DOI: 10.5281/zenodo.8246455
title: Open Avian Flu Dataset

description: Description: The Open Avian Flu Dataset (OAFD) is a collection of structured and curated data related to avian influenza (bird flu) outbreaks. It is designed to support research, analysis, and modeling efforts aimed at understanding the spread, impact, and control of avian flu. The dataset could encompass various aspects of avian flu, including viral strains, geographic distribution, host species, clinical outcomes, genetic sequences, and more.

Contents:



Geographic Data: Information about the locations of avian flu outbreaks, including latitude, longitude, country, region, and affected farms or regions.

Temporal Data: Dates of outbreak initiation, and detection.

Viral Strains: Information about the avian influenza virus strains involved in different outbreaks.

Host Species: Data on the types of bird species affected by each outbreak.

Clinical Data: Details on the clinical symptoms, morbidity, and mortality rates associated with different outbreaks.


Purpose: The purpose of the Open Avian Flu Dataset is to facilitate collaborative research, analysis, and modeling efforts aimed at understanding and mitigating the impact of avian flu outbreaks. By making this data openly accessible, researchers, epidemiologists, public health officials, and data scientists can work together to develop effective strategies for prevention, control, and response to avian flu outbreaks.

It's important to note that the specific content and structure of such a dataset can vary based on the sources of data, the objectives of the initiative, and the time frame of data collection. To find the most up-to-date and accurate information about any open dataset for avian flu, I recommend checking with reliable sources such as international health organizations, research institutions, or relevant data repositories.
description: Details of the OAFD files. 






Folder



Subfolder



File



Description





Africa



-



africa-outbreaks.csv



Number of HPAI detections in African countries not reporting via ADIS, by virus subtype and species [1].





Americas



Argentina



1.     argentina_aves_de_corral_cases.csv

2.     argentina_aves_no_corral_cases.csv



Number of HPAI detections in Argentine reported by Senasa, by province and species [2].





USA



1.     commercial-backyard-flocks.csv

2.     hpai-mammals.csv

3.     hpai-wild-birds.csv



Number of HPAI detections in USA reported by USDA/APHIS, by state, virus subtype and species [3].





-



americas-outbreaks.csv



Summary of HPAI detections in Americas, by country, virus subtype and species [1].





Asia



-



asia-outbreaks.csv



Number of HPAI detections in Asian countries not reporting via ADIS, by virus subtype and species [1].





Europe



Italy



1.     hpai-domestic-poultry-2021-2022.csv

2.     hpai-domestic-poultry-2022-2023.csv

3.     hpai-wild-birds-2021-2022.csv

4.     hpai-wild-birds-2022-2023.csv



Number of HPAI detections in Italy reported by IZSVe [4], by region, virus subtype and species.





United Kingdom



1.     human-potential-exposures.csv

2.     poultry-wildbirds-england.csv

3.     wild-mammals-england.csv

4.     wild-mammals-international.csv



Number of HPAI detections in United Kingdom reported by GOV.UK [5], by region, virus subtype and species.





-



europe-outbreaks.csv



Summary of HPAI detections in Europe, by country, virus subtype and species [1].





Line-lists



-



2023-03-01-avian-flu-linelist



This folder contains key information about reported human cases, with each row representing a case and each column representing a variable such as demographic, clinical, and epidemiologic information.





H5



1.     2022-10-21-avian-flu-linelist.csv

2.     2023-01-09-avian-flu-linelist.csv

3.     …





H5/H5N1



1.     2022-01-14-avian-flu-linelist.csv

2.     2022-05-06-avian-flu-linelist.csv

3.     …





 



H3N8



2023-03-27-avian-flu-linelist.csv





PDFs



-



Avian influenza overview:

1.     December 2021.pdf

2.     March – June 2022.pdf

3.     June – September 2022.pdf

4.     September – December 2022.pdf

5.     December 2022– March 2023.pdf

6.     Annex December 2022– March 2023 -Data on birds.pdf

7.     March – April 2023.pdf

8.     April – June 2023.pdf



This folder contains the main reports (in PDF format) [1] used to populate the dataset.

 





images



 



Fr6xLWsXoAA_gpj.jpeg

…



This folder contains

image files or graphics relevant to the repository's content. These images can be used for documentation, illustrations, or any visual assets that support the project.





-



-



README.md



This file contains information about the project and the other files stored in the repository.





-



-



data_dictionary.yml



This file describes the names and meanings of each variable (column), data types, possible value ranges, units of measurement, and any other relevant metadata that helps users understand the content and context of the data in the "Line-lists" files.





-



-



human-cases.csv



Summary of HPAI detections in human, by country [6].





-



-



summary-outbreaks-mammals.csv



Summary of HPAI detections in mammals, by country, virus subtype and species [7].





Abbreviation: ADIS: Animal Disease Information System; USDA: U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS); Senasa: Servicio Nacional de Sanidad y Calidad Agroalimentaria; IZSVe: Istituto Zooprofilattico Sperimentale delle Venezie; GOV.UK: United Kingdom government.

References

1.     European Food Safety Authority (EFSA) publications. Avian influenza overview. Available online: https://www.efsa.europa.eu/en/publications?s=avian+influenza+overview

 

2.     Argentina.gob.ar. Influenza aviar. Available online: https://www.argentina.gob.ar/senasa/influenza-aviar

 

3.     U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS). Avian influenza. Available online: https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/avian/avian-influenza

 

4.     Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe). Avian influenza in Italy: updates. Available online: https://www.izsvenezie.com/reference-laboratories/avian-influenza-newcastle-disease/italy-update

 

5.     GOV.UK. Avian influenza (influenza A H5N1): technical briefings. Available online: https://www.izsvenezie.com/reference-laboratories/avian-influenza-newcastle-disease/italy-update

 

6.     World Health Organization (WHO). Cumulative number of confirmed human cases for avian influenza A(H5N1) reported to WHO, 2003-2023. Available online: https://www.who.int/publications/m

 

7.     World Animal Health Information System (WAHIS). Events management. Available online: https://wahis.woah.org/ - /event-management