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

Autor:	Reneé Pieterse, Mushal Allam, Mpho Seleka, Florette K. Treurnicht, Michelle Seutloali, Cheryl Cohen, Ziyaad Valley-Omar, Sibongile Walaza, Arshad Ismail, Yusrah Salie‐Bassier, N. Govender, Kerrigan McCarthy, Lesley S. van Helden, Tasneem Anthony, Orienka Hellferscee, Phillip Senzo Mtshali, Mikhail Smith, Alicia Cloete
Rok vydání:	2020
Předmět:	Adult Male Pulmonary and Respiratory Medicine Adolescent Epidemiology Animals Wild Human pathogen 030312 virology Biology medicine.disease_cause Disease Outbreaks South Africa Young Adult 03 medical and health sciences H5N8 Phylogenetics Geese Influenza Human medicine Animals Humans Influenza A Virus H5N8 Subtype Clade Pathogen Phylogeny Poultry Diseases Struthioniformes 0303 health sciences Transmission (medicine) business.industry Influenza A Virus H3N2 Subtype Public Health Environmental and Occupational Health Outbreak Original Articles Middle Aged Poultry farming Virology Influenza A virus subtype H5N1 Ducks Infectious Diseases Influenza in Birds Epidemiological Monitoring Original Article Female avian influenza business Chickens
Zdroj:	Influenza and Other Respiratory Viruses
ISSN:	1750-2659 1750-2640
DOI:	10.1111/irv.12724
Popis:	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.
Databáze:	OpenAIRE
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