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

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.

Figure 1

Spatial distribution of thirteen sites investigated for IAV in wild birds in Gauteng Province. The sample size is indicated for those sites where ≥10 swab pools were collected (green points). Locations are indicated as follows: (a) Bon Accord Dam, (b) Zeekoegat, (c) Irene, (d) Baja Dam, (e) Leeukop Gevangenis Dam, (f) Zoo Lake, (g,h) Turffontein and Wemmerpan, (i) Grootvaly, (j) Rooikraal, (k) Heidelberg Dump, (l) Loch Vaal, (m) Klipdrift Dam.

Figure 2

Maximum likelihood phylogenetic tree of the H9 subtype HA genes. Viral sequences from the present study (black dots) and other South African viruses (grey dots) are highlighted.

Figure 3

Schematic overview of the ancestry and genomic reassortment between IAV field strains (black, solid lines) and their hypothetical recent common ancestors (grey, dotted lines) interpreted from the ML phylogenetic trees (Figure 2; Figures S1–S7) and tMRCA analyses (Table S2). The node dates are shown (see Table S2 for the 95% HPD).