Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm

The recent expansion of HPAIV H5N1 infections in terrestrial mammals in the Americas, most recently including the outbreak in dairy cattle, emphasizes the critical need for better epidemiological monitoring of zoonotic diseases. In this work, we detected, isolated, and characterized the HPAIV H5N1 f...

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Published in:Virus genes Vol. 60; no. 5; pp. 517 - 527
Main Authors: Singh, Gagandeep, Trujillo, Jessie D., McDowell, Chester D., Matias-Ferreyra, Franco, Kafle, Sujan, Kwon, Taeyong, Gaudreault, Natasha N., Fitz, Isaac, Noll, Lance, Morozov, Igor, Retallick, Jamie, Richt, Juergen A.
Format: Journal Article
Language:English
Published: New York Springer US 01.10.2024
Springer Nature B.V
Subjects:
Animals
Avian flu
Biomedical and Life Sciences
Biomedicine
birds
Cattle
Cattle Diseases - epidemiology
Cattle Diseases - virology
Dairy cattle
dairy farming
Dairy farms
Dairying
Environmental monitoring
Epidemiology
Farms
genes
Genetic analysis
genomics
Humans
Influenza A Virus, H5N1 Subtype - classification
Influenza A Virus, H5N1 Subtype - genetics
Influenza A Virus, H5N1 Subtype - isolation & purification
Influenza A Virus, H5N1 Subtype - pathogenicity
Kansas
Medical Microbiology
Original Paper
Phylogenetics
Phylogeny
Plant Sciences
Rare species
species
Virology
viruses
Whole genome sequencing
Zoonoses
Kansas
H5N1
Environmental
Highly pathogenic avian influenza virus
Bovine
Mammalian
ISSN:0920-8569, 1572-994X, 1572-994X
Online Access:Get full text
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Summary:The recent expansion of HPAIV H5N1 infections in terrestrial mammals in the Americas, most recently including the outbreak in dairy cattle, emphasizes the critical need for better epidemiological monitoring of zoonotic diseases. In this work, we detected, isolated, and characterized the HPAIV H5N1 from environmental swab samples collected from a dairy farm in the state of Kansas, USA. Genomic sequencing of these samples uncovered two distinctive substitutions in the PB2 (E249G) and NS1 (R21Q) genes which are rare and absent in recent 2024 isolates of H5N1 circulating in the mammalian and avian species. Additionally, approximately 1.7% of the sequence reads indicated a PB2 (E627K) substitution, commonly associated with virus adaptation to mammalian hosts. Phylogenetic analyses of the PB2 and NS genes demonstrated more genetic identity between this environmental isolate and the 2024 human isolate (A/Texas/37/2024) of H5N1. Conversely, HA and NA gene analyses revealed a closer relationship between our isolate and those found in other dairy cattle with almost 100% identity, sharing a common phylogenetic subtree. These findings underscore the rapid evolutionary progression of HPAIV H5N1 among dairy cattle and reinforces the need for more epidemiological monitoring which can be done using environmental sampling.
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ISSN:0920-8569
1572-994X
1572-994X
DOI:10.1007/s11262-024-02085-4