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GHL2024.D11.1E31

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aimeehan1 edited this page Jul 1, 2024 · 4 revisions

Influenza A (HxNy) outbreak

ID: GHL2024.D11.1E31
Tracking started: 2024-06-01
Tracking ended: ongoing

Data available here: EXPORT-LINK

Data dictionary available here: DATA-DICTIONARY

Schema

Case Demographics

  • Pathogen_name (string): Pathogen of case. ["Influenza A"].
  • Pathogen_subtype1 (string): pathogen subtype for Influenza A Hx.
  • Pathogen_subtype2 (string): pathogen subtype for Influenza A, further classification HxNy.
  • ID (string): Unique string identifying the case.
  • Case_status: Status of a case. Cases which are discarded were previously suspected but have now been confirmed negative, and should be excluded from case counts. Cases which are omit_error were incorrectly added and should be dismissed from any data interpretation. Must be one of: ["confirmed", "probable", "suspected", "discarded", "omit_error"].
  • Location_Admin0 (object): (GeoJSON) Admin 0 location [country]. Curators input an initial location where the case was reported from. This query results in a location structure returned from a geocoding API, such as Mapbox.
  • Location_Admin1 (object): (GeoJSON) Admin 1 location [state / province] for geocoding API, such as Mapbox.
  • Location_Admin2 (object): (GeoJSON) Admin 2 location [county / district] for geocoding API, such as Mapbox.
  • Location_Admin3 (object): (GeoJSON) Admin 3 location [city] for geocoding API, such as Mapbox.
  • Location_Comment (object): (GeoJSON) Location detail for case. For internal use only.
  • Age (string): Age of individual, specified as range, open-ended (<n, >n) or as a range delimited by a hyphen following 5 year increments (m-n).
  • Gender: Sex at birth of an individual. Must be one of: ["male", "female", "other"].
  • Occupation (string): Free response entry describing the individual's occupation.
  • Healthcare_worker: Whether individual is a healthcare worker. Must be one of: ["Y", "N"].

Medical History

  • Previous_infection: Did the individual test positive for the infection prior to the most recent diagnosis. Must be one of: ["Y", "N", "NA"].
  • Co_infection (array): If the individual tested positive for another pathogen, can select multiple.
  • Pre_existing_condition (array): If the individual has any pre-existing conditions. Must be one of: ["Y", "N"].
  • Pregnancy_Status: Is the case pregnant or post-partum? Must be one of: ["Y", "N", "NA"].
  • Vaccination: Has the individual received a dose of vaccine. Must be one of: ["Y", "N", "NA"].
  • Vaccine_name (string): Name of the first vaccine.
  • Vaccination_date (string, format: date): Date of first vaccination.
  • Vaccine_side_effects (array): List of symptoms experienced after receiving the vaccine.

Clinical Presentation

  • Symptoms (array): List of symptoms (i.e. cough, sore throat, etc.).
  • Date_report (string, format: date): Date case was first reported by Source. Suggest adding the date of first report, such as the date first included in a situation report or other official communication.
  • Date_onset (string, format: date): Date of onset of symptoms. May be difficult to infer from aggregate date reporting.
  • Date_confirmation (string, format: date): Date when case was confirmed.
  • Confirmation_method (string): Test used to perform diagnosis. Dependent on pathogen, and often already included in the definition.
  • Date_of_first_consultation (string, format: date): Date that the individual received first clinical consultation.
  • Hospitalised: Whether individual was hospitalised. Must be one of: ["Y", "N", "NA"].
  • Reason_for_hospitalisation (array): Reason why the individual was hospitalised, can select multiple.
    • Items: Must be one of: ["monitoring", "treatment"].
  • Date_hospitalisation (string, format: date): Date individual was hospitalised.
  • Date_discharge_hospital (string, format: date): Date that the individual was discharged from the hospital. Note: there is a separate field for ICU discharge.
  • Intensive_care: Whether individual admitted to an intensive care unit or high dependency unit at hospital. Must be one of: ["Y", "N", "NA"].
  • Date_admission_ICU (string, format: date): Date individual entered intensive care unit.
  • Date_discharge_ICU (string, format: date): Date that the individual was discharged from the ICU.
  • Home_monitoring: Whether individual is being remotely monitored by health officials at home without hospital admission. Must be one of: ["Y", "N", "NA"].
  • Isolated: Whether individual was isolated at home or in hospital. Dependent on context/pathogen. Must be one of: ["Y", "N", "NA"].
  • Date_isolation (string, format: date): Date individual entered isolation.
  • Outcome: Outcome of the disease, recovered includes inactive case counts. Must be one of: ["recovered", "death", "ongoing post-acute condition"].
  • Date_death (string, format: date): Date individual died.
  • Date_recovered (string, format: date): Date individual recovered, inactive case status.

Exposure

  • Contact_with_case: Has the individual had contact with a confirmed or suspected case. Must be one of: ["Y", "N", "NA"].
  • Contact_ID (string): If specified, the ID of the confirmed or suspected contact.
  • Contact_setting: Setting where contact occurred. HEALTH=healthcare, including laboratory exposure, PARTY=Sexual contact at night club/private party/sauna or similar setting, BAR=bar/restaurant/other small event where there was no sexual contact, LARGE=large event with no sexual contact (e.g. festival or sports event), LARGECONTACT=large event with sexual contact, UNK=unknown. Must be one of: ["HOUSE", "WORK", "SCHOOL", "HEALTH", "PARTY", "BAR", "LARGE", "LARGECONTACT", "OTHER", "UNK"].
  • Contact_setting_other (string): Contact setting not covered by Contact_setting.
  • Contact_animal: Whether the individual has known contact with animals. COMMERCIAL=animals raised on a farm for commercial or agricultural purposes at a larger scale including meat, milk, eggs, wool, labor and excludes backyard, BACKYARD=animals raised for agricultural purposes at smaller scale for family or community, PET=household pets excluding rodents, PETRODENTS=rodent pets, WILD=wild animals excluding rodents, WILDRODENTS=wild rodents. Must be one of: ["COMMERCIAL", "BACKYARD", "PET", "PETRODENTS", "WILD", "WILDRODENTS", "OTHER"].
  • Contact_animal_species (string): Free text describing animal species with known contact.
  • Contact_comment (string): Free text describing any additional contact information. For internal use only.
  • Transmission: Most likely mode of transmission. ANIMAL = Animal to human transmission. HAI = Healthcare-associated, LAB = Transmission in a laboratory due to occupational exposure, MTCT = Transmission from mother to child during pregnancy or at birth, OTHER = Other transmission, FOMITE = Contact with contaminated material (e.g bedding, clothing, objects), PTP = Person-to-person (excluding: mother-to-child, healthcare-associated or sexual transmission), SEX = Sexual transmission, TRANSFU = parenteral transmission including intravenous drug use and transfusion, UNK = Unknown. Must be one of: ["ANIMAL", "HAI", "LAB", "MTCT", "OTHER", "FOMITE", "PTP", "SEX", "TRANSFU", "UNK"].
  • Travel_history: Whether individual has travel history, domestic and/or international. Must be one of: ["Y", "N", "NA"].
  • Travel_history_entry (string, format: date): Date when individual entered the country.
  • Travel_history_start (string, format: date): Date when individual began travel.
  • Travel_history_location (object): (GeoJSON) Location of travel obtained from geocoding API such as Mapbox.

Laboratory Information

  • Genomics_Metadata (string): Which clade the viral strain belongs to.
  • Accession_Number (string): Accession number of the sequence uploaded to public database.

Source Information

  • Source (string, format: uri): URL of news story or government source where this case was confirmed.
  • Source_II (string, format: uri): URL of news story or government source where this case was confirmed.
  • Source_III (string, format: uri): URL of news story or government source where this case was confirmed.
  • Source_IV (string, format: uri): URL of news story or government source where this case was confirmed.
  • Date_entry (string, format: date): Date case was entered into line list.
  • Date_last_modified (string, format: date): Last date when case was modified in line list.

Changelog

Attribution

Data exports are published under the CC BY 4.0 license. If you use this data in a publication, please cite it as:

Global.health Influenza A (H5) [GHL2024.D11.1E31] accessed on YYYY-MM-DD

and please add the appropriate agency, paper, and/or individual in publications and/or derivatives using these data, contact them regarding the legal use of these data, and remember to pass-forward any existing license/warranty/copyright information.

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