1
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Russell SL, Andrew CL, Yang KC, Coombe M, McGregor G, Redford T, Jassem AN, Zlosnik JEA, Giacinti J, Kuchinski KS, Palmer JL, Tyson JR, Fjell C, Willie M, Ross MV, Winchester M, Wilson L, Berhane Y, Thacker C, Harms NJ, Soos C, Burns T, Prystajecky N, Himsworth C. Descriptive epidemiology and phylogenetic analysis of highly pathogenic avian influenza H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada, September 2022 to June 2023. Emerg Microbes Infect 2024; 13:2392667. [PMID: 39143912 PMCID: PMC11421163 DOI: 10.1080/22221751.2024.2392667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/23/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024]
Abstract
Surveillance data from wildlife and poultry was used to describe the spread of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada from September 2022 - June 2023 compared to the first "wave" of the outbreak in this region, which occurred April - August 2022, after the initial viral introduction. Although the number of HPAI-positive poultry farms and wildlife samples was greater in "Wave 2", cases were more tightly clustered in southwestern B.C. and the most commonly affected species differed, likely due to an influx of overwintering waterfowl in the area. Eight HPAI genetic clusters, representing seven genotypes and two inter-continental viral incursions, were detected, with significant variation in the relative abundance of each cluster between the waves. Phylogenetic data suggests multiple spillover events from wild birds to poultry and mammals but could not rule out transmission among farms and among mammals.
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Affiliation(s)
- Shannon L. Russell
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Cassandra L. Andrew
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Kevin C. Yang
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Public Health Agency of Canada (PHAC), Winnipeg, Canada
| | - Michelle Coombe
- Animal Health Centre, British Columbia Ministry of Agriculture and Food, Abbotsford, Canada
| | - Glenna McGregor
- Animal Health Centre, British Columbia Ministry of Agriculture and Food, Abbotsford, Canada
| | - Tony Redford
- Animal Health Centre, British Columbia Ministry of Agriculture and Food, Abbotsford, Canada
| | - Agatha N. Jassem
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - James E. A. Zlosnik
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jolene Giacinti
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada (ECCC), Ottawa, Canada
| | - Kevin S. Kuchinski
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
| | - John L. Palmer
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
| | - John R. Tyson
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Chris Fjell
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Megan Willie
- Canadian Wildlife Service, Environment and Climate Change Canada (ECCC), Delta, Canada
| | - Megan V. Ross
- Canadian Wildlife Service, Environment and Climate Change Canada (ECCC), Delta, Canada
| | - Maeve Winchester
- British Columbia Ministry of Water, Land and Resource Stewardship, Nanaimo, Canada
| | - Laurie Wilson
- Canadian Wildlife Service, Environment and Climate Change Canada (ECCC), Delta, Canada
| | | | - Caeley Thacker
- British Columbia Ministry of Water, Land and Resource Stewardship, Nanaimo, Canada
| | - N. Jane Harms
- Department of Environment, Government of Yukon, Whitehorse, Canada
| | - Catherine Soos
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada (ECCC), Ottawa, Canada
| | - Theresa Burns
- Animal Health Centre, British Columbia Ministry of Agriculture and Food, Abbotsford, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control (BCCDC) Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Chelsea Himsworth
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Animal Health Centre, British Columbia Ministry of Agriculture and Food, Abbotsford, Canada
- Canadian Wildlife Health Cooperative British Columbia, Abbotsford, Canada
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2
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Caserta LC, Frye EA, Butt SL, Laverack M, Nooruzzaman M, Covaleda LM, Thompson AC, Koscielny MP, Cronk B, Johnson A, Kleinhenz K, Edwards EE, Gomez G, Hitchener G, Martins M, Kapczynski DR, Suarez DL, Alexander Morris ER, Hensley T, Beeby JS, Lejeune M, Swinford AK, Elvinger F, Dimitrov KM, Diel DG. Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle. Nature 2024:10.1038/s41586-024-07849-4. [PMID: 39053575 DOI: 10.1038/s41586-024-07849-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus clade 2.3.4.4b has caused the death of millions of domestic birds and thousands of wild birds in the USA since January 2022 (refs. 1-4). Throughout this outbreak, spillovers to mammals have been frequently documented5-12. Here we report spillover of the HPAI H5N1 virus to dairy cattle across several states in the USA. The affected cows displayed clinical signs encompassing decreased feed intake, altered faecal consistency, respiratory distress and decreased milk production with abnormal milk. Infectious virus and viral RNA were consistently detected in milk from affected cows. Viral distribution in tissues via immunohistochemistry and in situ hybridization revealed a distinct tropism of the virus for the epithelial cells lining the alveoli of the mammary gland in cows. Whole viral genome sequences recovered from dairy cows, birds, domestic cats and a raccoon from affected farms indicated multidirectional interspecies transmissions. Epidemiological and genomic data revealed efficient cow-to-cow transmission after apparently healthy cows from an affected farm were transported to a premise in a different state. These results demonstrate the transmission of the HPAI H5N1 clade 2.3.4.4b virus at a non-traditional interface, underscoring the ability of the virus to cross species barriers.
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Affiliation(s)
- Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elisha A Frye
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Salman L Butt
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Lina M Covaleda
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Melanie Prarat Koscielny
- Ohio Animal Disease and Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA
| | - Brittany Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ashley Johnson
- Ohio Animal Disease and Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA
| | - Katie Kleinhenz
- Texas A&M Veterinary Medical Diagnostic Laboratory, Canyon, TX, USA
| | - Erin E Edwards
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Gabriel Gomez
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Gavin Hitchener
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Mathias Martins
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Darrell R Kapczynski
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, USA
| | - David L Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, USA
| | | | - Terry Hensley
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - John S Beeby
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Manigandan Lejeune
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Amy K Swinford
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - François Elvinger
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kiril M Dimitrov
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA.
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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3
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Paremskaia AI, Volchkov PY, Deviatkin AA. IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data. Viruses 2024; 16:873. [PMID: 38932165 PMCID: PMC11209090 DOI: 10.3390/v16060873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate analysis, it is necessary to select the most suitable reference for each segment. At the same time, there is no standardized method in the field of decoding sequencing results that allows the user to update the sequence databases to which the reads obtained by virus sequencing are compared. The IAVCP (influenza A virus consensus and phylogeny) was developed with the goal of automatically analyzing high-throughput sequencing data of influenza A viruses. Its goals include the extraction of a consensus genome directly from paired raw reads. In addition, the pipeline enables the identification of potential reassortment events in the evolutionary history of the virus of interest by analyzing the topological structure of phylogenetic trees that are automatically reconstructed.
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Affiliation(s)
- Anastasiia Iu. Paremskaia
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
| | - Pavel Yu. Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The MCSC Named after A. S. Loginov, 111123 Moscow, Russia
| | - Andrei A. Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia;
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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4
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Maqsood R, Smith MF, Holland LA, Sullins RA, Holland SC, Tan M, Hernandez Barrera GM, Thomas AW, Islas M, Kramer JL, Nordstrom L, Mulrow M, White M, Murugan V, Lim ES. Influenza Virus Genomic Surveillance, Arizona, USA, 2023-2024. Viruses 2024; 16:692. [PMID: 38793574 PMCID: PMC11125580 DOI: 10.3390/v16050692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Influenza viruses are constantly evolving and are therefore monitored worldwide in the hope to reduce the burden of disease by annual updates to vaccine recommendations. We conducted genomic sequencing of 110 influenza A and 30 influenza B viruses from specimens collected between October 2023 and February 2024 in Arizona, USA. We identified mutations in the hemagglutinin (HA) antigenic sites as well as the neuraminidase (NA) gene in our samples. We also found no unique HA and NA mutations in vaccinated yet influenza-infected individuals. Real-time genomic sequencing surveillance is important to ensure influenza vaccine effectiveness.
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Affiliation(s)
- Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Matthew F. Smith
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Regan A. Sullins
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Steven C. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Michelle Tan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Gabrielle M. Hernandez Barrera
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Alexis W. Thomas
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Mario Islas
- Arizona State University Health Services, Tempe, AZ 85281, USA
| | - Joanna L. Kramer
- Division of Primary, Complex, and Adolescent Medicine, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Lora Nordstrom
- Valleywise Health Medical Center, Phoenix, AZ 85008, USA
| | - Mary Mulrow
- Valleywise Health Medical Center, Phoenix, AZ 85008, USA
| | - Michael White
- Valleywise Health Medical Center, Phoenix, AZ 85008, USA
| | - Vel Murugan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- National Centre for Infectious Diseases, Singapore 308442, Singapore
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5
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Cronk BD, Caserta LC, Laverack M, Gerdes RS, Hynes K, Hopf CR, Fadden MA, Nakagun S, Schuler KL, Buckles EL, Lejeune M, Diel DG. Infection and tissue distribution of highly pathogenic avian influenza A type H5N1 (clade 2.3.4.4b) in red fox kits ( Vulpes vulpes). Emerg Microbes Infect 2023; 12:2249554. [PMID: 37589241 PMCID: PMC10512766 DOI: 10.1080/22221751.2023.2249554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Avian influenza H5N1 is a highly pathogenic virus that primarily affects birds. However, it can also infect other animal species, including mammals. We report the infection of nine juvenile red foxes (Vulpes vulpes) with Highly Pathogenic Avian Influenza A type H5N1 (Clade 2.3.4.4b) in the spring of 2022 in the central, western, and northern regions of New York, USA. The foxes displayed neurologic signs, and examination of brain and lung tissue revealed lesions, with brain lesions ranging from moderate to severe meningoencephalitis. Analysis of tissue tropism using RT-PCR methods showed a comparatively lower Ct value in the brain, which was confirmed by in situ hybridization targeting Influenza A RNA. The viral RNA labelling was highly clustered and overlapped the brain lesions, observed in neurons, and grey matter. Whole viral genome sequences obtained from the affected foxes were subjected to phylogenetic and mutation analysis to determine influenza A clade, host specificity, and potential occurrence of viral reassortment. Infections in red foxes likely occurred due to preying on infected wild birds and are unlikely due to transmission between foxes or other mammals.
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Affiliation(s)
- Brittany D. Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Rhea S. Gerdes
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kevin Hynes
- New York State Department of Environmental Conservation, Wildlife Health Program, Albany, NY, USA
| | - Cynthia R. Hopf
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa A. Fadden
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shotaro Nakagun
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Krysten L. Schuler
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elizabeth L. Buckles
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Manigandan Lejeune
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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6
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Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023; 9:vead052. [PMID: 37692894 PMCID: PMC10484056 DOI: 10.1093/ve/vead052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Evin Rothschild
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Stephanie E Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Kile
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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7
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Chon I, Saito R, Kyaw Y, Aye MM, Setk S, Phyu WW, Wagatsuma K, Li J, Sun Y, Otoguro T, Win SMK, Yoshioka S, Win NC, Ja LD, Tin HH, Watanabe H. Whole-Genome Analysis of Influenza A(H3N2) and B/Victoria Viruses Detected in Myanmar during the COVID-19 Pandemic in 2021. Viruses 2023; 15:v15020583. [PMID: 36851797 PMCID: PMC9964416 DOI: 10.3390/v15020583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
An influenza circulation was observed in Myanmar between October and November in 2021. Patients with symptoms of influenza-like illness were screened using rapid diagnostic test (RDT) kits, and 147/414 (35.5%) upper respiratory tract specimens presented positive results. All RDT-positive samples were screened by a commercial multiplex real-time polymerase chain reaction (RT-PCR) assay, and 30 samples positive for influenza A(H3N2) or B underwent further typing/subtyping for cycle threshold (Ct) value determination based on cycling probe RT-PCR. The majority of subtyped samples (n = 13) were influenza A(H3N2), while only three were B/Victoria. Clinical samples with low Ct values obtained by RT-PCR were used for whole-genome sequencing via next-generation sequencing technology. All collected viruses were distinct from the Southern Hemisphere vaccine strains of the corresponding season but matched with vaccines of the following season. Influenza A(H3N2) strains from Myanmar belonged to clade 2a.3 and shared the highest genetic proximity with Bahraini strains. B/Victoria viruses belonged to clade V1A.3a.2 and were genetically similar to Bangladeshi strains. This study highlights the importance of performing influenza virus surveillance with genetic characterization of the influenza virus in Myanmar, to contribute to global influenza surveillance during the COVID-19 pandemic.
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Affiliation(s)
- Irina Chon
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
- Correspondence: ; Tel.: +81-25-227-2129
| | - Reiko Saito
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
- Infectious Diseases Research Center of Niigata University (IDRC), Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yadanar Kyaw
- Respiratory Medicine Department, Thingangyun General Hospital, Yangon 110-71, Myanmar
| | - Moe Myat Aye
- National Health Laboratory, Department of Medical Services, Dagon Township, Yangon 111-91, Myanmar
| | - Swe Setk
- National Health Laboratory, Department of Medical Services, Dagon Township, Yangon 111-91, Myanmar
| | - Wint Wint Phyu
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Keita Wagatsuma
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Jiaming Li
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yuyang Sun
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Teruhime Otoguro
- Infectious Diseases Research Center of Niigata University (IDRC), Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Su Mon Kyaw Win
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon 111-91, Myanmar
| | - Sayaka Yoshioka
- Infectious Diseases Research Center of Niigata University (IDRC), Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Nay Chi Win
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon 111-91, Myanmar
| | - Lasham Di Ja
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon 111-91, Myanmar
| | - Htay Htay Tin
- National Health Laboratory, Department of Medical Services, Dagon Township, Yangon 111-91, Myanmar
| | - Hisami Watanabe
- Infectious Diseases Research Center of Niigata University (IDRC), Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
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8
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An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology. Microorganisms 2023; 11:microorganisms11020529. [PMID: 36838494 PMCID: PMC9967579 DOI: 10.3390/microorganisms11020529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken.
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9
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Goodman L, Lahmers K. Special issue on applied next-generation sequencing in veterinary diagnostic laboratories. J Vet Diagn Invest 2021; 33:177-178. [PMID: 33685332 DOI: 10.1177/1040638721995676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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