Information for this dataset was collected and built-in from two main animal well being databases: i) the Rising Illness Surveillance Program (ProMED-mail) (https://promedmail.org/), a program of the Worldwide Society for Infectious Illnesses (ISID, https://isid.org/) and ii) the World Animal Well being Data System (WAHIS) of the World Group for Animal Well being (WOAH, previously OIE) (https://wahis.woah.org/) .

Step 1: Integration of ProMED mail reviews

ProMED-mail (https://promedmail.org/) is the most important publicly obtainable system for reporting international outbreaks of infectious illnesses (outbreak means the prevalence of a number of circumstances in an epidemiological unit). It offers reviews (so-called “posts”) about outbreaks and occurrences of illnesses. The stream of knowledge resulting in the publication of ProMED-mail reviews is as follows: A illness occasion to be despatched is chosen from day by day outbreak notifications acquired by way of electronic mail, looking out the Web and conventional media, and looking out official and unofficial web sites. All incoming data is reviewed and filtered by an editor or deputy editor, who then passes it on to a multidisciplinary workforce of moderators of subject material consultants who assess the accountability and accuracy of the data, interpret, remark and cross-reference to earlier ProMED media. Mail reviews and the scientific literature35. A ProMED Mail report, recognized by a singular report identifier, can symbolize a single or a number of well being occasions.

The mixing of the curiosity messages from ProMED-mail happened in two steps:

i) Choice of ProMED mail reviews

By means of the “Search Posts” function on the ProMED-mail web site, we now have recognized reviews describing SARS-CoV-2 occasions in animals, ie presenting at the least one single case of SARS-CoV-2 in an animal. We used the key phrases “animal” and “COVID-19” (that are used within the “topic” of ProMED mail posts to report data associated to SARS-CoV-2 in animals) to naturalize the reviews and experimental infections or vaccination exams in animals, and common discussions of SARS-CoV-2 in animals (Notice: Though COVID-19 refers back to the illness brought on by SARS-CoV-2 in people and shouldn’t be utilized in animals, ProMED- mail conveniently makes use of this key phrase for each people and animals). Studies describing naturally occurring an infection (that means the presence of the virus is demonstrated by laboratory methodology(s)) or publicity (that means the presence of antibodies to SARS-CoV-2 is demonstrated by laboratory methodology(s)) of a person or group of People had been manually filtered and included for information extraction. On the time of submission (June 22, 2022), the ProMED-mail database contained 232 reviews of SARS-CoV-2 in animals.

ii) Hyperlink to earlier reviews

If a well being occasion is ongoing, ProMED-mail publishes follow-up reviews that hyperlink to earlier ProMED-mail reviews (on the finish of the report or within the “See additionally” part on the finish of the article). We used this data to determine the potential relationship of every reported occasion to a earlier one (e.g. medical follow-up, additional unfold of the virus and therapy consequence) and entered this information into the ultimate dataset.

Step 2: Integration of WAHIS reviews

WAHIS (https://wahis.woah.org/) is a web-based pc system that processes animal illness information in actual time. The WAHIS information displays the data collected by the veterinary companies of WOAH member (previously OIE) and non-member nations and territories on WOAH-listed home, wild animal, rising and zoonotic illnesses. In keeping with the WOAH Terrestrial Animal Well being Code36, proof of SARS-CoV-2 an infection in animals meets the factors for reporting to WOAH as an rising an infection (https://www.woah.org/app/uploads/2021/03 /a-reporting-sars-cov-2-to-the-oie.pdf). Solely approved customers, ie WOAH member nation delegates and their approved representatives, can enter information into the WAHIS platform to tell the WOAH of related animal illness data.

A WAHIS report, recognized by a singular report identifier, could comprise a single or a number of outbreaks, every recognized by a singular outbreak identifier. All data is publicly obtainable on the WAHIS interface.

The WAHIS messages of curiosity had been built-in in two steps:

i) Choice of WAHIS reviews

We used the WAHIS animal illness occasions dashboard (https://wahis.woah.org/#/occasions) to extract circumstances of SARS-CoV-2 an infection in animals reported by WOAH member states and non-member states. WAHIS publishes immediate notifications (INs) and follow-up reviews (FURs), recognizable by the prefix “IN” and “FUR” of their respective names. Immediate reviews present details about newly reported occasions, whereas FURs typically present updates about beforehand reported ongoing occasions (e.g. variety of newly contaminated animals and new deaths, new management measures launched).

We utilized filters to the DISEASE discipline (“SARS-CoV-2 in animals (inf. with)”) and REPORT DATE to pick out reviews of SARS-CoV-2 occasions from December 1, 2019 to the current. The reviews might be seen on-line or downloaded as a single PDF or Excel file, with every file equivalent to a rustic report (ie a number of outbreaks might be included in a single report). On the time of submitting (June 22, 2022), the WAHIS dashboard contained 311 reviews associated to SARS-CoV-2.

ii) Identification of gaps and completion of the dataset

ProMED-mail searches all kinds of knowledge sources, together with WAHIS reviews. The ProMED Mail posts point out the Occasion ID of the WAHIS report(s) used as a supply of knowledge, permitting the unique supply to be consulted on the WAHIS dashboard. Due to this fact, we determined to first determine SARS-CoV-2 occasions in animals within the ProMED mail database. In a second step, we used the WAHIS dashboard to determine gaps, i.e. to finish the beforehand recorded SARS-CoV-2 occasions (hereinafter known as sibling occasions) and to search out extra occasions that weren’t reported in ProMED-mail had been (Fig. 1).

Fig. 1illustration 1

Schematic overview of the methodology: report integration and validation steps.

For every nation (utilizing the “COUNTRY/TERRITORY” filter on the WAHIS dashboard), we recognized sibling occasions by evaluating the WAHIS reviews to the entire nation’s beforehand entered ProMED Mail reviews, utilizing data on species, subnational Administration and date of laboratory affirmation (a buffer of ±7 days was thought of attributable to attainable discrepancies when it comes to affirmation by totally different laboratories) or date of publication if the date of laboratory affirmation was lacking (on this case a buffer of 30 days was thought of because of the date of the publication is extremely database dependent). Now we have not used metropolis data right here as reviews could inconsistently seek advice from the town/village of outbreak prevalence attributable to privateness considerations.

Though this technique was time consuming, it was persistently utilized all through the information extraction course of to make sure complete assortment of knowledge for every outbreak, information accuracy, and methodology reproducibility.

information extraction

ProMED-mail offers detailed, text-based (narrative) reviews on well being occasions. This information is unstructured, whereas WAHIS makes use of each semi-structured (.pdf file divided into sections together with free textual content) and structured information (.xlsx format) to show the reviews. Every chosen report has undergone a handbook assessment by a veterinarian, making certain a full understanding of the content material and context. Data was extracted manually and coded by hand.

The next occasion data was extracted (if obtainable) and entered right into a structured template in a devoted .csv file:

  • – animal host: widespread title (ie most particular title of the supply(s) in English) and scientific title as talked about within the supply(s) (scientific names are harmonized in order that solely the primary letter of the genus is capitalized) ;

  • – Geographical location: nation, sub-national authorities, metropolis;

  • – SARS-CoV-2 variant;

  • – Dates: when the case was confirmed within the laboratory, reported by WAHIS and printed;

  • – Metrics: variety of circumstances, variety of deaths, variety of prone animals.

As well as, the next animal affected person/case data was extracted to populate the dataset:

  • – Age;

  • – intercourse;

  • – Dwelling circumstances;

  • – Primary purpose for the take a look at;

  • – suspected supply of an infection;

  • – Signs: The primary reported medical indicators allegedly related to SARS-CoV-2 have been summarized with one to extra key phrases talked about within the textual content. A number of signs have been separated by the “and” operator.

The extracted information described above was entered into the dataset as talked about within the report and no data was subjected to any interpretation previous to entry. To make the information simpler to grasp, combine with different sources, and analyze, we have additionally added the next 5 affected person attributes:

  • – The widespread and scientific title (resolved to species or subspecies degree, relying on obtainable data) of the animal host, harmonized with the Nationwide Middle for Biotechnology Data (NCBI) taxonomic backbone37;

  • – The host’s colloquial title, ie the title utilized in technical jargon to determine the animal (e.g. “tiger” for “Sumatran tiger”);

  • – The scientific title of the host resolved to the species degree;

  • – The upper taxonomy (ie household) of the animal host, taken from the report, knowledgeable data or the literature.

Lastly, for every SARS-CoV-2 occasion captured within the information set, we now have supplied the first and secondary supply of knowledge i.e. supply title (ProMED-Mail or WAHIS) and hyperlink to the web report, in addition to the unique supply of knowledge given by the first supply. A duplicate of every report used in the course of the information extraction course of was downloaded and saved as a PDF file. We timestamped the saved file (ProMED Mail reviews) or the obtain date was specified within the filename (inserting a timestamp for WAHIS reviews was not attainable).

The info documenting every occasion corresponds to the data obtainable within the ProMED Mail and/or WAHIS report when the report is seen (see timestamp or obtain date). Any subsequent editions or modifications of the report by ProMED-mail and/or WAHIS weren’t taken under consideration.

Disclaimer

Use of the information from the WAHIS platform requires point out of the next assertion: “The World Group for Animal Well being (WOAH) bears no duty for the integrity or accuracy of the information contained herein, together with however not restricted to, deletion, manipulation or reformatting of knowledge that will have occurred past its management”.

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