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GHL2024.D11.1E31

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aimeehan1 edited this page Mar 12, 2025 · 26 revisions

Influenza A (HxNy) outbreak

ID: GHL2024.D11.1E31
Tracking started: 2024-04
Tracking ended: ongoing

U.S. Linelist Data available here: EXPORT-LINK (Data is refreshed once per day at midnight UTC)

U.S. Outbreak Timeline: LINK

U.S. Outbreak Map: LINK

About

The following links provide information from the U.S. Centers for Disease Control and Prevention (CDC) to help you understand the virus, outbreak, and risk to animals and people.

Schema

Case Demographics

  • ID (string): Unique string identifying the case.
  • 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. Sources will often refer to cases as avian influenza, Influenza A/H5, A(H5), A(H5N1), H5N1 and use these terms interchangeably regardless of testing or confirmatory neuraminidase (NA) status. NA subtype is not always able to be determined due to low viral RNA levels in samples. Sources will also describe cases in the context of the animal outbreaks among poultry and cattle, which are reported as H5N1 outbreaks. Global.health has only classified the N1 neuraminidase when it has been confirmed and sequenced by the U.S. CDC.
  • Case_status (string): Status of a case. "Confirmed" cases test positive for H5 from confirmatory laboratory evidence conducted by the U.S. CDC. "Probable" cases are when a case tests positive for H5 at a public health laboratory but testing at CDC is not able to confirm H5 infection, per Council of State and Territorial Epidemiologists (CSTE) guidance. 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 (string): (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 (string): (GeoJSON) Admin 1 location [state / province] for geocoding API, such as Mapbox.
  • Location_Admin2 (string): (GeoJSON) Admin 2 location [county / district] for geocoding API, such as Mapbox.
  • Location_Admin3 (string): (GeoJSON) Admin 3 location [city] for geocoding API, such as Mapbox.
  • Location_Comment (string): 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). Open-ended values for 'adult' is >=18 and 'child' is <18.
  • Gender (string): 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 (string): Whether individual is a healthcare worker. Must be one of: ["Y", "N"].

Medical History

  • Previous_infection (string): Did the individual test positive for the infection prior to the most recent diagnosis. Must be one of: ["Y", "N"].
  • Co_infection (array): If the individual tested positive for another pathogen, can list multiple.
  • Pre_existing_condition (string): If the individual has any pre-existing conditions. Must be one of: ["Y", "N"].
  • Pregnancy_Status: (string) Is the case pregnant or post-partum? Must be one of: ["Y", "N"].
  • Treatment_antiviral: (string) Has the individual received antiviral treatment. Must be one of: ["Y", "N"].
  • Treatment_antiviral_name: (string) Name of antiviral drug.
  • Vaccination: (string) Has the individual received a dose of vaccine. Must be one of: ["Y", "N"].
  • Vaccine_name (string): Name of the first vaccine.
  • Vaccine_date (string, format: iso8601date): Date of first vaccination.
  • Vaccine_side_effects (array): List of symptoms experienced after receiving the vaccine.

Clinical Presentation

  • Symptoms (array): Comma separated list of symptoms as described by source (i.e. cough, sore throat, etc.).
  • Date_onset (string, format: iso8601date): Date of onset of symptoms. May be difficult to infer from aggregate date reporting.
  • Date_confirmation (string, format: iso8601date): Date when case was confirmed.
  • Confirmation_method (string): Test used to perform diagnosis.
  • Confirmation_comment (string): Testing or confirmation detail for case. For internal use only.
  • Date_of_first_consultation (string, format: iso8601date): Date that the individual received first clinical consultation.
  • Hospitalised (string): Whether individual was hospitalised. Must be one of: ["Y", "N"].
  • Date_hospitalisation (string, format: date): Date individual was hospitalised.
  • Intensive_care (string): Whether individual admitted to an intensive care unit or high dependency unit at hospital. Must be one of: ["Y", "N"].
  • Date_admission_ICU (string, format: iso8601date): Date individual entered intensive care unit.
  • Date_discharge_ICU (string, format: iso8601date): Date that the individual was discharged from the ICU.
  • Isolated: Whether individual was isolated at home or in hospital. Dependent on context/pathogen. Must be one of: ["Y", "N"].
  • Date_isolation (string, format: iso8601date): Date individual entered isolation.
  • Outcome: Outcome of the disease, recovered includes inactive case counts. Must be one of: ["recovered", "death", "ongoing post-acute condition"]. "recovered" includes 'recovering' Outcome status, as described by Source.
  • Date_death (string, format: iso8601date): Date individual died.
  • Date_recovered (string, format: iso8601date): 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"].
  • 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"].
  • Travel_history_entry (string, format: iso8601date): Date when individual entered the country.
  • Travel_history_start (string, format: iso8601date): Date when individual began travel.
  • Travel_history_location (object): (GeoJSON) Location of travel obtained from geocoding API such as Mapbox.
  • Travel_history_comment (string): Travel history detail for case. For internal use only.

Laboratory Information

  • Genomics_Sequence (string): Sequence name and accession number(s) uploaded to public database.
  • Genomics_Clade (string): Which clade the viral strain belongs to.
  • Genomics_Genotype (string): Which genotype the viral strain belongs to.

Source Information

  • Source (string, format: url): URL of news story or government source where this case was confirmed.
  • Source_Date report (string, format: iso8601date): Date of Report for Source (I).
  • Source_Government (string): Indicate whether Source (I) is an official government source. Must be one of: ["Y", "N"].
  • Source_II (string, format: url): URL of news story or government source where this case was confirmed.
  • Source_III (string, format: url): URL of news story or government source where this case was confirmed.
  • Source_IV (string, format: url): URL of news story or government source where this case was confirmed. Additional sources may be added using consecutive numbering as roman numerals.
  • Date_entry (string, format: iso8601date): Date case was entered into line list.
  • Date_last_modified (string, format: iso8601date): Last date when case was modified in line list.
  • Curator_comment (string): Curator notes about case. For internal use only.
  • Verified (string): Must be one of: ["Y", "N"]. For internal use only.
  • Verified_by (string): Curator initials for verification. For internal use only.

Changelog

Public linelist for U.S. cases released 2025-01-30

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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