Surveillance and Phylogenetic Characterisation of Avian Influenza Viruses Isolated from Wild Waterfowl in Zambia in 2015, 2020, and 2021

Abstract

In recent years, the southern African region has experienced repeated incursions of highly pathogenic avian influenza viruses (HPAIVs), with wild migratory birds being implicated in the spread. To understand the profile of avian influenza viruses (AIVs) circulating in Zambia, we surveyed wild waterfowl for AIVs and phylogenetically characterised the isolates detected in 2015, 2020, and 2021. A total of 2,851 faecal samples of wild waterfowl were collected from Lochinvar National Park in the Southern Province of Zambia. During the study period, 85 (3.0%) low pathogenicity AIVs belonging to various subtypes were isolated, with H2N9, H8N4, and H10N8 being reported for the first time in avian species in Africa. The majority of the isolates were detected from glossy ibis (order Pelecaniformes) making it the first report of AIV from these birds in Zambia. Phylogenetic analysis of all eight gene segments of the 30 full genomes obtained in this study revealed that all the isolates belonged to the Eurasian lineage with their closest relatives being viruses isolated from wild and/or domestic birds in Bangladesh, Belgium, Egypt, Georgia, Mongolia, the Netherlands, and South Africa. Additionally, the Zambian viruses were grouped into distinct clusters based on the year of isolation. While no notifiable AIVs of the H5 or H7 subtypes were detected in wild birds in Zambia, viral internal protein genes of some viruses were closely related to H7 low pathogenicity AIVs. This study shows that periodically, a considerable diversity of AIV subtypes are introduced into the Zambian ecosystem by wild migratory waterfowl. The findings highlight the importance of continuous surveillance and monitoring of AIVs in wild waterfowl, including birds traditionally not considered to be major AIV reservoirs, for a better understanding of the eco-epidemiology and evolutionary dynamics of AIVs in Africa.

Outbreaks of H5N1 High Pathogenicity Avian Influenza in South Africa in 2023 Were Caused by Two Distinct Sub-Genotypes of Clade 2.3.4.4b Viruses

“…H6N2 and H12N2 viruses detected in ostriches indicated that these subtypes were also circulating in the local wild bird reservoir in 2023. The identity of the other subtypes could not be established, but H1Nx, H2Nx, and H10Nx viruses are likely as these were identified in Zambian wild birds in recent years [ 29 ].…”

Phylogenetic Analysis of Newcastle Disease Virus Isolated from Poultry in Live Bird Markets and Wild Waterfowl in Zambia

“…The study samples were collected in 2015, 2020, and 2021 from wild waterfowl and poultry in Zambia ( Table 1 ) as part of the AIV surveillance activities. Results for AIV surveillance in wild waterfowl have been published elsewhere [ 22 ]. A total of 2851 fresh faecal samples were collected from the wild birds in Lochinvar National Park (LNP), a bird sanctuary that is home to migratory birds.…”

“…Faecal samples were processed as per the previously described protocol [ 13 , 22 ]. About 0.5 mL of supernatant fluid from each sample was inoculated in duplicate into the allantoic cavity of 9 to 11-day-old embryonated chicken eggs.…”

“…Sequencing was performed as previously described [ 22 ]. Viral RNA was extracted from the HA-positive and HI-confirmed allantoic fluids using the QIAamp Viral RNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.…”