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
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Abstract	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.
AbstractList	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. 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.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.
Author	Retallick, Jamie McDowell, Chester D. Matias-Ferreyra, Franco Richt, Juergen A. Noll, Lance Trujillo, Jessie D. Kafle, Sujan Kwon, Taeyong Fitz, Isaac Singh, Gagandeep Gaudreault, Natasha N. Morozov, Igor
AuthorAffiliation	1 Department of Diagnostic Medicine/Pathobiology (DMP), College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA 2 Kansas State Veterinary Diagnostic Laboratory (KSVDL), College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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SubjectTerms	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
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Title	Detection and characterization of H5N1 HPAIV in environmental samples from a dairy farm
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