SARS-ANI VIS

Informing Scientists, Stakeholders, and the Public

The SARS-ANI VIS provides intuitive insights into specific aspects of SARS-CoV-2 events in animals at-a-glance.

Data Sources

Information displayed in the SARS-ANI dashboard is collected from reports published in two major databases: i) the Program for Monitoring Emerging Diseases ProMED-mail, which is a program of the International Society for Infectious Diseases (ISID), and ii) the World Animal Health Information System (WAHIS) of the World Organisation for Animal Health (WOAH, formerly OIE).

One ProMED-mail or WAHIS report, identified via a unique report identifier, may depict one single or several health events (or outbreaks). ProMED-mail and WAHIS also publish follow-up reports of outbreaks (describing e.g. clinical follow-up, further spread of the virus, treatment outcome, number of newly infected animals and new deaths, newly implemented control measures) that have also been entered in the dataset.

Remarks

The number of reported SARS-CoV-2 events in animals in each country depends on the reporting strategy of the country to the WOAH, the intensity of the research and surveillance strategy in the different animal hosts (e.g. whether pets from infected households are systematically investigated or not), the media coverage on the diagnosed cases, and the uptake of the reported event by the ProMED-mail team.

If an event/outbreak is not published in WAHIS and/or ProMED-mail then it will not be included in the dataset.

Number of cases and deaths in farmed mink are inconsistently reported, therefore data on SARS-CoV-2 events in mink are partial and does not allow accurate estimation of the impact of SARS-CoV-2 in the mink population.

Data documenting each event corresponds to information available in the ProMED-mail and/or WAHIS report when consulting the report. Potential subsequent editions or modifications of the report by ProMED-mail and/or WAHIS is not considered.

Definitions

SARS-CoV-2 event: We consider as an event when one single case or several epidemiologically related cases were identified by the presence of viral RNA (proof of infection) and/or antibodies (proof of exposure) in an animal. Epidemiologically related cases include e.g. animals belonging to the same farm, captive animals housed together, pets belonging to the same household, or animals sampled within the same (generally transversal) study, featuring similar event and patient attributes, i.e. they underwent the same laboratory test(s) and showed the same results (including variant), exhibited the same symptoms and disease outcome, and were confirmed, reported (when applicable), and published on the same date (e.g. when pets of the same species sharing the same household showed different symptoms, they are reported as two distinct events). Events include follow-up history reports of outbreaks (e.g. follow-up on the clinical status of the animal, variant identification after case confirmation).

Infection: The presence of the virus is evidenced through laboratory method(s).

Exposure: The presence of antibodies against SARS-CoV-2 is evidenced through laboratory method(s).

Outbreak: Occurrence of one or more cases in an epidemiological unit (e.g. one farm, one household). The number of outbreaks is lower than the number of events because distinct events i) may belong to the same epidemiological unit (e.g. animals that are living together) or ii) may be follow-ups of the same outbreak.

Case fatality rate: The CFR for each animal host and country is obtained by dividing the total number of reported deaths in one animal host by the total number of reported cases for this host in the country. Animals culled as part of a control strategy are excluded (not all were diagnosed as infected). Similarly, mink are not included here because data on case and death numbers are partial. The CFR depends strongly on testing and does not give information on the infection fatality rate (IFR, number of deaths divided by the total number of infected individuals) or mortality rate (MR, number of deaths divided by the total at-risk population).

Date confirmed: When the SARS-CoV-2 infection or exposure was laboratory confirmed.

Date reported: When the SARS-CoV-2 event was reported by the WAHIS.

Date published: When the primary source published the SARS-CoV-2 event (date published = date reported when WAHIS is primary source).

Not applicable: Used when the information does not apply to the event. For example when only one laboratory test is conducted, “Not applicable” is reported for the second and third tests.

Not specified: Used when the information is relevant for the event but has not been specified in the report(s). For example, when a PCR test is performed for diagnostic purpose but the report(s) does not mention which sample was used, the sample type is “Not specified”.

Animal host names and taxonomy

The SARS-ANI VIS displays recognized common and scientific names for the animal hosts, all harmonized against the National Center for Biotechnology Information (NCBI) backbone.

Raw data

A dynamic version of the dataset, which is weekly updated, can be accessed via GitHub https://github.com/amel-github/sars-ani/.

Disclaimer

The World Organisation for Animal Health (WOAH) bears no responsibility for the integrity or accuracy of the data contained herein, in particular due, but not limited to, any deletion, manipulation, or reformatting of data that may have occurred beyond its control.