{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:57:45Z","timestamp":1790859465846,"version":"4.1.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":263,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82330103"],"award-info":[{"award-number":["82330103"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"China Mega-Project for Infectious Diseases grant","award":["2025ZD01900102"],"award-info":[{"award-number":["2025ZD01900102"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Nairobi sheep disease virus (NSDV) is a tick-borne orthonairovirus causing severe hemorrhagic gastroenteritis in small ruminants, with case fatality rate up to 90% among naive populations. Despite its veterinary and zoonotic importance, the evolution and spatiotemporal dynamics of NSDV remain poorly understood. We analysed S, M, and L segment sequences collected from the 1950s to 2024 in China, India, and Kenya, and identified three geographically structured lineages (Lineage A from India, Lineage B from China, and Lineage C from Kenya). No host-specific clustering was observed, indicating geographic isolation, rather than host adaptation, is the primary driver of diversification. Recombination events exhibited strong geographic structuring, with Jilin province as a major hotspot (likely reflecting higher sampling density in the region). Occasional intercontinental gene flow from Africa into China contributed parental lineages, and recombinant strains were detected in ticks, with parental contributions from sheep and saiga antelope hosts. Selection analyses revealed strong purifying selection on L segment (dN\/dS\u2009=\u20090.365), but relaxed or positive selection on M glycoprotein (dN\/dS\u2009=\u20093.020) and S segment (dN\/dS\u2009=\u20095.360). Substitution rates ranged from 1.56\u2009\u00d7\u200910\u22124 (L) to 6.81\u2009\u00d7\u200910\u22124 (S) substitutions\/site\/year. Time-to-most-recent-common-ancestor (tMRCA) of all NSDV strains was estimated at ~\u20091732\u00a0ce (95% highest posterior density [HPD]: 1624\u20131833), representing the divergence between the Chinese lineage and the common ancestor of the Indian and Kenyan lineages. The Indian and Kenyan lineages subsequently diverged from their common ancestor ~\u20091763\u00a0ce (95% HPD: 1677\u20131845), followed by the Indian lineage (~1883\u00a0ce) and the Chinese lineage (~1934\u00a0ce). The ancestral location at the root node is highly uncertain (maximum a posteriori, MAP\u2009=\u2009India_Karnataka), and sparse sampling from intermediate regions limits robust phylogeographic inference. Among the well-supported intra-continental routes, migration from India (Maharashtra\/Karnataka) to eastern China (Liaoning, Shandong) received moderate support (BF\u2009=\u20096.40\u201322.57). A route from Liaoning to Kenya was also detected (BF\u2009=\u200911.84), but this inference should be interpreted with caution given the limited Kenyan sampling and potential unsampled intermediate populations.<\/jats:p>","DOI":"10.1093\/ve\/veag061","type":"journal-article","created":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T11:39:01Z","timestamp":1789817941000},"source":"Crossref","is-referenced-by-count":0,"title":["Phylogeography and evolutionary dynamics of Nairobi sheep disease virus"],"prefix":"10.1093","volume":"12","author":[{"given":"Han-Zheng","family":"Mu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Si-Qian","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei-Qi","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gui-Yan","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun-Dong","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]},{"name":"Department of Epidemiology and Health Statistics, School of Public Health, Anhui Medical University , 81 Mei-Shan Road, Shushan District, Hefei 230032 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Health Statistics, School of Public Health, Anhui Medical University , 81 Mei-Shan Road, Shushan District, Hefei 230032 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Ai","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6937-2430","authenticated-orcid":false,"given":"Wei","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science , 20 Dong-Da Street, Fengtai District, Beijing 100071 ,","place":["China"]},{"name":"Department of Epidemiology and Health Statistics, School of Public Health, Anhui Medical University , 81 Mei-Shan Road, Shushan District, Hefei 230032 ,","place":["China"]},{"name":"The First Affiliated Hospital of Anhui Medical University , 218 Ji-Xi Road, Shushan District, Hefei 230032 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"2026100108160970600_ref1","doi-asserted-by":"publisher","first-page":"9727","DOI":"10.1093\/nar\/gkae650","article-title":"Molecular basis of RNA recombination in the 3'UTR of chikungunya virus genome","volume":"52","author":"Bardossy","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026100108160970600_ref2","doi-asserted-by":"publisher","first-page":"411","DOI":"10.20506\/rst.34.2.2367","article-title":"Nairobi sheep disease virus\/Ganjam virus","volume":"34","author":"Baron","year":"2015","journal-title":"Rev Sci Tech (International Office of Epizootics)"},{"key":"2026100108160970600_ref3","doi-asserted-by":"publisher","first-page":"2167","DOI":"10.1093\/molbev\/msw082","article-title":"SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes","volume":"33","author":"Bielejec","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref4","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1016\/j.ympev.2010.01.006","article-title":"Ancient common ancestry of Crimean-Congo hemorrhagic fever virus","volume":"55","author":"Carroll","year":"2010","journal-title":"Mol Phylogenet Evol"},{"key":"2026100108160970600_ref5","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1099\/vir.0.049379-0","article-title":"Molecular evolution of Crimean-Congo hemorrhagic fever virus based on complete genomes","volume":"94","author":"Chen","year":"2012","journal-title":"J Gen Virol"},{"key":"2026100108160970600_ref6","first-page":"799","article-title":"Ganjam virus: a new arbovirus isolated from ticks Haemaphysalis intermedia Warburton and Nuttall, 1909 in Orissa, India","volume":"57","author":"Dandawate","year":"1969","journal-title":"Indian J Med Res"},{"key":"2026100108160970600_ref7","first-page":"975","article-title":"Isolation of Ganjam virus from a human case of febrile illness: a report of a laboratory infection and serological survey of human sera from three different states of India","volume":"57","author":"Dandawate","year":"1969","journal-title":"Indian J Med Res"},{"key":"2026100108160970600_ref8","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1093\/molbev\/msz189","article-title":"ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models","volume":"37","author":"Darriba","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref9","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1016\/0021-9975(78)90005-1","article-title":"The serological relationships of Nairobi sheep disease virus","volume":"88","author":"Davies","year":"1978","journal-title":"J Comp Pathol"},{"key":"2026100108160970600_ref10","doi-asserted-by":"publisher","first-page":"8834","DOI":"10.1128\/JVI.00752-06","article-title":"Crimean-Congo hemorrhagic fever virus genomics and global diversity","volume":"80","author":"Deyde","year":"2006","journal-title":"J Virol"},{"key":"2026100108160970600_ref11","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1007\/BF02383239","article-title":"The distribution and prevalence of Nairobi Sheep disease and other tick-borne infections of sheep and goats in northern Somalia","volume":"7","author":"Edelsten","year":"1975","journal-title":"Trop Anim Health Prod"},{"key":"2026100108160970600_ref12","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2026100108160970600_ref13","doi-asserted-by":"publisher","first-page":"718","DOI":"10.3201\/eid2104.141602","article-title":"Nairobi sheep disease virus RNA in ixodid ticks, China, 2013","volume":"21","author":"Gong","year":"2015","journal-title":"Emerg Infect Dis"},{"key":"2026100108160970600_ref14","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.3390\/v13071250","article-title":"Diagnosis and Pathogenesis of Nairobi Sheep Disease Orthonairovirus Infections in Sheep and Cattle","volume":"13","author":"Hartlaub","year":"2021","journal-title":"Viruses"},{"key":"2026100108160970600_ref15","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.clinmicnews.2021.02.002","article-title":"Norovirus: Molecular Epidemiology, Viral Culture, Immunity, and Vaccines","volume":"43","author":"Hasing","year":"2021","journal-title":"Clin Microbiol Newsl"},{"key":"2026100108160970600_ref16","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.3390\/v17081054","article-title":"Molecular Evolution and Phylogeography of the Crimean-Congo Hemorrhagic Fever Virus","volume":"17","author":"Iglesias-Rivas","year":"2025","journal-title":"Viruses"},{"key":"2026100108160970600_ref17","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"2026100108160970600_ref18","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref19","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2026100108160970600_ref20","doi-asserted-by":"publisher","first-page":"419","DOI":"10.3389\/fvets.2020.00419","article-title":"Nairobi Sheep Disease Virus: A Historical and Epidemiological Perspective","volume":"7","author":"Krasteva","year":"2020","journal-title":"Front Vet Sci"},{"key":"2026100108160970600_ref21","first-page":"001974","article-title":"ICTV Virus Taxonomy Profile: Nairoviridae 2024","volume":"105","author":"Kuhn","year":"2024","journal-title":"J Gen Virol"},{"key":"2026100108160970600_ref22","doi-asserted-by":"publisher","first-page":"3276","DOI":"10.1093\/bioinformatics\/btu531","article-title":"AliView: a fast and lightweight alignment viewer and editor for large datasets","volume":"30","author":"Larsson","year":"2014","journal-title":"Bioinf (Oxf)"},{"key":"2026100108160970600_ref23","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1007\/s00705-013-1940-z","article-title":"The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses","volume":"159","author":"Lasecka","year":"2013","journal-title":"Arch Virol"},{"key":"2026100108160970600_ref24","doi-asserted-by":"publisher","first-page":"110734","DOI":"10.1016\/j.ygeno.2023.110734","article-title":"Genomics evolution of Jingmen viruses associated with ticks and vertebrates","volume":"115","author":"Li","year":"2023","journal-title":"Genomics"},{"key":"2026100108160970600_ref25","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1146\/annurev-ento-010715-023819","article-title":"Rift Valley Fever: An Emerging Mosquito-Borne Disease","volume":"61","author":"Linthicum","year":"2016","journal-title":"Annu Rev Entomol"},{"key":"2026100108160970600_ref26","doi-asserted-by":"publisher","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":"2026100108160970600_ref27","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref28","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/S0368-1742(17)80002-3","article-title":"On a Tick-Borne Gastro-Enteritis of Sheep and Goats Occurring in British East Africa","volume":"30","author":"Montgomery","year":"1917","journal-title":"J Comp Pathol Ther"},{"key":"2026100108160970600_ref29","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1080\/00034983.1996.11813031","article-title":"Nairobi sheep disease virus isolated from Haemaphysalis intermedia ticks collected in Sri Lanka","volume":"90","author":"Perera","year":"1996","journal-title":"Ann Trop Med Parasitol"},{"key":"2026100108160970600_ref30","doi-asserted-by":"publisher","first-page":"msae173","DOI":"10.1093\/molbev\/msae173","article-title":"Ecological Changes Exacerbating the Spread of Invasive Ticks has Driven the Dispersal of Severe Fever with Thrombocytopenia Syndrome Virus Throughout Southeast Asia","volume":"41","author":"P\u00e9rez","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref31","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst Biol"},{"key":"2026100108160970600_ref32","first-page":"319","article-title":"Laboratory infections with Ganjam virus","volume":"74","author":"Rao","year":"1981","journal-title":"Indian J Med Res"},{"key":"2026100108160970600_ref33","first-page":"1572","article-title":"MrBayes 3: Bayesian phylogenetic inference under mixed models","volume":"19","author":"Ronquist","year":"2003","journal-title":"Bioinf (Oxf)"},{"key":"2026100108160970600_ref34","doi-asserted-by":"publisher","first-page":"3118","DOI":"10.1093\/bioinformatics\/btac287","article-title":"SimPlot++: a Python application for representing sequence similarity and detecting recombination","volume":"38","author":"Samson","year":"2022","journal-title":"Bioinf (Oxf)"},{"key":"2026100108160970600_ref35","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nrmicro2614","article-title":"Why do RNA viruses recombine?","volume":"9","author":"Simon-Loriere","year":"2011","journal-title":"Nat Rev Microbiol"},{"key":"2026100108160970600_ref36","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":"2026100108160970600_ref37","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref38","doi-asserted-by":"publisher","first-page":"102375","DOI":"10.1016\/j.ttbdis.2024.102375","article-title":"Identification and phylogenetic analysis of Nairobi sheep disease virus from Haemaphysalis longicornis ticks in Shandong Province, China","volume":"15","author":"Wang","year":"2024","journal-title":"Ticks Tick-borne Dis"},{"key":"2026100108160970600_ref39","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/S0368-1742(58)80018-1","article-title":"An epizootic of Nairobi sheep disease in Uganda","volume":"68","author":"Weinbren","year":"1958","journal-title":"J Comp Pathol"},{"key":"2026100108160970600_ref40"},{"key":"2026100108160970600_ref41","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1016\/j.meegid.2011.04.001","article-title":"Genomic analysis reveals Nairobi sheep disease virus to be highly diverse and present in both Africa, and in India in the form of the Ganjam virus variant","volume":"11","author":"Yadav","year":"2011","journal-title":"Infect Genet Evol"},{"key":"2026100108160970600_ref42","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic Analysis by Maximum Likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"key":"2026100108160970600_ref43","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1016\/j.virol.2019.01.026","article-title":"Genomes and seroprevalence of severe fever with thrombocytopenia syndrome virus and Nairobi sheep disease virus in Haemaphysalis longicornis ticks and goats in Hubei, China","volume":"529","author":"Yang","year":"2019","journal-title":"Virology"},{"key":"2026100108160970600_ref44","doi-asserted-by":"publisher","first-page":"e0000625","DOI":"10.1128\/jvi.00006-25","article-title":"Epidemiological, virological, and pathogenic insights into Nairobi sheep disease virus infection in sheep and goats in China","volume":"99","author":"Yao","year":"2025","journal-title":"J Virol"},{"key":"2026100108160970600_ref45","doi-asserted-by":"publisher","first-page":"e79663","DOI":"10.1371\/journal.pone.0079663","article-title":"Bayesian phylogeography of Crimean-Congo hemorrhagic fever virus in Europe","volume":"8","author":"Zehender","year":"2013","journal-title":"PLoS One"},{"key":"2026100108160970600_ref46","doi-asserted-by":"publisher","first-page":"e00330-26","DOI":"10.1128\/jvi.00330-26","article-title":"Nairobi sheep disease virus: an emerging threat with unresolved pathogenesis and zoonotic potential","volume":"100","author":"Zhang","year":"2026","journal-title":"J Virol"},{"key":"2026100108160970600_ref47","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/s41579-022-00845-3","article-title":"The human-infection potential of emerging tick-borne viruses is a global public health concern","volume":"21","author":"Zhou","year":"2023","journal-title":"Nat Rev Microbiol"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veag061\/71281216\/veag061.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/12\/1\/veag061\/71281216\/veag061.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/12\/1\/veag061\/71281216\/veag061.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:16:21Z","timestamp":1790856981000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veag061\/8824250"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,19]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veag061","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"veag061"}}