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. 2024 May 31;16(6):896.
doi: 10.3390/v16060896.

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

Celia Abolnik  1 , Laura Christl Roberts  1   2   3 , Christine Strydom  4 , Albert Snyman  5 , David Gordon Roberts  5
Affiliations

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

Celia Abolnik et al. Viruses. .

Abstract

In 2023, South Africa continued to experience sporadic cases of clade 2.3.4.4b H5N1 high-pathogenicity avian influenza (HPAI) in coastal seabirds and poultry. Active environmental surveillance determined that H5Nx, H7Nx, H9Nx, H11Nx, H6N2, and H12N2, amongst other unidentified subtypes, circulated in wild birds and ostriches in 2023, but that H5Nx was predominant. Genome sequencing and phylogenetic analysis of confirmed H5N1 HPAI cases determined that only two of the fifteen sub-genotypes that circulated in South Africa in 2021-2022 still persisted in 2023. Sub-genotype SA13 remained restricted to coastal seabirds, with accelerated mutations observed in the neuraminidase protein. SA15 caused the chicken outbreaks, but outbreaks in the Paardeberg and George areas, in the Western Cape province, and the Camperdown region of the KwaZulu-Natal province were unrelated to each other, implicating wild birds as the source. All SA15 viruses contained a truncation in the PB1-F2 gene, but in the Western Cape SA15 chicken viruses, PA-X was putatively expressed as a novel isoform with eight additional amino acids. South African clade 2.3.4.4b H5N1 viruses had comparatively fewer markers of virulence and pathogenicity compared to European strains, a possible reason why no spillover to mammals has occurred here yet.

Keywords: H5N1; PA-X isoform; PB1-F2 truncation; clade 2.3.4.4b; high-pathogenicity avian influenza; phylogenetic analysis; poultry; seabirds; wild bird disease surveillance.

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Conflict of interest statement

Author Christine Strydom is employed by the company SMT Veterinary Laboratory (Pty) Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Time-scaled maximum clade credibility tree of the complete genomes of southern African clade 2.3.4.4B H5N1 HPAI viruses. Sub-genotypes of the clades are in italics.
Figure 2
Figure 2
Enlarged view of the concatenated genome time-scaled MCC tree showing sub-genotype SA13 viruses. Sub-clades designated as groups A, B (B1 and B2), and C are indicated.
Figure 3
Figure 3
Map showing the locations of clade 2.3.4.4b H5N1 outbreaks in South Africa in 2023.
Figure 4
Figure 4
Enlarged view of the concatenated genome time-scaled MCC tree showing sub-genotype SA15 viruses. Sub-clades designated as groups D, E, and F are indicated. WC—Western Cape province; KZN—KwaZulu-Natal province.
Figure 5
Figure 5
Results of environmental wild bird surveillance in 2023. Pie chart sizes are proportional to the numbers of samples tested. Inset: comparison of the cycle threshold (Ct) values for the real-time rRT-PCR AIV screening assay vs. the H5 subtyping assay.
See this image and copyright information in PMC

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