Wild Bird Surveillance in the Gauteng Province of South Africa during the High-Risk Period for Highly Pathogenic Avian Influenza Virus Introduction

Celia Abolnik; Thandeka P Phiri; Gerbrand van der Zel; Jade Anthony; Nadine Daniell; Liesl de Boni

doi:10.3390/v14092027

Wild Bird Surveillance in the Gauteng Province of South Africa during the High-Risk Period for Highly Pathogenic Avian Influenza Virus Introduction

Viruses. 2022 Sep 13;14(9):2027. doi: 10.3390/v14092027.

Authors

Celia Abolnik¹, Thandeka P Phiri¹, Gerbrand van der Zel², Jade Anthony¹, Nadine Daniell¹, Liesl de Boni²

Affiliations

¹ Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.
² Gauteng Department of Agriculture and Rural Development, Johannesburg 2000, South Africa.

Abstract

Migratory birds carried clade 2.3.4.4B H5Nx highly pathogenic avian influenza (HPAI) viruses to South Africa in 2017, 2018 and 2021, where the Gauteng Province is a high-risk zone for virus introduction. Here, we combined environmental faecal sampling with sensitive rRT-PCR methods and direct Ion Torrent sequencing to survey wild populations between February and May 2022. An overall IAV incidence of 42.92% (100/231) in water bird faecal swab pools or swabs from moribund or dead European White Storks (Ciconia ciconia) was detected. In total, 7% of the IAV-positive pools tested H5-positive, with clade 2.3.4.4B H5N1 HPAI confirmed in the storks; 10% of the IAV-positive samples were identified as H9N2, and five complete H9N2 genomes were phylogenetically closely related to a local 2021 wild duck H9N2 virus, recent Eurasian LPAI viruses or those detected in commercial ostriches in the Western and Eastern Cape Provinces since 2018. H3N1, H4N2, H5N2 and H8Nx subtypes were also identified. Targeted surveillance of wild birds using environmental faecal sampling can thus be effectively applied under sub-Saharan African conditions, but region-specific studies should first be used to identify peak prevalence times which, in southern Africa, is linked to the peak rainfall period, when ducks are reproductively active.

Keywords: H5N1; H9N2; avian influenza; environmental faecal sampling; wild bird surveillance.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Animals, Wild
Ducks
Influenza A Virus, H5N1 Subtype*
Influenza A Virus, H5N2 Subtype*
Influenza A Virus, H9N2 Subtype*
Influenza in Birds* / epidemiology
Phylogeny
South Africa / epidemiology
Struthioniformes*
Water

Substances

Water

Grants and funding

The study was funded by the National Department of Science and Innovation (DSI) and National Research Foundation (NRF) grant no. N00705/114612 and the National Department of Trade and Industry (DTI) grant “Healthy Flocks-Quality Leather”, with contributions from the Gauteng Department of Agriculture and Rural Development.