The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021–2022

Abstract

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021–2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho’s outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana’s outbreaks in 2021 were unrelated, but viruses of Botswana’s unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA’s commercial poultry cases in 2021–2022 were point introductions from wild birds. Like H5N8 HPAI in 2017–2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

“…], and prion species [small petrels in the genera Pachyptila and Halobaena ]), which nest in separated burrow systems and may limit spread. Penguins are also susceptible to HPAIV, and mortality has been observed following infection 68 . Penguin species nest in high densities (dependent upon species ranging between 0.25 - 1.7 nests per m 2 ) 69, 70 , and although limited impact has been seen to date, if HPAIV does start to impact more significantly on penguin colonies, it could show rapid infection and spread.…”

Unexpected delayed incursion of highly pathogenic avian influenza H5N1 (clade 2.3.4.4b) in the Antarctic region

“…Compared to previous HPAIV subtypes and clades, H5N1 2.3.4.4b has significantly improved replication in wild birds (3), and increased fitness through continuous reassortments (4). Also, the virus is able to infect an unusually broad variety of wild bird species (3), which has likely facilitated this spread. In addition to their role as viral spreaders, wild birds are suffering huge losses following mass mortality events, and the scale of mortality amongst wild birds is likely in the millions rather than tens of thousands reported (5).…”

“…Wild bird movements have underpinned the rapid spread of this virus that swept across most continents within two years (2). Compared to previous HPAIV subtypes and clades, H5N1 2.3.4.4b has significantly improved replication in wild birds (3), and increased fitness through continuous reassortments (4). Also, the virus is able to infect an unusually broad variety of wild bird species (3), which has likely facilitated this spread.…”

“…Furthermore, while mainly ducks were previously central to HPAIV outbreaks, the global panzootic includes a large range of bird species, and increasingly novel species groups like seabirds (11). Notably in breeding colonies of seabirds, there have been extensive outbreaks in Europe in 2022 and 2023, and the southward expansion of HPAIV H5N1 in South America was largely driven through outbreaks in coastal seabirds, including pelicans and cormorants, as well as spill-overs to coastal marine mammals with the deaths of >20,000 South American sea lions (3,9,12,13).…”

Utilising citizen science data to rapidly assess potential wild bridging hosts and reservoirs of infection: avian influenza outbreaks in Great Britain

“…Although the host range for HPAI H5Nx are known to be broad based on challenge studies and wild-bird surveillance (Lee et al 2017, Empress-i 2023), virulence and transmissibility appear to be highly variable across taxa. Mass mortality events attributed to H5 clade 2.3.4.4b have been recorded in several groups such as wildfowl, shorebirds, seabirds, and raptors (Abolnik et al 2023, Adlhoch & Baldinelli 2023, Lane et al 2023, Pohlmann et al 2023), whereas in other groups, such as passerines, such reports are lacking. However, passerines have demonstrated moderate to high seroprevalence against older clades of HPAI H5Nx, likely indicative of past infection (Kou et al 2005, Kaplan & Webby 2013), and detecting increased mortality in these less conspicuous species is likely to be more difficult.…”