Wild bird surveillance in the Gauteng Province of South Africa during the high-risk period for highly pathogenic avian influenza virus introduction

Abolnik, CeliaPhiri, T.P.Van der Zel, GerbrandAnthony, JadeDaniell, NadineDe Boni, Liesl2023-03-242023-03-242022-09-13Abolnik, C.; Phiri, T.P.; van der Zel, G.; Anthony, J.; Daniell, N.; de Boni, L.Wild Bird Surveillance in the Gauteng Province of South Africa during the High-Risk Period for Highly Pathogenic Avian Influenza Virus Introduction. Viruses 2022, 14, 2027. https://DOI.org/10.3390/v14092027.1999-4915 (online)10.3390/v14092027http://hdl.handle.net/2263/90191DATA AVAILABILITY STATEMENT : Sequences generated in this study are deposited in the GISAID EpiFlu database under the accession numbers EPI2131759-EPI2131784, EPI2121793-EPI2131801, EPI2131810- EP12131826, EP12131838-EPI2131851 and EPI2131857-EPI2131864.SUPPLEMENTARY MATERIAL : FIGURE S1 (a): Maximum likelihood phylogenetic tree of the PB2 genes (2153 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; Figure S1 (b): Maximum likelihood phylogenetic tree of the PB2 genes (839 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S2: Maximum likelihood phylogenetic tree of the PB1 genes (2271 bp alignment). Viral sequences from the present study are indicated with black dots; FIGURE S3: Maximum likelihood phylogenetic tree of the PA genes (1940 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S4: Maximum likelihood phylogenetic tree of the NP genes (1372 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S5: Maximum likelihood phylogenetic tree of the N2 subtype NA genes (902 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S6: Maximum likelihood phylogenetic tree of the M genes (979 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; FIGURE S7: Maximum likelihood phylogenetic tree of the NS genes (832 bp alignment). Viral sequences from the present study are indicated with black dots, with other South African virus sequences indicated by grey dots; TABLE S1: Samples analysed in the study and summary of results; TABLE S2: tMRCA analysis.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.en© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.Wild bird surveillanceH9N2H5N1Environmental faecal samplingAvian influenza virusHighly pathogenic avian influenza (HPAI)Wild bird surveillance in the Gauteng Province of South Africa during the high-risk period for highly pathogenic avian influenza virus introductionArticle