{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:27:09Z","timestamp":1787164029660,"version":"build-2736575974"},"update-to":[{"DOI":"10.1371\/journal.pntd.0014565","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000}}],"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T00:00:00Z","timestamp":1785715200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["328498\/Z\/25\/Z"],"award-info":[{"award-number":["328498\/Z\/25\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>\n                    Spanning almost\u00a0six decades (1966\u20132024), 23 whole-genome sequences of Chandipura virus (CHPV), a neurotropic rhabdovirus associated with acute encephalitis primarily in India, have been analyzed. The virus is believed to be transmitted mainly by\n                    <jats:italic>Sergentomyia<\/jats:italic>\n                    and\n                    <jats:italic>Phlebotomus<\/jats:italic>\n                    sandflies. An epidemiological geographical map was developed showing global CHPV detection in sandflies, district-level human encephalitis reports in India, and sandfly species distribution across the country. This integrated landscape links viral occurrence with vector ecology and outbreak potential. To investigate evolutionary dynamics, we analyzed 23 complete genomes, comprising 5 human-derived isolates from India, 17 sandfly-derived isolates from Senegal and Kenya, and one hedgehog-derived isolate from Nigeria. Phylogenetic reconstruction revealed clear lineage segregation between Indian and African strains, indicating region-specific evolution. Despite this divergence, overall genomic variability remained low. Among all genes, the phosphoprotein exhibited relatively higher variability, while human-derived Indian sequences showed lower genetic diversity than the predominantly sandfly-derived African sequences; however, this comparison is confounded by differences in geography, sampling period, and host origin. Selection pressure analyses indicated predominantly purifying selection across coding regions. Episodic diversification analysis detected adaptive events in structural proteins. In the glycoprotein, all diversification sites (P272H, L424W, K503R) overlapped with predicted B-cell epitopes. In the matrix protein, both sites (K20R, D97N) mapped to predicted B-cell epitope regions. In contrast, among the two diversification sites in the nucleoprotein (N35E, A187V), only A187V overlapped with an epitope, whereas N35E was outside predicted antigenic domains. Collectively, these findings provide a comprehensive evolutionary and epidemiological perspective on CHPV and highlight the urgent need for systematic genomic surveillance to inform future diagnostic, vaccine and public health intervention strategies.\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0014565","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T17:33:18Z","timestamp":1785778398000},"page":"e0014565","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Unravelling the genomic epidemiology and antigenic evolution of Chandipura virus: A genetically constrained neurotropic threat"],"prefix":"10.1371","volume":"20","author":[{"given":"Pooja Rani","family":"Kuri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3305-0034","authenticated-orcid":true,"given":"Amit","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,3]]},"reference":[{"key":"pntd.0014565.ref001","unstructured":"Ghosh S, Basu A. Neuropathogenesis by Chandipura virus: an acute encephalitis syndrome in India. 2017:21\u20135."},{"key":"pntd.0014565.ref002","doi-asserted-by":"crossref","unstructured":"Kumar K, Rajasekharan S, Gulati S, Rana J, Gabrani R, Jain CK. Elucidating the interacting domains of Chandipura virus nucleocapsid protein. 2013;2013:594319\u201329.","DOI":"10.1155\/2013\/594319"},{"issue":"2","key":"pntd.0014565.ref003","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.biochi.2012.09.009","article-title":"Characterization of the chandipura virus leader RNA-phosphoprotein interaction using single tryptophan mutants and its detection in viral infected cells","volume":"95","author":"A Roy","year":"2013","journal-title":"Biochimie"},{"key":"pntd.0014565.ref004","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.actatropica.2015.04.027","article-title":"Host interactions of Chandipura virus matrix protein","volume":"149","author":"S Rajasekharan","year":"2015","journal-title":"Acta Trop"},{"issue":"3","key":"pntd.0014565.ref005","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004756","article-title":"Structure of the low pH conformation of Chandipura virus G reveals important features in the evolution of the vesiculovirus glycoprotein","volume":"11","author":"E Baquero","year":"2015","journal-title":"PLoS Pathog"},{"key":"pntd.0014565.ref006","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1099\/vir.0.019307-0","article-title":"The HR motif in the RNA-dependent RNA polymerase L protein of Chandipura virus is required for unconventional mRNA-capping activity","volume":"91","author":"T Ogino","year":"2010","journal-title":"J Gen Virol"},{"issue":"12","key":"pntd.0014565.ref007","first-page":"1295","article-title":"Chandipura: a new Arbovirus isolated in India from patients with febrile illness","volume":"55","author":"PN Bhatt","year":"1967","journal-title":"Indian J Med Res"},{"key":"pntd.0014565.ref008","first-page":"395","article-title":"Chandipura virus encephalitis outbreak among children in Nagpur division, Maharashtra, 2007","volume":"132","author":"YK Gurav","year":"2010","journal-title":"Indian J Med Res"},{"issue":"9437","key":"pntd.0014565.ref009","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/S0140-6736(04)16982-1","article-title":"A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus","volume":"364","author":"BL Rao","year":"2004","journal-title":"Lancet"},{"issue":"9452","key":"pntd.0014565.ref010","doi-asserted-by":"crossref","first-page":"2175","DOI":"10.1016\/S0140-6736(04)17579-X","article-title":"Chandipura virus, encephalitis, and epidemic brain attack in India","volume":"364","author":"TJ John","year":"2004","journal-title":"Lancet"},{"issue":"1","key":"pntd.0014565.ref011","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.actatropica.2012.06.001","article-title":"Chandipura virus: an emerging tropical pathogen","volume":"124","author":"S Menghani","year":"2012","journal-title":"Acta Trop"},{"key":"pntd.0014565.ref012","doi-asserted-by":"crossref","first-page":"44","DOI":"10.2174\/1874357901812010044","article-title":"Chandipura viral encephalitis: a brief review","volume":"12","author":"GN Sapkal","year":"2018","journal-title":"Open Virol J"},{"issue":"4","key":"pntd.0014565.ref013","doi-asserted-by":"crossref","DOI":"10.1099\/jgv.0.001837","article-title":"The role of sand flies as vectors of viruses other than phleboviruses","volume":"104","author":"M Jancarova","year":"2023","journal-title":"J Gen Virol"},{"issue":"5","key":"pntd.0014565.ref014","first-page":"769","article-title":"Isolation of Chandipura virus (Vesiculovirus: Rhabdoviridae) from Sergentomyia species of sandflies from Nagpur, Maharashtra, India","volume":"139","author":"AB Sudeep","year":"2014","journal-title":"Indian J Med Res"},{"key":"pntd.0014565.ref015","first-page":"817","article-title":"Geographical distribution & density of phlebotominae sandflies in surat district","volume":"77","author":"AP Pandya","year":"1983","journal-title":"Indian J Med Res"},{"issue":"6","key":"pntd.0014565.ref016","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.4269\/ajtmh.2006.75.1151","article-title":"Venereal transmission of Chandipura virus by Phlebotomus papatasi (Scopoli)","volume":"75","author":"MS Mavale","year":"2006","journal-title":"Am J Trop Med Hyg"},{"issue":"3","key":"pntd.0014565.ref017","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1603\/0022-2585(2005)042[0495:DOCVFS]2.0.CO;2","article-title":"Detection of chandipura virus from sand flies in the genus Sergentomyia (Diptera: Phlebotomidae) at Karimnagar District, Andhra Pradesh, India","volume":"42","author":"G Geevarghese","year":"2005","journal-title":"J Med Entomol"},{"issue":"2","key":"pntd.0014565.ref018","doi-asserted-by":"crossref","first-page":"241","DOI":"10.11646\/zootaxa.5093.2.7","article-title":"A report on occurrence of Phlebotomine sand flies (Diptera: Psychodidae) and two new country records from Andaman & Nicobar Islands, a Union territory of India","volume":"5093","author":"P Jambulingam","year":"2022","journal-title":"Zootaxa"},{"issue":"2","key":"pntd.0014565.ref019","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.actatropica.2008.04.025","article-title":"Breeding ecology of visceral leishmaniasis vector sandfly in Bihar state of India","volume":"107","author":"R Singh","year":"2008","journal-title":"Acta Trop"},{"issue":"2","key":"pntd.0014565.ref020","first-page":"131","article-title":"Phlebotomus of Senegal: survey of the fauna in the region of Kedougou. Isolation of arbovirus","volume":"92","author":"Y Ba","year":"1999","journal-title":"Bull Soc Pathol Exot"},{"key":"pntd.0014565.ref021","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2334-8-168","article-title":"Development and evaluation of a real-time one step reverse-transcriptase PCR for quantitation of Chandipura virus","volume":"8","author":"S Kumar","year":"2008","journal-title":"BMC Infect Dis"},{"issue":"3","key":"pntd.0014565.ref022","doi-asserted-by":"crossref","first-page":"247","DOI":"10.7883\/yoken.JJID.2017.397","article-title":"Molecular evidence of Chandipura virus from Sergentomyia species of Sandflies in Gujarat, India","volume":"71","author":"RG Damle","year":"2018","journal-title":"Jpn J Infect Dis"},{"issue":"5","key":"pntd.0014565.ref023","doi-asserted-by":"crossref","first-page":"193","DOI":"10.4103\/1995-7645.377740","article-title":"Faunal richness and checklist of sandflies (Diptera)","volume":"16","author":"HK Shah","year":"2023","journal-title":"Asian Pac J Trop Med"},{"key":"pntd.0014565.ref024","volume-title":"QGIS Geographic Information System (Version 3.28)","author":"QGIS Development Team","year":"2023"},{"issue":"12","key":"pntd.0014565.ref025","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msae263","article-title":"MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing","volume":"41","author":"S Kumar","year":"2024","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pntd.0014565.ref026","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pntd.0014565.ref027","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"I Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pntd.0014565.ref028","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"A Rambaut","year":"2016","journal-title":"Virus Evol"},{"issue":"4","key":"pntd.0014565.ref029","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"R Bouckaert","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"pntd.0014565.ref030"},{"issue":"3","key":"pntd.0014565.ref031","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/molbev\/msx335","article-title":"Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes","volume":"35","author":"S Weaver","year":"2018","journal-title":"Mol Biol Evol"},{"key":"pntd.0014565.ref032","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1093\/nar\/gkx346","article-title":"BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"MC Jespersen","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"8016","key":"pntd.0014565.ref033","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"J Abramson","year":"2024","journal-title":"Nature"},{"key":"pntd.0014565.ref034","author":"LLC Schr\u00f6dinger","year":"2023"},{"issue":"2","key":"pntd.0014565.ref035","first-page":"179","article-title":"Isolation of Chandipura virus from sandflies in Aurangabad","volume":"58","author":"V Dhanda","year":"1970","journal-title":"Indian J Med Res"},{"issue":"5","key":"pntd.0014565.ref036","doi-asserted-by":"crossref","first-page":"570","DOI":"10.4269\/ajtmh.1994.50.570","article-title":"First isolations of arboviruses from phlebotomine sand flies in West Africa","volume":"50","author":"D Fontenille","year":"1994","journal-title":"Am J Trop Med Hyg"},{"key":"pntd.0014565.ref037","volume-title":"Acute encephalitis syndrome due to Chandipura virus \u2010 India","author":"World Health Organisation\u2013Disease Outbreak News","year":"2024"},{"key":"pntd.0014565.ref038","volume-title":"DGHS, Union Health Ministry, along with experts reviews the Chandipura virus cases and acute encephalitis syndrome cases in Gujarat, Rajasthan, and Madhya Pradesh","author":"Press Information Beauraue"},{"issue":"1","key":"pntd.0014565.ref039","doi-asserted-by":"crossref","first-page":"2421218","DOI":"10.1080\/21505594.2024.2421218","article-title":"Re-emergence of Chandipura virus infection in India","volume":"15","author":"N Kumar","year":"2024","journal-title":"Virulence"},{"issue":"101507","key":"pntd.0014565.ref040","article-title":"Re-emergence of Chandipura virus in India: urgent need for public health vigilance and proactive management","volume":"62","author":"A Pareek","year":"2024","journal-title":"New Microbes New Infect"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0014565","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0014565","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T17:47:29Z","timestamp":1787161649000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0014565"}},"subtitle":[],"editor":[{"given":"Brianna R","family":"Beechler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,3]]},"references-count":40,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0014565","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,3]]}}}