Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017

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Influenza Other Respir Viruses. 2020 Feb 14. doi: 10.1111/irv.12724. [Epub ahead of print] Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017.

Valley-Omar Z^1,2, Cloete A¹, Pieterse R³, Walaza S¹, Salie-Bassier Y¹, Smith M¹, Govender N¹, Seleka M¹, Hellferscee O¹, Mtshali PS¹, Allam M¹, Ismail A¹, Anthony T³, Seutloali M³, McCarthy K¹, van Helden L⁴, Cohen C^1,5, Treurnicht FK^1,6.
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Abstract

BACKGROUND:

In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces.
OBJECTIVES:

We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak.
METHODS:

Influenza A(H5N8)-positive veterinary specimens were used to evaluate the ability of real-time PCR-based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next-generation sequencing for phylogenetic characterization and screening for mammalian-adaptive mutations.
RESULTS:

Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real-time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation.
CONCLUSIONS:

Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low-risk human pathogen.
? 2020 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.


KEYWORDS:

H5N8; South Africa; avian influenza

PMID: 32058677 DOI: 10.1111/irv.12724
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