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GHL2024.D11.1E71

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aimeehan1 edited this page Dec 20, 2024 · 21 revisions

Mpox outbreak

ID: GHL2024.D11.1E71
Tracking started: 2024-08
Tracking ended: 2024-12-18 (WHO data as of 2024-12-08)

This repository contains dated records of curated Mpox cases starting January 2024 using publicly available data from the Africa Centres for Disease Control and Prevention Epidemic Intelligence Weekly Reports. The Global.health sourcing strategy pivoted to align with the WHO mpox dasbhoard as the primary source of data in October 2024.

2024 Data available here: EXPORT-LINK Data is refreshed once per day at 12a (midnight) UTC

The process for data curation is described in the Outbreak-data Wiki.

Data dictionary, see Schema below.

Schema

Case Demographics

  • Pathogen_name (string): Pathogen of case. ["Mpox"].
  • 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"].
  • 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"].
  • Treatment_antiviral: Has the individual received antiviral treatment. Must be one of: ["Y", "N"].
  • Treatment_antiviral_name: (string): Name of the antiviral.
  • 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.

Clinical Presentation

  • Symptoms (array): List of symptoms (i.e. cough, sore throat, etc.).
  • 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.
  • Hospitalised: Whether individual was hospitalised. Must be one of: ["Y", "N"].
  • 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"].
  • Home_monitoring: Whether individual is being remotely monitored by health officials at home without hospital admission. Must be one of: ["Y", "N"].
  • Isolated: Whether individual was isolated at home or in hospital. Dependent on context/pathogen. Must be one of: ["Y", "N"].
  • 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"].
  • 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_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: 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.
  • Travel_history_comment (object): Free text describing any additional travel information. For internal use only.

Laboratory Information

  • Genomics_Metadata (string): Which clade the viral strain belongs to.
  • Accession_Number (string): Accession number of the sequence uploaded to public database.
  • Confirmation_comment (object): Free text describing any additional confirmation information. For internal use only.

Source Information

  • Source_I (string, format: uri): URL of news story or government source where this case was confirmed.
  • Date_report_ource_I (string, format: date): Date of report.
  • Source_I_Government (string, format: uri): Must be one of: ["Y", "N"].
  • 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 by curator.
  • Date_last_modified (string, format: date): Last date when case was modified in line list by curator.

Changelog

In December, G.h reached 100 days of active outbreak response for mpox and will transition to offer resources available from the WHO (Mpox dashboard) and Africa CDC (Reports) through our platform. We aim to complement, not replace, existing systems. Users may access the G.h linelist archive here (Link pending). WHO data as of 08 December 2024. WHO notes that 'In the Democratic Republic of the Congo, confirmed and suspected cases reported at the national level are not updated as of the 17th November 2024. Efforts are ongoing to update this data' (n=9,513 confirmed cases).

Footnotes are provided in G.h Briefing Reports to provide insight and transparency into the curation process.

*Case Status_'Discarded' On 05 November 2024, G.h updated our case status definition for ‘suspected’ cases to align with WHO’s description from their website and SitReps, “In some countries, suspected cases that undergo testing are not removed from the count, regardless of whether the test result is positive (confirmed case) or negative (discarded case). Moreover, not all countries have robust surveillance systems for mpox, meaning reported case counts likely underestimate the extent of community transmission." "In the absence of more detailed information, it is currently not possible to correctly subtract confirmed cases from the total number of suspected cases reported; therefore, the confirmed cases represent a subset of suspected cases"

G.h has adjusted our discarded / suspected case numbers in our linelist database, for most countries, to align with WHO case numbers for suspected cases. G.h is using official data for suspected cases from the Rwanda Ministry of Health since WHO has not included suspected cases for Rwanda in their reporting.

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 Mpox data [GHL2024.D11.1E71] 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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