Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis
The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as...
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2024-11-01
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| author | Patil Tawidian Mia K. Torchetti Mary L. Killian Kristina Lantz Krista E. Dilione Jourdan M. Ringenberg Sarah N. Bevins Julianna B. Lenoch Hon S. Ip |
| author_facet | Patil Tawidian Mia K. Torchetti Mary L. Killian Kristina Lantz Krista E. Dilione Jourdan M. Ringenberg Sarah N. Bevins Julianna B. Lenoch Hon S. Ip |
| author_sort | Patil Tawidian |
| collection | DOAJ |
| description | The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 and December 2023 to visualize the genotypic diversity of viruses in poultry and wildlife populations. Our results reveal that ordination- and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on the genotypic diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment. |
| format | Article |
| id | doaj-art-23af83c9fa4c461581e84ba9c5dc84ea |
| institution | OA Journals |
| issn | 1999-4915 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-23af83c9fa4c461581e84ba9c5dc84ea2025-08-20T02:01:19ZengMDPI AGViruses1999-49152024-11-011612181810.3390/v16121818Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination AnalysisPatil Tawidian0Mia K. Torchetti1Mary L. Killian2Kristina Lantz3Krista E. Dilione4Jourdan M. Ringenberg5Sarah N. Bevins6Julianna B. Lenoch7Hon S. Ip8U.S. Geological Survey, National Wildlife Health Center Madison, Madison, WI 53711, USANational Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA 50010, USANational Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA 50010, USANational Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA 50010, USAWildlife Service, National Wildlife Disease Program, U.S. Department of Agriculture, Fort Collins, CO 80521, USAWildlife Service, National Wildlife Disease Program, U.S. Department of Agriculture, Fort Collins, CO 80521, USAWildlife Service, National Wildlife Disease Program, U.S. Department of Agriculture, Fort Collins, CO 80521, USAWildlife Service, National Wildlife Disease Program, U.S. Department of Agriculture, Fort Collins, CO 80521, USAU.S. Geological Survey, National Wildlife Health Center Madison, Madison, WI 53711, USAThe introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 and December 2023 to visualize the genotypic diversity of viruses in poultry and wildlife populations. Our results reveal that ordination- and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on the genotypic diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment.https://www.mdpi.com/1999-4915/16/12/1818avian influenzahigh pathogenic influenza virus (HPAI)H5N1 virusvirus reassortmentH5N1 genotypesvirus nomenclature |
| spellingShingle | Patil Tawidian Mia K. Torchetti Mary L. Killian Kristina Lantz Krista E. Dilione Jourdan M. Ringenberg Sarah N. Bevins Julianna B. Lenoch Hon S. Ip Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis Viruses avian influenza high pathogenic influenza virus (HPAI) H5N1 virus virus reassortment H5N1 genotypes virus nomenclature |
| title | Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis |
| title_full | Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis |
| title_fullStr | Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis |
| title_full_unstemmed | Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis |
| title_short | Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis |
| title_sort | genotypic clustering of h5n1 avian influenza viruses in north america evaluated by ordination analysis |
| topic | avian influenza high pathogenic influenza virus (HPAI) H5N1 virus virus reassortment H5N1 genotypes virus nomenclature |
| url | https://www.mdpi.com/1999-4915/16/12/1818 |
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