites; or other abnormal findings. Stool specimen codo:VGO_StructuralProteinOfSARS-CoV-2 Structural protein of SARS-CoV-2 codo:VGO_SwabSpecimen A swab specimen is a sample of cells or secretions collected from an individual's body using a swab, which is a small stick with a cotton or synthetic tip. Swab specimens can be collected from various parts of the body, such as the nose, throat, vagina, or rectum, depending on the type of test being performed. They are commonly used diagnostic tools to detect and diagnose infections such as COVID-19, influenza, and sexually transmitted infections. Swab specimen codo:VGO_TissueSpecimen A tissue specimen is a sample of tissue collected from an individual for medical testing or diagnosis. It is a commonly used diagnostic tool to detect and diagnose various medical conditions such as cancer, infections, and autoimmune diseases. Tissue specimens can be collected from different parts of the body, such as the skin, organs, or bones, using various techniques, including biopsies and surgical procedures. The collected specimen is then analyzed in a laboratory to detect any abnormalities or signs of disease in the tissue. Tissue specimens are an important tool for clinicians and researchers to better understand the nature of diseases and develop effective treatments. Tissue specimen codo:VGO_TrachealSwabSpecimen A tracheal swab specimen is a sample of secretions collected from the trachea, which is the tube that carries air to and from the lungs. The collection of a tracheal swab specimen involves the insertion of a swab through the nose or mouth into the trachea to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used to diagnose respiratory infections such as COVID-19 or tuberculosis. Tracheal swab specimen codo:VGO_UGENEv.33 UGENE Features Creating, editing, and annotating nucleic acid and protein sequences Fast search in a sequence Multiple sequence alignment: ClustalW, ClustalO, MUSCLE, Kalign, MAFFT, T-Coffee PCR in silico Search through online databases: NCBI, PDB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, DAS servers Local and NCBI Genbank BLAST search Open reading frames finder Restriction enzyme finder with integrated REBASE restriction enzymes list Integrated Primer3 package for PCR primer design Plasmid construction and annotation Cloning in silico by designing cloning vectors Genome mapping short reads with Bowtie, BWA, and UGENE Genome Aligner Raw NGS data processing Visualization of next-generation sequencing data (BAM files) using UGENE Assembly Browser Variant calling with SAMtools RNA-seq data analysis with Tuxedo pipeline (TopHat, Cufflinks, etc.) SPAdes de novo assembler HMMER2 and HMMER3 packages integration Chromatogram viewer Search for transcription factor binding sites (TFBS) with weight matrix and SITECON algorithms Search for direct, inverted, and tandem repeats in DNA sequences Local sequence alignment with optimized Smith-Waterman algorithm Building (using integrated IQ-TREE, PHYLIP Neighbor Joining, MrBayes or PhyML Maximum Likelyhood) and editing phylogenetic trees Combining various algorithms into custom workflows with UGENE Workflow Designer Contigs assembly with CAP3 3D Structure viewer for files in PDB and MMDB formats, anaglyph view support Protein secondary structure prediction with GOR IV and PSIPRED algorithms Constructing dotplots for nucleic acid sequences mRNA alignment with Spidey Search for a pattern of various algorithms’ results in a nucleic acid sequence with UGENE Query Designer Unipro UGENE is a free cross-platform genome analysis suite. It is distributed under the terms of the GNU General Public License. UGENEv.33 codo:VGO_UnknownBiospecimen codo:VGO_UpperRespiratoryTractSwabSpecimen An upper respiratory tract swab specimen is a sample of secretions collected from the upper respiratory tract, which includes the nasal cavity, pharynx, and larynx. The collection of an upper respiratory tract swab specimen involves the insertion of a swab into the nostril or mouth to collect a sample of secretions, which is then sent to a laboratory for analysis. It is commonly used to diagnose respiratory infections such as COVID-19 or influenza. Upper respiratory tract swab specimen codo:VGO_UrineSpecimen A urine specimen is a sample of urine collected from an individual for medical testing, diagnosis, or monitoring. It is a non-invasive and commonly used diagnostic tool to detect and diagnose various medical conditions such as urinary tract infections, kidney diseases, and diabetes. Urine specimen codo:VGO_Variant A variant is a viral genome (genetic code) that may contain one or more mutations. In some cases, a group of variants with similar genetic changes, such as a lineage or group of lineages, may be designated by public health organizations as a Variant Being Monitored (VBM), Variant of Concern (VOC) or a Variant of Interest (VOI) due to shared attributes and characteristics that may require public health action. Variant codo:VGO_Virus An infectious agent which consists of two parts, genetic material and a protein coat. These organisms lack independent metabolism, and they must infect the cells of other types of organisms to reproduce. Most viruses are capable of passing through fine filters that retain bacteria, and are not visible through a light microscope. (NCI) Group of minute infectious agents characterized by a lack of independent metabolism and by the ability to replicate only within living host cells; have capsid, may have DNA or RNA (not both). (CSP) Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. (MSH) Virus codo:VGO_WasteWaterSurveillanceSpecimen Wastewater surveillance specimen is a type of environmental specimen that refers to samples taken from the sewage or wastewater system to monitor the presence and prevalence of pathogens, such as SARS-CoV-2. Waste water surveillance specimen codo:VGO_WastewaterTesting Wastewater testing involves analyzing samples of wastewater to detect and monitor the presence of specific pathogens, such as SARS-CoV-2, in a population or geographic area. Wastewater testing codo:VaccinationStatistics Vaccination statistics refer to numerical data that provides information about the number of people who have received one or more doses of a vaccine. These statistics are used to monitor and track the progress of vaccination programs and to assess the effectiveness of vaccination campaigns and interventions. Vaccination statistics typically include the total number of doses administered, the number of people who have received one or more doses of the vaccine, the percentage of the population that has been vaccinated, and other relevant data points such as age, gender, and geographical location of the vaccinated population. Vaccination statistics codo:Vaccine An immunogen consisting of a suspension of weakened or dead pathogenic cells injected in order to stimulate the production of antibodies. Vaccine vaccinum codo:VaccineShot A vaccine is a substance that helps the body develop immunity to a specific disease by introducing a small, harmless piece of the virus or bacteria that causes the disease. Vaccines are usually given in multiple doses, spaced out over time, to ensure that the body develops a strong and long-lasting immune response. Each dose of a vaccine is called a "vaccine shot" or simply a "shot." For example, the Pfizer-BioNTech COVID-19 vaccine is given in two doses, three weeks apart, and each dose is a "vaccine shot." It's important to note that getting the full series of vaccine shots is usually necessary to achieve full immunity to a disease, and it's important to follow the recommended schedule for vaccine doses to ensure maximum protection. Vaccine shot Vaccine dose codo:VitalSign The vital signs of a suspected covid-19 patient as found through clinical evidences. sign of life; usually an indicator of a person's general physical condition; "he was still alive but his vital signs were weak" Vital sign Vital sign VitalSign codo:VulnerableToCOVID-19 COVID-19 is often more severe in people who are older than 60 years or who has certain bad health habit or who have health conditions like lung or heart disease, diabetes or conditions that affect their immune system.​ Defined as per WHO recommended Risk Factors, i.e., Obesity, Smoking, Alcohol, Physical Inactivity, Pollution, Diabetes, Cardiovascular Disease, Respiratory Disease, and Cancer. (COVID-19 and NCD risk factors, https://www.who.int/docs/default-source/ncds/un-interagency-task-force-on-ncds/uniatf-policy-brief-ncds-and-covid-030920-poster.pdf) Vulnerable to COVID-19 codo:WEAR_GovernanceAndSocio-economicMeasures Governance and socio-economic measures codo:WEAR_Measure Measure codo:WEAR_MovementRestriction Movement restriction codo:WEAR_PreventiveMeasure Preventive measure to contain the surge in COVID-19 cases. Preventive measure codo:WEAR_PublicHealthMeasure Public health measure codo:WEAR_Response Response measures are actions, policies, and programmes that. countries, as Parties to the UN Framework Convention on. Climate Change (UNFCCC), undertake in response to climate. change, mostly for mitigation of greenhouse gas (GHG) emissions. Response measures means any reasonable measures taken by any person in relation to a particular incident to prevent or minimize transboundary harm. Response codo:WEAR_ResponseComponent Part of a response. Response component codo:WEAR_SocialDistancing Social distancing codo:WEAR_WeatherCondition One-word description of the observed weather condition. Weather condition 1 1 1 1 1 codo:WEAR_WeatherInformation Weather information Weather information codo:Woman A women. Woman Drug-drug interatction between Ritonavir-Boosted Nirmatrelvir and Amiodarone Ritonavir-BoostedNirmatrelvir/Amiodarone DDI Drug-drug interatction between Ritonavir-BoostedNirmatrelvir and Carbamazepine Ritonavir-BoostedNirmatrelvir/Carbamazepine DDI Drug-drug interatction between Ritonavir-Boosted Nirmatrelvir and Clopidogrel Ritonavir-BoostedNirmatrelvir/Clopidogrel DDI Drug-drug interatction between Ritonavir-Boosted Nirmatrelvir and Clozapine Ritonavir-BoostedNirmatrelvir/Clozapine DDI Drug-drug interatction between Ritonavir-Boosted Nirmatrelvir and Disopyramide Ritonavir-BoostedNirmatrelvir/Disopyramide DDI Ritonavir-BoostedNirmatrelvir/Dofetilide DDI Ritonavir-BoostedNirmatrelvir/Dronedarone DDI Ritonavir-BoostedNirmatrelvir/Eplerenone DDI Ritonavir-BoostedNirmatrelvir/Flecainide DDI Ritonavir-BoostedNirmatrelvir/Ivabradine DDI Ritonavir-BoostedNirmatrelvir/Lurasidone DDI Ritonavir-BoostedNirmatrelvir/Midazolam DDI Ritonavir-BoostedNirmatrelvir/Phenobarbital DDI Ritonavir-BoostedNirmatrelvir/Phenytoin DDI Ritonavir-BoostedNirmatrelvir/Pimozide DDI Ritonavir-BoostedNirmatrelvir/Primidone DDI Ritonavir-BoostedNirmatrelvir/Propafenone DDI Ritonavir-BoostedNirmatrelvir/Quinidine DDI Ritonavir-BoostedNirmatrelvir/Rifampin DDI Drug-drug interaction between Ritonavir-BoostedNirmatrelvir and Rifapentine Ritonavir-BoostedNirmatrelvir/Rifapentine DDI Ritonavir-BoostedNirmatrelvir/Sildenafil DDI Ritonavir-BoostedNirmatrelvir/Vardenafil DDI Ritonavir-BoostedNirmatrelvir/Voclosporin DDI Ritonavir-BoostedNirmatrelvir/Glecaprevir/pibrentasvir DDI a vaccine intended to provide acquired immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), , the virus that causes coronavirus disease 2019 (COVID-19). COVID‑19 vaccine A27S A27S A51V A51V A63T A63T SCTID: 82991003 Generalized aches and pains (finding) 0-2 months Ahmedabad 23.03 72.58 Ahmedabad Ajmer 26.4499 74.6399 Ajmer Amsterdam 52.366667 4.9 Amsterdam Anantapur Anantapur Andaman and Nicobar Islands A union territory of India comprising 572 islands of which 37 are inhabited, are a group of islands at the juncture of the Bay of Bengal and the Andaman Sea. Andaman and Nicobar Islands Andhra Pradesh Andhra Pradesh Argentina Argentina Assam Assam Oxford-AstraZeneca COVID-19 vaccine AZD1222 ChAdOx1 nCoV19 Covishield Athens 37.983972 23.727806 Athens Bagalkote 16.1817 75.6958 Bagalkote Bahrain Bahrain Bangalore 12.983333 77.583333 Bangalore Bangalore-Urban Bangalore-Urban Bangalore Rural Bangalore Rural Bangladesh Bangladesh Baroda 22.3 73.2 Baroda Belagavi 15.85 74.5 Belagavi Bellary District 15.1 76.916667 Bellary Bengaluru Urban Bengaluru Urban Bhatkal 13.967 74.567 Bhatkal Bidar 17.9 77.5 Bidar Bihar Bihar Botswana Brazil Brazil Breathing without difficulty A dyspneic condition. Breathlessness Shortness of breath C90Y C90Y COVAXIN BBV152 COVID-19 A Coronavirus infection that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2 (source: obo). A disease caused by severe acute respiratory syndrome coronavirus 2.  Disease caused by 2019 novel coronavirus Disease caused by 2019-nCoV NCI:C171133 SCTID: 840539006 2019 Novel Coronavirus The body responds to a viral infection by producing antibodies that help neutralize the virus. Blood tests (also called serology tests or serology immunoassays) can detect the presence of such antibodies. COVID-19 Antibody Tests Serology blood test Serology test serological test utoimmune lymphoproliferative syndrome (ALPS) is a rare immune disorder first described by NIH scientists in the mid-1990s that can cause numerous autoimmune problems, such as low levels of red blood cells, clot-forming platelets, and infection-fighting white blood cells. These problems can increase the risk of infection and hemorrhage. Read more about autoimmune lymphoproliferative syndrome (ALPS). Autoimmune lymphoproliferative syndrome Autoimmune polyglandular syndrome type 1 (APS-1), also called autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), causes a diverse range of symptoms, including autoimmunity against different types of organs and increased susceptibility to candidiasis, a fungal infection caused by Candida yeast. Read more about APS-1 (APECED). Autoimmune polyglandular syndrome type 1 Aches and pains BENTA disease is a rare genetic disorder of the immune system caused by mutations in the gene CARD11. The disease is characterized by high levels of certain immune cells starting in infancy, an enlarged spleen, enlarged lymph nodes, immunodeficiency, and an elevated risk of lymphoma, a type of cancer Read more about BENTA disease BENTA-Disease Breathing without difficulty Breathlessness Caspase eight deficiency state, or CEDS, is a very rare genetic disorder of the immune system caused by mutations in the CASP8 gene. CEDS is characterized by an enlarged spleen and lymph nodes, recurrent sinus and lung infections, recurrent viral infections, and a low level of infection-fighting antibodies. NIH researchers first described this condition in two siblings in 2002. CEDS Caspase eight deficiency state COVID-19 2019 Novel Coronavirus Cardiovascular Disease (CVD) Chronic Kidney Disease (CKD) Chronic Kidney Insufficiency (CKI) Chronic Liver Disease (CLD) Chronic Obstructive Pulmonary Disease (COPD) Cough Diabetes mellitus Dyspnea Fever HIV Human Immunodeficiency Virus High-Titer COVID-19 convalescent plasma Hypertension Ischemic heart disease Malaise Molnupiravir Not reported 70 true 17 15 44 77 67 80 22 66 90 14 68 90 Pain Pneumonia Remdesivir Ritonavir-Boosted Nirmatrelvir Paxlovid Runny nose Severe pneumonia Sneezing Sore throat Upper Respiratory Tract Infection URTI 25 67 55 70 88 30 a medical imaging technique used in radiology (x-ray) to obtain detailed internal images of the body noninvasively for diagnostic purposes. formerly known as computed axial tomography or CAT scan CT scan Cardiovascular Disease (CVD) Carwar Carwar

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Chamarajanagar 11.926 76.9402 Chamarajanagar Channagiri 14.03 75.93 Channagiri Chattisgadh Chattisgadh Chennai 13.0825 80.275 Chennai Chikkaballapur 13.43 77.72 Chikkaballapur Chikmagalur 13.313 75.737 Chikmagalur Chitradurga 14.23 76.4 Chitradurga Chronic Kidney Disease (CKD) Chronic Kidney Insufficiency (CKI) Chronic Liver Disease (CLD) Chronic Obstructive Pulmonary Disease (COPD) Cloud Colombo 6.934444 79.842778 Colombo Conjunctivitis red eyes Containment Zones : The patients who were contacts of Conatinment Zones and their contacts. Some patients have the Ward represented in the Reason column. SCTID: 49727002 Cough Any facility, such as hotels/lodges/hostels/stadiums for providing care to COVID-19 patients are reffered as Covid Care Centre (CCC). Covid Care Centre (CCC) D3N D3N D405N D405N D614G D614G D796Y D796Y D99del D99del Dadra And Nagar Haveli And Daman And Diu Dadra and Nagar Haveli and Daman and Diu (DNHDD) is a union territory in western India. Dadra And Nagar Haveli And Daman And Diu Dakshina Kannada District Dakshina Kannada Daman And Diu Until June 2019, Daman and Diu was an Union Territory of India. But since July 2019 it was merged to another Union Territory of India "Dadra and Nagar Haveli" and togtrehr formed a single union territory "Dadra and Nagar Haveli and Daman and Diu (DNHDD)." Daman And Diu Dammam 26.433333 50.1 Dammam Davangere Davangere District 14.4666 75.9242 Davangere Debaspete Debaspete The Dedicated COVID Health Centre are hospitals that shall offer care for all cases that have been clinically assigned as moderate. Dedicated Covid Health Centre (DCHC) The Dedicated COVID Hospitals are hospitals that shall offer comprehensive care primarily for those who have been clinically assigned as severe. Dedicated Covid Hospital (DCH) Delhi 28.61 77.23 Delhi Dharwad Dharwad District 15.458333 75.008333 Dharwad Diabetes Mellitus (DM) SCTID: 62315008 Diarrhea Diu 20.71 70.98 Diu Doha 25.286667 51.533333 Doha Domestic Travel History Absent : The patients for whom the information was given as "Travel History-Domestic" SCTID: 11833005 Dry cough Dubai 25.263056 55.297222 Dubai difficult or labored respiration Dyspnea Dyspnoea E gene E31del E31del E484A E484A Edinburgh 55.953 -3.189 Edinburgh F108del F108del F157L F157L F486V F486V F490P F490P F490S F490S F59W F59W F63L F63L F66del F66del F694Y F694Y SCTID: 386661006 Fever Fog France France G1001S G1001S G100C G100C G100H G100H G100del G100del G107del G107del G1099D G1099D G142D G142D G204R G204R G257S G257S G339D G339D G339H G339H G446S G446S G489S G489S G66A G66A G66del G66del G671S G671S Gadag 15.4167 75.6167 Gadag Gadag-Betageri 15.4167 75.6167 Gadag-Betageri Germany Germany Goa 15.5 73.83 Goa Greece Greece Gujarat Gujarat From Gujarat : The patients with travel history to Gujarat and their contacts. Gulbarga 17.329 76.825 Gulbarga Guyana officially the Co‑operative Republic of Guyana, is a country on the northern mainland of South America. Guyana H655Y H655Y H69del H69del H83del H83del H882R H882R H882Y H882Y SCTTID: 59994004 Hacking cough Hail Haryana Haryana Hassan 13.012 76.068 Hassan Haveri 14.793889 75.403889 Haveri Himachal Pradesh Himachal Pradesh Hindupur 13.83 77.49 Hindupur Hong Kong Hubballi 15.350217 75.137625 Hubballi Hubli 15.350217 75.137625 Hubli, officially known as Hubballi, is a city in the Indian state of Karnataka. Hubli Humnabad 17.77 77.13 a City and municipal council in the Bidar District of the Indian state of Karnataka and city is a headquarters of Humnabad taluk. Humnabad Hyderabad 17.37 78.48 Hyderabad Hypertension (HTN) I1013T I1013T I103C I103C I106T I106T I106V I106V I107M I107M I210V I210V I223M I223M I42V I42V India India India Indonesia Indonesia Influenza like illness : The patients showing influenza like symptoms and their contacts. Influenza Like Illness ILI Iraq Republic of Iraq A country in Western Asia, bordered by Turkey to the north, Iran to the east, Kuwait to the southeast, Saudi Arabia to the south, Jordan to the southwest and Syria to the west. Iraq Republic of Iraq Ireland Ireland Ischemic Heart Disease (IHD) Italy Italy Jalgaon Jalgaon District 20.997984 75.566711 Jalgaon Jammu 32.73 74.87 Jammu is the winter capital and the largest city in Jammu district of the Indian union territory of Jammu and Kashmir. Jammu Jammu And Kashmir Jammu And Kashmir Jeddah 21.543333 39.172778 Jeddah Jharkhand Jharkhand 2020-06-27T00:00:00 2020-06-27T00:00:00 27-June Trace History Absent : On this day, no trace history information was given for the patients. Patients who were contacts of these individuals are also in this cluster. 2020-06-28T00:00:00 2020-06-28T00:00:00 28-June Trace History Absent : On this day, no trace history information was given for the patients. Patients who were contacts of these individuals are also in this cluster. 2020-06-29T00:00:00 2020-06-29T00:00:00 29-June Trace History Absent : On this day, no trace history information was given for the patients. Patients who were contacts of these individuals are also in this cluster. K147E K147E K411R K411R K417N K417N K417T K417T Kalaburagi 17.329 76.825 Kalaburagi Kalburgi 17.329 76.825 Kalburgi Karnataka Karnataka Karnataka Karwara Karwara Kashmir Kashmir Kerala Kerala Coorg Kodagu Kodagu District Kodagu, also called Coorg, is a district in Karnataka State. Coorg Kodagu Kolhapur 16.691667 74.233333 Kolhapur Kolkata 22.5726 88.3639 Kolkata Koppal Koppala 15.35 76.15 a city in Koppala district in the Indian state of Karnataka. Koppal Koppala Koppala District Koppala Kuwait Kuwait L14del L14del L177F L177F L24del L24del L264F L264F L438F L438F L452Q L452Q L452R L452R Light Cloud Light RainSun London 51.507222 -0.1275 London M gene M101I M101I M1050I M1050I M124I M124I Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Madhya Pradesh Madhya Pradesh Madikeri 12.4209 75.7397 Madikeri Madrid 40.416667 -3.716667 Madrid Madurai Madurai District 9.9 78.1 Madurai Maharashtra Maharashtra From Maharashtra : The patients with travel history to Maharashtra and their contacts. physical discomfort (as mild sickness or depression) (Source: WordNet) SNOMED CT Malaise SCTID: 367391008 Malaysia Malaysia Mandya 12.52 76.9 Mandya Mangalore 12.78563 74.84108 Mangalore Mangaluru 12.78563 74.84108 Mangaluru Manipur Manipur Mecca 21.4225 39.823333 Mecca Membrane Protein M Middle East Middle East From Middle East : The patients with travel to the Middle East and their contacts. MiddleEastCluster Mumbai 18.975 72.825833 Mumbai Muscat 23.588889 58.408333 Muscat Mysore Mysore N gene N118S N118S N440K N440K N448D N448D N450D N450D N460K N460K N481K N481K N501Y N501Y N618Y N618Y N679K N679K N679del N679del N734D N734D N764K N764K N82del N82del N84K N84K N856S N856S N89I N89I N95S N95S N969K N969K Nagaland Nagaland Nandurbar Nandurbar District 21.37 74.25 Nandurbar Nanjangud 12.12 76.68 Nanjangud Nelamangala 13.102 77.374 Nelamangala Nepal Nepal Nerve damage Netherlands Netherlands New York City 40.71274 -74.005974 New York City New York State New York State Not reported Oman Oman Other sexual orientation Overcast P132H P132H P13L P13L P25del P25del P26del P26del P323L P323L P681H P681H P681R P681R P822S P822S SCTID: 22253000 Pain Palghar Palghar Panvel 18.994444 73.113889 a locality in Raigad district of Maharashtra in India. Panvel Paris 48.856613 2.352222 Paris Partly Cloud Persistent pain in chest Persistent pressure in chest Pharmaceutical Company In Nanjangud Pharmaceutical Company in Nanjangud : This patients who were workers of a Pharmaceutical Company in Nanjangud, Mysore along with their contacts. Philippines Philippines Pneumonia is classified as severe when the heart, the kidneys or the circulatory system are at risk of failing, or if the lungs can no longer take in enough oxygen. http://snomed.info/id/406521002 Postoperative diagnosis The patient was discovered to have a disease as a result of tests given during pregnancy. Pregnancy scanning SCTID: 406520001 The patient was discovered to have another disease as the result of tests given before surgery. Preoperative diagnosis Pune 18.520278 73.856667 Pune Punjab Punjab Q19E Q19E Q498R Q498R Q954H Q954H R183E R183E R203K R203K R32del R32del R392C R392C R408S R408S R41P R41P R41del R41del R43C R43C R4H R4H R507G R507G R52C R52C R595S R595S R683del R683del R68I R68I R712K R712K R726K R726K R75K R75K R78C R78C R810C R810C R914K R914K R93H R93H R96I R96I R99K R99K The Molecular test, commonly known as the RT-PCR test, is a method of testing that is used to directly detect the presence of the virus in the sample a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using polymerase chain reaction (PCR). RT-PCR tests Reverse transcription polymerase chain reaction Raichore Raichur 16.2 77.37 a city municipality in the district of Raichur in the Indian state of Karnataka. Raichore Raichur Rayachuru Raigad Raigadh Raigad District (formerly Kolába district), is a district in the Konkan division of Maharashtra, India. Raigad Raigadh Rain Rajasthan Rajasthan From Rajasthan : The patients with travel history to Rajasthan and their contacts. Ramanagara Ramanagara District 12.723 77.286 a city and a city municipal council in the Indian state of Karnataka. Ramanagara Ramanagara District A COVID-19 antigen refers to any foreign matter or viral proteins in the body that triggers an immune response. a rapid diagnostic test suitable for point-of-care testing that directly detects the presence or absence of an antigen. Rapid antigen test (RAT) Antigen rapid test (ART) Rapid antigen detection test (RADT) Rapid test rapid antigen test Ratnagiri Ratnagiri District 16.994444 73.3 Ratnagiri Ratnagiri District Reduced consciousness Rest Of Europe Rest Of Europe From the rest of Europe : The patients with travel history to Europe but not to UK and their contacts. RestOfEuropeCluster Riyadh 24.633333 46.716667 Riyadh SCTID: 267101005 Nasal discharge presen Nose dripping Nose running S106del S106del S135R S135R S221L S221L S33del S33del S371F S371F S373P S373P S375F S375F S403L S403L S413R S413R S477N S477N Saudi Arabia Saudi Arabia Scotland Scotland Second Generation Contact Absent : The patients whose information was given as "Contact" without giving the patient ID of the individual they were a contact of. SecondGenerationContactCluster rendering an organism sensitive to a serum by a series of injections. Sensitisation Sensitization Severe Acute Respiratory Infection: This includes patients with a history of Severe Acute Respiratory Infection whose symptoms have resurfaced and their contacts. Severe Acute Respiratory Infections SARI Shahapur 16.7 76.83 a city and taluka headquarter located in the Yadgir district of Indian state of Karnataka. Shahapur Sharjah 25.3575 55.390833 Sharjah Shikharaji 23.9611 86.1371 Shikharaji Shivamogga 13.933333 75.566667 Shivamogga Singapore 1.283333 103.833333 Singapore Sleep disorders Sleet SCTID: 76067001 Sneezing Snow Solapur 17.68 75.92 Solapur SCTID: 162397003 Sore throat Pain in throat Raw throat Republic of South Africa Republic of South Africa South America South America From South America : The patients with travel history to South America and their contacts. SouthAmericaCluster From the Southern States : The patients with travel to Kerala, Tamil Nadu, Andhra Pradesh or Telengana and their contacts. This doesn't contain patients with interdistrict travel in Karnataka Southern States Of India Kerala, Tamil Nadu, Andhra Pradesh or Telengana. This doesn't contain Karnataka Southern States Of India Spain Spain EPI_ISL_14916130 2022-09-01T00:00:00 Data source- GISAID EPI_SET ID: EPI_SET_230329vz DOI: https://doi.org/10.55876/gis8.230329vz EPI_ISL_14810239 2022-08-08T00:00:00 Data source- GISAID EPI_SET ID: EPI_SET_230329vz DOI: https://doi.org/10.55876/gis8.230329vz EPI_ISL_14810204 2022-11-08T00:00:00 Data source- GISAID EPI_SET ID: EPI_SET_230329vz DOI: https://doi.org/10.55876/gis8.230329vz EPI_ISL_14810205 2022-11-08T00:00:00 Data source- GISAID EPI_SET ID: EPI_SET_230329vz DOI: https://doi.org/10.55876/gis8.230329vz EPI_ISL_14810202 2022-11-08T00:00:00 Data source- GISAID EPI_SET ID: EPI_SET_230329vz DOI: https://doi.org/10.55876/gis8.230329vz Sri Lanka Sri Lanka Sun Surat 21.17024 72.831061 Surat Switzerland Switzerland T112I T112I T11A T11A T17A T17A T19I T19I T223I T223I T24I T24I T327I T327I T376A T376A T478K T478K T492I T492I 2020-03-13T00:00:00 2020-03-18T00:00:00 2020-03-18T00:00:00 2020-03-13T00:00:00 TJ Congregation from 13th to 18th March in Delhi : The patients with travel history to the TJ Congregation in Delhi and their contacts. Tamil Nadu Tamil Nadu Telangana Telangana Texas Texas Thane Thane District 19.172431 72.957019 Thane Thane District The World Represents the geographic region of the entire world. The World Thunder SCTID: 224960004 Feeling tired Fatigue Trivandrum 8.4875 76.9525 Trivandrum Tumkur 13.34 77.1 Tumkur Turkey Turkey Uttar Pradesh UP UP SCTID: 54150009 URTI Upper Respiratory Tract Infection USA USA From USA : The patients who had travel history to USA and their contacts. USACluster Udupi 13.3389 74.7451 Udupi The patient was identified as at risk for the disease (e.g., Covid-19) and was tested as part of tracing people identified to be at risk. Under tracing United Arab Emirates United Arab Emirates United Kingdom United Kingdom UK From United Kingdom : The patients with travel history to UK and their contacts. UnitedKingdomCluster Unknown : The patients who have been listed in the Media Bulletins as "Contact Under Tracing"and their contacts. Uttar Kannada Uttar Kannada Uttar Pradesh Uttar Pradesh North Canara Uttara Kannada Uttara Kannada, formerly known as North Canara, is a district in the Indian state of Karnataka. North Canara Uttara Kannada V213G V213G taking a vaccine as a precaution against contracting a disease Vaccination Inoculation Vadodara District Vadodara Vadodara District Vellore Vellore District 12.920219 79.133306 Vellore Vellore District Vijayapura 13.29 77.8 Vijayapura Vishakapatnam 17.704167 83.297778 Vishakapatnam W152R W152R West Bengal West Bengal Western Province is one of the nine provinces of Sri Lanka, the first level administrative division of the country. Western Province Wuhan Y144del Y144del Y505H Y505H Yadgir Yadgir ins104P ins104P ins108GstopYstop ins108GstopYstop p000001-kar-codo p000002-kar-codo p000003-kar-codo p000004-kar-codo p000005-kar-codo Insertion of 4 nucleotides when compared to the reference WIV04 sequence. Gap of 15 nucleotides when compared to the reference WIV04 sequence. 39 2021-01-28T10:00:00 V B GR B.1.1 GRA BA.2 VOC Omicron GRA BA.2.10 VOC Omicron GRA BA.2.10.1 VOC Omicron 18-44 years 45 years and above This specification describes CODO, an integrated ontological data model, a formal Ontology for collection and analysis of COVID-19 and related data. The Introduction section further provides the overall scope of the ontology and its usage. It is designed using W3C's RDF technology. 2020-04-27 Biswanath Dutta Debanjali Bain https://creativecommons.org/licenses/by/4.0/ 2022-04-16 2023-03-31 2023-07-11 Indian Statistical Institute CODO: an Ontology for collection and analysis of COviD-19 data https://w3id.org/codo codo https://w3id.org/codo CQ 1: What mutations were discovered in patient p1's genomic testing results? CQ 2: Which patient's test result revealed the N501Y mutation? CQ 3: Which SARS-CoV-2 variant has patient p1 been diagnosed with? CQ 4: Which sequencing method was used in the genome sequencing test for patient p1? CQ 5: Who has been diagnosed as an Omicron patient? CQ 6: Which patients' nasopharyngeal swabs have been collected? CQ 7: A person's genomic sequence report reveals that the spike protein has a del69-70 mutation. Which variants might there be? CQ 8: What are the characteristic mutations found in the test result of a person (p2) diagnosed with the B.1.1.529 variant? CQ 9: What are all the substitution mutations that occurred in B.1.1.7? CQ 10: What mutations are detected in Delta? CQ 11: Where and when was the initial B.1.351 variant discovered? CQ 12: What structural proteins are present in SARS-CoV-2? CQ 13. Which therapeutics are recommended for COVID-19 patients with specific underlying health conditions? CQ 14. What are the potential adverse effects of specific COVID-19 drugs? CQ 15. Identify the drug interactions that may occur with a particular COVID-19 therapeutic. CQ 16. What are the risk factors associated with severe COVID-19 infection? CQ 17. How does the choice of COVID-19 therapeutics vary based on patient characteristics? CQ 18. Which drugs should be avoided due to known interactions with commonly prescribed COVID-19 medications? codo:COVIDRO_Obesity Overweight (defined as a body mass index (BMI) is 25 kg/m2 or higher, but under 30 kg/m2), obesity (BMI is 30 kg/m2 or higher, but under 40 kg/m2), or severe obesity (BMI is 40 kg/m2 or higher), can make you more likely to get very sick from COVID-19. The risk of severe illness from COVID-19 increases sharply with higher BMI. Obesity The location of for example where a person is situated, an organization (covid-19 dedicated facilities, medical clinics) is located. location