{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T16:40:24Z","timestamp":1782146424735,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pntd.0014204","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T00:00:00Z","timestamp":1776038400000}}],"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/W010755\/1"],"award-info":[{"award-number":["BB\/W010755\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI167048"],"award-info":[{"award-number":["R01AI167048"]}],"id":[{"id":"10.13039\/100000060","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                    Crimean-Congo haemorrhagic fever virus (CCHFV) is an important human tick-borne pathogen, able to cause severe haemorrhagic fever. CCHFV is endemic in Tajikistan, which records between 5\u201338 cases of CCHF a year from southern regions. Molecular surveillance of CCHFV is crucial to implement effective prevention and control strategies, understand viral evolution, study transmission dynamics, and develop effective diagnostics, therapeutics, and vaccines. While the presence of Asia-1 and Asia-2 genotypes has been previously reported, only two historical samples from Tajikistan have been fully sequenced. In this study we developed and applied a genotype IV-specific tiling PCR enrichment approach recovering 52 CCHFV genome segment sequences from clinical and\n                    <jats:italic>Hyalomma<\/jats:italic>\n                    tick samples collected between 2017\u20132023. Most sequences belonged to the Asia-2 genotype, but one virus exhibited an Asia-1 S segment combined with Asia-2 M and L segments, representing the first evidence of such viral reassortment event in Tajikistan.\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0014204","type":"journal-article","created":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T17:38:23Z","timestamp":1775583503000},"page":"e0014204","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomic characterisation of Crimean-Congo haemorrhagic fever virus (CCHFV) in Tajikistan identifies a novel reassortant virus"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2249-2942","authenticated-orcid":true,"given":"Jake","family":"D\u2019Addiego","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farida","family":"Tishkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manija","family":"Mullojonova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktoriya","family":"Dzhuraeva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grant","family":"Lythe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart","family":"Dent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Molina-Par\u00eds","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Leitner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roger","family":"Hewson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,4,7]]},"reference":[{"issue":"10","key":"pntd.0014204.ref001","article-title":"Promotion of order Bunyavirales to class Bunyaviricetes to accommodate a rapidly increasing number of related polyploviricotine viruses","volume":"98","author":"JH Kuhn","year":"2024","journal-title":"J Virol"},{"issue":"3","key":"pntd.0014204.ref002","first-page":"143","article-title":"Experimental transmission of Crimean-Congo hemorrhagic fever virus by Rhipicephalus evertsi evertsi (Acarina:Ixodidae)","volume":"92","author":"O Faye","year":"1999","journal-title":"Bull Soc Pathol Exot"},{"issue":"11","key":"pntd.0014204.ref003","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1007\/s00436-017-5616-6","article-title":"Molecular detection of Crimean-Congo hemorrhagic fever virus in ticks, Greece, 2012-2014","volume":"116","author":"A Papa","year":"2017","journal-title":"Parasitol Res"},{"issue":"6","key":"pntd.0014204.ref004","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.jinf.2022.09.016","article-title":"Widespread exposure to Crimean-Congo haemorrhagic fever in Uganda might be driven by transmission from Rhipicephalus ticks: Evidence from cross-sectional and modelling studies","volume":"85","author":"SA Lule","year":"2022","journal-title":"J Infect"},{"issue":"4","key":"pntd.0014204.ref005","doi-asserted-by":"crossref","first-page":"654","DOI":"10.3201\/eid3004.231155","article-title":"Crimean-Congo hemorrhagic fever virus diversity and reassortment, Pakistan, 2017-2020","volume":"30","author":"M Umair","year":"2024","journal-title":"Emerg Infect Dis"},{"issue":"4","key":"pntd.0014204.ref006","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.3201\/eid2704.203462","article-title":"Fatal case of crimean-congo hemorrhagic fever caused by reassortant virus, Spain, 2018","volume":"27","author":"A Negredo","year":"2021","journal-title":"Emerg Infect Dis"},{"issue":"9","key":"pntd.0014204.ref007","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1017\/S0950268808001878","article-title":"Genetic relationship in southern African Crimean-Congo haemorrhagic fever virus isolates: evidence for occurrence of reassortment","volume":"137","author":"FJ Burt","year":"2009","journal-title":"Epidemiol Infect"},{"key":"pntd.0014204.ref008","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1099\/vir.0.80121-0","article-title":"Evidence of segment reassortment in Crimean-Congo haemorrhagic fever virus","volume":"85","author":"R Hewson","year":"2004","journal-title":"J Gen Virol"},{"issue":"11","key":"pntd.0014204.ref009","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0166744","article-title":"Phylogeography of crimean congo hemorrhagic fever virus","volume":"11","author":"AN Lukashev","year":"2016","journal-title":"PLoS One"},{"issue":"5","key":"pntd.0014204.ref010","first-page":"854","article-title":"Crimean-congo hemorrhagic fever virus for clinicians-epidemiology, clinical manifestations, and prevention","volume":"30","author":"State of the Clinical Science Working Group of the National Emerging Pathogens T, Education Center\u2019s Special Pathogens Research N, State of the Clinical Science Working Group of the National Emerging Pathogens Training Education Center\u2019s Special Pathogens Research N","year":"2024","journal-title":"Emerg Infect Dis"},{"key":"pntd.0014204.ref011","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.antiviral.2018.09.009","article-title":"The WHO R&D Blueprint: 2018 review of emerging infectious diseases requiring urgent research and development efforts","volume":"159","author":"MS Mehand","year":"2018","journal-title":"Antiviral Res"},{"issue":"11","key":"pntd.0014204.ref012","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.1017\/ice.2021.343","article-title":"Crimean-Congo hemorrhagic fever outbreak in Turkey amid the coronavirus disease 2019 (COVID-19) pandemic; A debacle for the healthcare system of Turkey","volume":"43","author":"Q Mehmood","year":"2022","journal-title":"Infect Control Hosp Epidemiol"},{"issue":"1","key":"pntd.0014204.ref013","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s41182-023-00559-z","article-title":"The new wave of Congo virus in Pakistan: Emerging threat","volume":"51","author":"I Masood","year":"2023","journal-title":"Trop Med Health"},{"issue":"9","key":"pntd.0014204.ref014","doi-asserted-by":"crossref","DOI":"10.1016\/S1473-3099(23)00478-4","article-title":"The largest reported outbreak of CCHF in hospital settings: Lessons from Kandahar, Afghanistan","volume":"23","author":"A Gaina","year":"2023","journal-title":"Lancet Infect Dis"},{"key":"pntd.0014204.ref015","doi-asserted-by":"crossref","first-page":"100019","DOI":"10.1016\/j.ijidoh.2024.100019","article-title":"Another Crimean-Congo hemorrhagic fever outbreak in Uganda: Ongoing challenges with prevention, detection, and response","volume":"2","author":"JF Zalwango","year":"2024","journal-title":"IJID One Health"},{"key":"pntd.0014204.ref016","doi-asserted-by":"crossref","DOI":"10.31646\/gbio.203","article-title":"An Outbreak of Crimean-Congo hemorrhagic fever (CCHF) in South Africa in 2022","volume":"5","author":"U Betodkar","year":"2023","journal-title":"Global Biosecurity"},{"issue":"1","key":"pntd.0014204.ref017","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1186\/s12879-024-10199-1","article-title":"Crimean-Congo haemorrhagic fever among healthcare workers in Iran 2000-2023, a report of National Reference Laboratory","volume":"24","author":"M Fazlalipour","year":"2024","journal-title":"BMC Infect Dis"},{"key":"pntd.0014204.ref018","doi-asserted-by":"crossref","first-page":"100588","DOI":"10.1016\/j.ijregi.2025.100588","article-title":"Crimean-Congo hemorrhagic fever, a real health problem in Iraq?","volume":"14","author":"MA Abdulrahman","year":"2025","journal-title":"IJID Reg"},{"key":"pntd.0014204.ref019","author":"European Centre for Disease Prevention and Control","year":"2025"},{"key":"pntd.0014204.ref020","unstructured":"Semper AE, Olver J, Warner J, Cehovin A, Fay PC, Hart PJ, et al. Research and product development for Crimean-Congo haemorrhagic fever: priorities for 2024-30. Lancet Infect Dis. 2024."},{"issue":"2","key":"pntd.0014204.ref021","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.virs.2023.01.001","article-title":"Crimean-Congo hemorrhagic fever virus in Central, Eastern, and South-eastern Asia","volume":"38","author":"M Fereidouni","year":"2023","journal-title":"Virol Sin"},{"issue":"8","key":"pntd.0014204.ref022","doi-asserted-by":"crossref","first-page":"841","DOI":"10.3390\/pathogens11080841","article-title":"The Prevalence and Genetic Variants of the CCHF Virus Circulating among Ticks in the Southern Regions of Kazakhstan","volume":"11","author":"KT Sultankulova","year":"2022","journal-title":"Pathogens"},{"key":"pntd.0014204.ref023","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijid.2021.12.286","article-title":"Results of genotyping of the Congo-Crimean hemorrhagic fever virus circulating in Southern Kazakhstan","volume":"116","author":"G Abuova","year":"2022","journal-title":"International Journal of Infectious Diseases"},{"key":"pntd.0014204.ref024","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1099\/vir.0.18805-0","article-title":"Genetic variability of Crimean-Congo haemorrhagic fever virus in Russia and Central Asia","volume":"84","author":"L Yashina","year":"2003","journal-title":"J Gen Virol"},{"issue":"9","key":"pntd.0014204.ref025","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1089\/vbz.2011.0769","article-title":"Crimean-Congo hemorrhagic fever in Tajikistan","volume":"12","author":"FH Tishkova","year":"2012","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"11","key":"pntd.0014204.ref026","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijid.2013.04.008","article-title":"Identification and analysis of Crimean-Congo hemorrhagic fever virus from human sera in Tajikistan","volume":"17","author":"B Atkinson","year":"2013","journal-title":"Int J Infect Dis"},{"issue":"3","key":"pntd.0014204.ref027","first-page":"29","article-title":"Genetic variants of the Crimean-Congo hemorrhagic fever virus circulating in endemic areas of the southern Tajikistan in 2009","author":"ID Petrova","year":"2013","journal-title":"Mol Gen Mikrobiol Virusol"},{"key":"pntd.0014204.ref028","doi-asserted-by":"crossref","first-page":"114833","DOI":"10.1016\/j.jviromet.2023.114833","article-title":"Recovery of complete genome sequences of Crimean-Congo haemorrhagic fever virus (CCHFV) directly from clinical samples: A comparative study between targeted enrichment and metagenomic approaches","volume":"323","author":"J D\u2019Addiego","year":"2024","journal-title":"J Virol Methods"},{"issue":"2","key":"pntd.0014204.ref029","doi-asserted-by":"crossref","first-page":"313","DOI":"10.3201\/eid3102.241249","article-title":"Two human infections with diverse Europe-1 Crimean-Congo hemorrhagic fever virus strains, North Macedonia, 2024","volume":"31","author":"D Jakimovski","year":"2025","journal-title":"Emerg Infect Dis"},{"key":"pntd.0014204.ref030"},{"key":"pntd.0014204.ref031"},{"key":"pntd.0014204.ref032"},{"key":"pntd.0014204.ref033"},{"issue":"2","key":"pntd.0014204.ref034","article-title":"Investigating the effect of ribavirin treatment on genetic mutations in Crimean-Congo haemorrhagic fever virus (CCHFV) through next-generation sequencing","volume":"95","author":"J D\u2019Addiego","year":"2023","journal-title":"J Med Virol"},{"issue":"6","key":"pntd.0014204.ref035","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"J Quick","year":"2017","journal-title":"Nat Protoc"},{"issue":"14","key":"pntd.0014204.ref036","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"18","key":"pntd.0014204.ref037","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"H Li","year":"2018","journal-title":"Bioinformatics"},{"issue":"2","key":"pntd.0014204.ref038","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"P Danecek","year":"2021","journal-title":"Gigascience"},{"issue":"1","key":"pntd.0014204.ref039","doi-asserted-by":"crossref","first-page":"1567","DOI":"10.1038\/s41598-017-01703-6","article-title":"BAMClipper: Removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing","volume":"7","author":"CH Au","year":"2017","journal-title":"Sci Rep"},{"issue":"7","key":"pntd.0014204.ref040","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"K Tamura","year":"2021","journal-title":"Mol Biol Evol"},{"key":"pntd.0014204.ref041","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: A multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"pntd.0014204.ref042","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":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"pntd.0014204.ref043","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1023\/B:DOBI.0000046647.18163.22","article-title":"Study of the genetic variability of Crimean-Congo hemorrhagic fever virus in Central Asia","volume":"398","author":"SV Seregin","year":"2004","journal-title":"Dokl Biochem Biophys"},{"issue":"2","key":"pntd.0014204.ref044","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1023\/B:VIRU.0000016857.94136.89","article-title":"Genetic characterization of the M RNA segment of Crimean-Congo hemorrhagic fever virus strains isolated in Russia and Tajikistan","volume":"28","author":"SV Seregin","year":"2004","journal-title":"Virus Genes"},{"issue":"3","key":"pntd.0014204.ref045","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1007\/s00705-005-0648-0","article-title":"Complete L segment coding-region sequences of Crimean Congo hemorrhagic fever virus strains from the Russian Federation and Tajikistan","volume":"151","author":"JD Meissner","year":"2006","journal-title":"Arch Virol"},{"issue":"3","key":"pntd.0014204.ref046","first-page":"11","article-title":"Characteristics of Crimean-Congo hemorrhagic fever virus circulating in Russia and Central Asia","volume":"47","author":"LN Iashina","year":"2002","journal-title":"Vopr Virusol"},{"issue":"6","key":"pntd.0014204.ref047","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.3201\/eid1906.120771","article-title":"Crimean-Congo hemorrhagic fever Asia-2 genotype, Pakistan","volume":"19","author":"MM Alam","year":"2013","journal-title":"Emerg Infect Dis"},{"issue":"1","key":"pntd.0014204.ref048","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/s12879-025-10728-6","article-title":"Molecular characterization and phylogenetic analysis of Crimean-Congo hemorrhagic fever virus, northwestern of Iran","volume":"25","author":"N Soozangar","year":"2025","journal-title":"BMC Infect Dis"},{"issue":"8","key":"pntd.0014204.ref049","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.3390\/v17081054","article-title":"Molecular evolution and phylogeography of the crimean-congo hemorrhagic fever virus","volume":"17","author":"P Iglesias-Rivas","year":"2025","journal-title":"Viruses"},{"issue":"4","key":"pntd.0014204.ref050","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0302224","article-title":"Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts","volume":"19","author":"S S Celina","year":"2024","journal-title":"PLoS One"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0014204","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T00:00:00Z","timestamp":1776038400000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0014204","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T17:46:07Z","timestamp":1776102367000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0014204"}},"subtitle":[],"editor":[{"given":"Brianna R","family":"Beechler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,7]]},"references-count":50,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0014204","relation":{},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,7]]}}}