Avian Flu

This repository contains the most updated information on HPAI outbreaks in domestic poultry and captive birds and HPAI positive cases in wild birds in

1. Europe, according to official reporting sources (ADIS – Animal Disease Information System)
2. USA, according to official reporting sources (USDA - United States Department of Agriculture)
3. Italy, according to official reporting sources (IZSVe - Istituto Zooprofilattico Sperimentale delle Venezie)
4. Argentina, according to official reporting sources (SENASA - DIRECCIÓN NACIONAL DE SANIDAD ANIMAL)
5. England, according to official reporting sources (GOV.UK)

Repository structure

avian-flu/
│
├── */
│   ├── Africa/
│   │   ├── africa-outbreaks.csv
│   ├── Americas/
│   │   ├── Argentina/
│   │   │   ├── argentina-aves-de-corral-cases.csv
│   │   │   ├── argentina-aves-no-corral-cases.csv
│   │   ├── USA/
│   │   │   ├── commercial-backyard-flocks.csv
│   │   │   ├── hpai-mammals.csv
│   │   │   ├── hpai-wild-birds.csv
│   │   ├── americas-outbreaks.csv
│   ├── Asia/
│   │   ├── asia-outbreaks.csv
│   ├── Europe/
│   │   ├── Italy/
│   │   │   ├── HPAI/
│   │   │   │   ├── 2021-2022/
│   │   │   │   │   ├── hpai-domestic-poultry-2021-2022.csv
│   │   │   │   │   ├── hpai-wild-birds-2021-2022.csv
│   │   │   │   ├── 2022-2023/
│   │   │   │   │   ├── hpai-domestic-poultry-2022-2023.csv
│   │   │   │   │   ├── hpai-wild-birds-2022-2023.csv
│   │   ├── United Kingdom/
│   │   │   ├── human-potential-exposures.csv
│   │   │   ├── poultry-wildbirds-england.csv
│   │   │   ├── wild-mammals-england.csv
│   │   │   ├── wild-mammals-international.csv
│   ├── Line-lists/
│   │   ├── H3N8/
│   │   │   ├── 2023-03-27-avian-flu-linelist.csv
│   │   ├── H5/
│   │   │   ├── H5N1/
│   │   │   │   ├── 2022-01-14-avian-flu-linelist.csv
│   │   │   │   ├── 2022-05-06-avian-flu-linelist.csv
│   │   │   │   ├── ...
│   │   │   ├── 2022-10-21-avian-flu-linelist.csv
│   │   │   ├── 2023-01-09-avian-flu-linelist.csv
│   │   │   ├── ...
│   ├── PDFs/
│   ├── images/
│   ├── human-cases.csv
│   ├── summary-outbreaks-mammals.csv

Information on data files

1. The Argentina folder was added on March 12
2. The Americas, Asia, Africa folders was added on March 15
3. The United Kingdom folder was added on March 16

Visualization

1. Italy Map
   
   

Data dictionary

The data dictionary contains information about columns/fields in the list files.

Data schema

Filename: europe-cases.csv

Field	Format	Description
Confirmed date	YYYY-MM-DD	Date of notification
Country	String	Name of the country
Lat	WGS84	Latitude of the country
Long	WGS84	Longitude of the country
HPAI strain	String	Name of the HPAI strain
WOAH Classification	String	Name of the species
Outbreaks	Integer	Number of outbreaks

Directory: Italy
Filename: hpai-wild-birds-#.csv (example: hpai-wild-birds-2021-2022.csv)

Field	Format	Description
n	Integer	Number of the row
ID ADIS	String	ADIS Reference is a unique identification code authomatically created by the EU Animal Disease Information System (Regolations (EU) 2016/429 e 2020/2002) when Competent Autority of each Member State notifies an animal disease outbreak. The actual number of outbreaks is the one indicated in the first column of the table.
Region	String	Name of the region
Province	String	Name of the province
Latitude	WGS84	Latitude of the province
Longitude	WGS84	Longitude of the province
No. animals	Integer	Number of cases
Species	String	Name of the species
HPAI strain	String	Name of the HPAI strain
Confirmation date	YYYY-MM-DD	Date of notification

Directory: Italy
Filename: hpai-domestic-poultry-#.csv (example: hpai-domestic-poultry-2021-2022)

Field	Format	Description
n	Integer	Number of the row
ID ADIS	String	ADIS Reference is a unique identification code authomatically created by the EU Animal Disease Information System (Regolations (EU) 2016/429 e 2020/2002) when Competent Autority of each Member State notifies an animal disease outbreak. The actual number of outbreaks is the one indicated in the first column of the table.
Region	String	Name of the region
Province	String	Name of the province
Latitude	WGS84	Latitude of the province
Longitude	WGS84	Longitude of the province
No. animals	Integer	Number of cases
Species	String	Name of the species
HPAI strain	String	Name of the HPAI strain
Confirmation date	YYYY-MM-DD	Date of notification
Extinction date	YYYY-MM-DD	Termination date surveillance
Measures Protection Zone in force until	YYYY-MM-DD	The boundaries of the protection and surveillance zones and the date on which the measures applied will be lifted, were decided according to art 21 point 2 ‘The competent authority shall adapt the boundaries of the initial restricted zone, including the boundaries of the protection, surveillance and the further restricted zones, in the case of the overlapping of two or more restricted zones due to further outbreaks of the category A disease.’, and art 39 point 1 a) and b) of the Commission Delegated Regulation (EU) 687/2020 ‘The competent authority may lift the measures provided for in Section 1 and 2 of this Chapter only if the minimum period set out in Annex X has elapsed and the following conditions are fulfilled: (a) the preliminary cleaning and disinfection and, where relevant, control of insects and rodents, has been performed in accordance with Article 15 in the affected establishment; and (b) in all establishments keeping animals of listed species in the protection zone, animals of listed species have undergone, with favourable results, clinical and when necessary laboratory examination in accordance with Article 26.’ The amendments to these zone will be published regularly with the Commission Implementing Decision (EU) 2021/641.
Measures Surveillance Zone in force until	YYYY-MM-DD	The boundaries of the protection and surveillance zones and the date on which the measures applied will be lifted, were decided according to art 21 point 2 ‘The competent authority shall adapt the boundaries of the initial restricted zone, including the boundaries of the protection, surveillance and the further restricted zones, in the case of the overlapping of two or more restricted zones due to further outbreaks of the category A disease.’, and art 39 point 1 a) and b) of the Commission Delegated Regulation (EU) 687/2020 ‘The competent authority may lift the measures provided for in Section 1 and 2 of this Chapter only if the minimum period set out in Annex X has elapsed and the following conditions are fulfilled: (a) the preliminary cleaning and disinfection and, where relevant, control of insects and rodents, has been performed in accordance with Article 15 in the affected establishment; and (b) in all establishments keeping animals of listed species in the protection zone, animals of listed species have undergone, with favourable results, clinical and when necessary laboratory examination in accordance with Article 26.’ The amendments to these zone will be published regularly with the Commission Implementing Decision (EU) 2021/641.

Getting the data

Direct download (CSV): https://raw.githubusercontent.com/fbranda/avian-flu/main/europe-cases.csv

Python (requires pandas):

import pandas as pd
df = pd.read_csv("https://raw.githubusercontent.com/fbranda/avian-flu/main/europe-cases.csv")

R:

df <- read.csv("https://raw.githubusercontent.com/fbranda/avian-flu/main/europe-cases.csv")

Contributions

1. Branda F, Mazzoli S. The importance of rapid and robust availability of epidemiological data for real-time mapping of the risk of avian influenza a (H5N1) spread. Pathogens and Global Health. 2023 Jun 22:1-4.

2. Branda, F.; Mazzoli, S.; Pierini, M.; Ciccozzi, M. Trends and Spatiotemporal Patterns of Avian Influenza Outbreaks in Italy: A Data-Driven Approach. Infect. Dis. Rep. 2024, 16, 1-12.

License and attribution

This repository and data exports are published under the CC BY 4.0 license.

Please cite as: Francesco Branda. (2023). Open Avian Flu Dataset [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8246456