{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:15:13Z","timestamp":1787030113425,"version":"build-2736575974"},"reference-count":64,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T00:00:00Z","timestamp":1717718400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003141","name":"CONACyT \u201cEstrategia para la evaluaci\u00f3n geo-temporal de la diversidad gen\u00e9tica de virus dengue y chikungunya para el apoyo a la vigilancia epidemiol\u00f3gica\u201d","doi-asserted-by":"publisher","award":["261775"],"award-info":[{"award-number":["261775"]}],"id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Chikungunya virus (CHIKV) is transmitted by mosquito bites and causes chikungunya fever (CHIKF). CHIKV has a single-stranded RNA genome and belongs to a single serotype with three genotypes. The Asian lineage has recently emerged in the Western Hemisphere, likely due to travel-associated introduction. Genetic variation accumulates in the CHIKV genome as the virus replicates, creating new lineages. Whole genome sequencing is ideal for studying virus evolution and spread but is expensive and complex. This study investigated whether specific, highly variable regions of the CHIKV genome could recapitulate the phylogeny obtained with a complete coding sequence (CDS). Our results revealed that concatenated highly variable regions accurately reconstructed CHIKV phylogeny, exhibiting statistically indistinguishable branch lengths and tree confidence compared to CDS. In addition, these regions adequately inferred the evolutionary relationships among CHIKV isolates from the American outbreak with similar results to the CDS. This finding suggests that highly variable regions can effectively capture the evolutionary relationships among CHIKV isolates, offering a simpler approach for future studies. This approach could be particularly valuable for large-scale surveillance efforts.<\/jats:p>","DOI":"10.3390\/v16060926","type":"journal-article","created":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T08:05:17Z","timestamp":1717747517000},"page":"926","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Accurate Recapitulation of Chikungunya Virus Complete Coding Sequence Phylogeny Using Variable Genome Regions for Genomic Surveillance"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2824-8924","authenticated-orcid":false,"given":"Eduardo D.","family":"Rodr\u00edguez-Aguilar","sequence":"first","affiliation":[{"name":"Center for Infectious Disease Research, National Institute of Public Health of Mexico, Av. Universidad 655, Cuernavaca 62100, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Everardo","family":"Guti\u00e9rrez-Mill\u00e1n","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Research, National Institute of Public Health of Mexico, Av. Universidad 655, Cuernavaca 62100, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5361-2877","authenticated-orcid":false,"given":"Mario H.","family":"Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Research, National Institute of Public Health of Mexico, Av. Universidad 655, Cuernavaca 62100, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,7]]},"reference":[{"key":"ref_1","unstructured":"(2015). Chikungunya: Case Definitions for Acute, Atypical and Chronic Cases. 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