{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T11:44:55Z","timestamp":1782819895194,"version":"3.54.5"},"reference-count":31,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"USDA NACA","award":["58-3022-3-042"],"award-info":[{"award-number":["58-3022-3-042"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Vesicular stomatitis virus (VSV) causes clinical disease in livestock that mimics Foot-and-Mouth Disease, necessitating its status as a reportable pathogen to the World Organization for Animal Health. Given the importance of accurate classification for epidemiological surveillance, this study aims to update VSV taxonomic organization using whole-genome sequence criteria to better monitor disease dynamics. Using phylogenetic analysis and the Species Demarcation Tool (SDT), we analyzed pairwise identity across publicly available sequences, constructing a rooted maximum likelihood tree to cluster strains based on robust genetic identity scores. The results demonstrate that nucleotide divergences exceeding 30% define distinct species within the Vesiculovirus genus. Within a species, divergences between 10% and 30% successfully delineate genotypes, while differences between 6% and 10% identify specific subtypes. These quantitative benchmarks provide a precise framework for viral classification, significantly enhancing genomic surveillance and the ability to track the evolution and transmission of VSV genotypes and subtypes across diverse geographic regions.<\/jats:p>","DOI":"10.3390\/pathogens15070689","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T10:01:17Z","timestamp":1782813677000},"page":"689","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Revised Classification of Vesicular Stomatitis Virus (VSV) Genotypes and Subtypes"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0070-6746","authenticated-orcid":false,"given":"Bernal","family":"Le\u00f3n","sequence":"first","affiliation":[{"name":"Laboratorio Bioseguridad, Departamento Diagn\u00f3stico Veterinario, Laboratorio Nacional de Servicios Veterinarios, Servicio Nacional de Salud Animal, Ministerio de Agricultura y Ganader\u00eda, Ulloa, Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2180-2120","authenticated-orcid":false,"given":"Gabriel","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Institute for Vaccine Research and Development, Hokkaido University, Sapporo 001-0021, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3214-4599","authenticated-orcid":false,"given":"Bradd","family":"Mendoza-Guido","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones en Salud, Universidad de Costa Rica, Montes de Oca, San Jos\u00e9 11501, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Consuelo","family":"Carrillo","sequence":"additional","affiliation":[{"name":"Independent Researcher, Westbrook, CT 06498, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis L.","family":"Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6481-2639","authenticated-orcid":false,"given":"Kathryn A.","family":"Hanley","sequence":"additional","affiliation":[{"name":"Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2106-1166","authenticated-orcid":false,"given":"Nidia S.","family":"Trovao","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA"},{"name":"Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA"},{"name":"National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,30]]},"reference":[{"key":"ref_1","unstructured":"Knipe, D.M., and Howley, P. (2013). Rhabdoviridae. Fields Virology, Lip-pincott Williams & Wilkins."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3103","DOI":"10.1128\/jvi.67.6.3103-3110.1993","article-title":"A Small Highly Basic Protein Is Encoded in Overlapping Frame within the P Gene of Vesicular Stomatitis Virus","volume":"67","author":"Spiropoulou","year":"1993","journal-title":"J. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/S1369-5274(03)00084-5","article-title":"Contributions of Vesicular Stomatitis Virus to the Understanding of RNA Virus Evolution","volume":"6","author":"Novella","year":"2003","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_4","unstructured":"(2025, October 26). Genus: Vesiculovirus|ICTV. Available online: https:\/\/ictv.global\/report\/chapter\/rhabdoviridae\/rhabdoviridae\/vesiculovirus."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Velazquez-Salinas, L., Zarate, S., Eschbaumer, M., Pereira Lobo, F., Gladue, D.P., Arzt, J., Novella, I.S., and Rodri-guez, L.L. (2016). Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arbo-viruses. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0159943"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1007\/s00705-012-1420-x","article-title":"Full-Length Genome Analysis of Vesicular Stomatitis New Jersey Virus Strains Representing the Phylogenetic and Geographic Diversity of the Virus","volume":"157","author":"Pauszek","year":"2012","journal-title":"Arch. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1099\/0022-1317-83-10-2475","article-title":"Full-Length Genome Analysis of Natural Isolates of Vesicular Stomatitis Virus (Indiana 1 Serotype) from North, Central and South America","volume":"83","author":"Rodriguez","year":"2002","journal-title":"J. Gen. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4873","DOI":"10.1128\/jvi.64.10.4873-4883.1990","article-title":"Polymerase Errors Accumulating during Natural Evolution of the Glycoprotein Gene of Vesicular Stomatitis Virus Indiana Serotype Isolates","volume":"64","author":"Bilsel","year":"1990","journal-title":"J. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e01454-20","DOI":"10.1128\/MRA.01454-20","article-title":"Near-Complete Genome Sequences of Vesicular Stomatitis Vi-rus Isolates from the 2020 Outbreak in Kansas","volume":"10","author":"Doerksen","year":"2021","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1099\/0022-1317-73-5-1201","article-title":"Comparison of the Amino Acid Se-quences of Nine Different Serotypes of Hepatitis B Surface Antigen and Genomic Classification of the Corre-sponding Hepatitis B Virus Strains","volume":"73","author":"Norder","year":"1992","journal-title":"J. Gen. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e00737-22","DOI":"10.1128\/mra.00737-22","article-title":"Vesicular Stomatitis Virus Isolated from a Bovine Brain Sample in Costa Rica","volume":"11","year":"2022","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Sievers, F., and Higgins, D.G. (2014). Clustal Omega. Current Protocols in Bioinformatics, John Wiley & Sons, Inc.","DOI":"10.1002\/0471250953.bi0313s48"},{"key":"ref_14","first-page":"95","article-title":"BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95\/98\/NT","volume":"41","author":"Hall","year":"1999","journal-title":"Nucleic Acids Symp. Ser."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and Analysis of Recombination Patterns in Virus Genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Muhire, B.M., Varsani, A., and Martin, D.P. (2014). SDT: A Virus Classification Tool Based on Pairwise Sequence Align-ment and Identity Calculation. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0108277"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"msae263","DOI":"10.1093\/molbev\/msae263","article-title":"MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing","volume":"41","author":"Kumar","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"ref_18","first-page":"268","article-title":"IQ-TREE: A Fast and Effective Stochastic Algo-rithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"J. Mol. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian Phylogenetic and Phylodynamic Data Integration Using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1053\/tvjl.1998.0303","article-title":"Vesicular Stomatitis","volume":"157","author":"Letchworth","year":"1999","journal-title":"Vet. J."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1177\/104063870601800201","article-title":"a Detection and Serotype-Specific Differentiation of Vesicular Stomatitis Virus Using a Multiplex, Real-Time, Reverse Transcription-Polymerase Chain Reaction Assay","volume":"18","author":"Hole","year":"2006","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1006\/viro.2000.0289","article-title":"Re-Emergence of Vesicular Stomatitis in the Western United States Is Associated with Distinct Viral Genetic Lineages","volume":"271","author":"Rodriguez","year":"2000","journal-title":"Virology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1099\/vir.0.82644-0","article-title":"Molecular Epidemiology of Vesicular Stoma-titis New Jersey Virus from the 2004\u20132005 US Outbreak Indicates a Common Origin with Mexican Strains","volume":"88","author":"Pauszek","year":"2007","journal-title":"J. Gen. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Mendoza-Guido, B., Montiel-Mora, J.R., Ure\u00f1a-Salazar, C., Barrantes, K., and Chac\u00f3n, L. (2025). Molecular Epidemiology of Aquatic Environments: Challenges from Sampling to Implementation of Surveillance Programs. Front. Public Health, 13.","DOI":"10.3389\/fpubh.2025.1652535"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1159\/000074988","article-title":"Classifying Hepatitis B Virus Genotypes","volume":"46","author":"Miyakawa","year":"2003","journal-title":"Intervirology"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2575","DOI":"10.1099\/0022-1317-69-10-2575","article-title":"Typing Hepatitis B Virus by Homology in Nucleotide Sequence: Comparison of Surface Antigen Subtypes","volume":"69","author":"Okamoto","year":"1988","journal-title":"J. Gen. Virol."},{"key":"ref_28","first-page":"305","article-title":"Genotype F Prevails in {HBV} Infected Patients of Hispanic Origin in Central America and May Carry the Precore Stop Mutants","volume":"54","author":"Norder","year":"1997","journal-title":"J. Med. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1159\/000360947","article-title":"Genotypes and Genetic Variability of Hepatitis B Virus","volume":"57","author":"Kramvis","year":"2014","journal-title":"Intervirology"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1099\/jgv.0.001387","article-title":"Analysis of Genomic-Length HBV Sequences to Determine Genotype and Subgenotype Reference Sequences","volume":"101","author":"McNaughton","year":"2020","journal-title":"J. Gen. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.3390\/v3081358","article-title":"Homologous Recombination in Negative Sense RNA Viruses","volume":"3","author":"Han","year":"2011","journal-title":"Viruses"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/7\/689\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T10:51:02Z","timestamp":1782816662000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/7\/689"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,30]]},"references-count":31,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["pathogens15070689"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15070689","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,30]]}}}