{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:16:04Z","timestamp":1787030164165,"version":"build-2736575974"},"reference-count":50,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,12,27]],"date-time":"2022-12-27T00:00:00Z","timestamp":1672099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Council of Thailand"},{"name":"Center of Excellence in Clinical Virology at Chulalongkorn University"},{"name":"King Chulalongkorn Memorial Hospital"},{"name":"MK Restaurant Group x Aunt Thongkam Foundation"},{"name":"BJC Big C Foundation"},{"name":"Chulalongkorn University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Coxsackievirus (CV)-A6 infections cause hand, foot, and mouth disease (HFMD) in children and adults. Despite the serious public health threat presented by CV-A6 infections, our understanding of the mechanisms by which new CV-A6 strains emerge remains limited. This study investigated the molecular epidemiological trends, evolutionary dynamics, and recombination characteristics of CV-A6-associated HFMD in Thailand between 2019 and 2022. In the HFMD patient samples collected during the 4-year study period, we identified enterovirus (EV) RNA in 368 samples (48.7%), of which CV-A6 (23.7%) was the predominant genotype, followed by CV-A4 (6%), EV-A71 (3.7%), and CV-A16 (3.4%). According to the partial viral protein (VP) 1 sequences, all these CV-A6 strains belonged to the D3 clade. Based on the viral-RNA-dependent RNA polymerase (RdRp) gene, four recombinant forms (RFs), RF-A (147, 84.5%), RF-N (11, 6.3%), RF-H (1, 0.6%), and newly RF-Y (15, 8.6%), were identified throughout the study period. Results from the similarity plot and bootscan analyses revealed that the 3D polymerase (3Dpol) region of the D3\/RF-Y subclade consists of sequences highly similar to CV-A10. We envisage that the epidemiological and evolutionarily insights presented in this manuscript will contribute to the development of vaccines to prevent the spread of CV-A6 infection.<\/jats:p>","DOI":"10.3390\/v15010073","type":"journal-article","created":{"date-parts":[[2022,12,28]],"date-time":"2022-12-28T08:42:22Z","timestamp":1672216942000},"page":"73","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["Evolutionary and Genetic Recombination Analyses of Coxsackievirus A6 Variants Associated with Hand, Foot, and Mouth Disease Outbreaks in Thailand between 2019 and 2022"],"prefix":"10.3390","volume":"15","author":[{"given":"Jiratchaya","family":"Puenpa","sequence":"first","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nutsada","family":"Saengdao","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"},{"name":"Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nongkanok","family":"Khanarat","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sumeth","family":"Korkong","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jira","family":"Chansaenroj","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9391-663X","authenticated-orcid":false,"given":"Ritthideach","family":"Yorsaeng","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nasamon","family":"Wanlapakorn","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2337-6807","authenticated-orcid":false,"given":"Yong","family":"Poovorawan","sequence":"additional","affiliation":[{"name":"Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand"},{"name":"FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok 10300, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.3201\/eid1509.090438","article-title":"Coxsackievirus A6 and hand, foot, and mouth disease, Finland","volume":"15","author":"Osterback","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1099\/vir.0.000062","article-title":"Genetic characterization of human coxsackievirus A6 variants associated with atypical hand, foot and mouth disease: A potential role of recombination in emergence and pathogenicity","volume":"96","author":"Gaunt","year":"2015","journal-title":"J. Gen. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.3201\/eid1810.120813","article-title":"Hand, foot, and mouth disease caused by coxsackievirus a6","volume":"18","author":"Flett","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"5491","DOI":"10.1038\/s41598-017-05618-0","article-title":"Persistent circulation of Coxsackievirus A6 of genotype D3 in mainland of China between 2008 and 2015","volume":"7","author":"Song","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"O150","DOI":"10.1111\/1469-0691.12361","article-title":"Molecular epidemiology of enterovirus 71, coxsackievirus A16 and A6 associated with hand, foot and mouth disease in Spain","volume":"20","author":"Cabrerizo","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2451","DOI":"10.1007\/s00705-014-2071-x","article-title":"Coxsackievirus A6 and enterovirus 71 causing hand, foot and mouth disease in Cuba, 2011\u20132013","volume":"159","author":"Fonseca","year":"2014","journal-title":"Arch. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"105245","DOI":"10.1016\/j.jcv.2022.105245","article-title":"Hand, foot, and mouth disease outbreak by Coxsackievirus A6 during COVID-19 pandemic in 2021, S\u00e3o Paulo, Brazil","volume":"154","author":"Carmona","year":"2022","journal-title":"J. Clin. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"105378","DOI":"10.1016\/j.meegid.2022.105378","article-title":"Genetic characteristics of Coxsackievirus A6 from children with hand, foot and mouth disease in Beijing, China, 2017\u20132019","volume":"106","author":"Zhang","year":"2022","journal-title":"Infect. Genet. Evol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2100978","DOI":"10.2807\/1560-7917.ES.2021.26.43.2100978","article-title":"A large-scale outbreak of hand, foot and mouth disease, France, as at 28 September 2021","volume":"26","author":"Mirand","year":"2021","journal-title":"Euro Surveill."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.jcv.2018.09.002","article-title":"Molecular epidemiology of coxsackievirus A6 circulating in Hong Kong reveals common neurological manifestations and emergence of novel recombinant groups","volume":"108","author":"Lau","year":"2018","journal-title":"J. Clin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1007\/s13337-020-00567-1","article-title":"Isolation and molecular characterization of coxsackievirus A6 and coxsackievirus A16 from a case of recurrent Hand, Foot and Mouth Disease in Mumbai, Maharashtra, India, 2018","volume":"31","author":"Saxena","year":"2020","journal-title":"Virusdisease"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1016\/j.vaccine.2018.12.065","article-title":"Phylogenetic and antigenic analyses of coxsackievirus A6 isolates in Yamagata, Japan between 2001 and 2017","volume":"37","author":"Mizuta","year":"2019","journal-title":"Vaccine"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"165","DOI":"10.33073\/pjm-2019-016","article-title":"Hand, Foot, and Mouth Disease Caused by Coxsackievirus A6: A Preliminary Report from Istanbul","volume":"68","author":"Ceylan","year":"2019","journal-title":"Pol. J. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1002\/jmv.25590","article-title":"Hand-foot-and-mouth disease in uruguay: Coxsackievirus A6 identified as causative of an outbreak in a rural childcare center","volume":"92","author":"Lizasoain","year":"2020","journal-title":"J. Med. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"8273","DOI":"10.1016\/j.vaccine.2020.11.031","article-title":"Coxsackieviruses A6 and A16 associated with hand, foot, and mouth disease in Vietnam, 2008\u20132017: Essential information for rational vaccine design","volume":"38","author":"Dao","year":"2020","journal-title":"Vaccine"},{"key":"ref_16","first-page":"140","article-title":"Atypical hand, foot, and mouth disease caused by Coxsackievirus A6 in Argentina in 2015","volume":"51","author":"Cisterna","year":"2019","journal-title":"Rev. Argent. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"104307","DOI":"10.1016\/j.jcv.2020.104307","article-title":"Atypical hand-foot-mouth disease in Bel\u00e9m, Amazon region, northern Brazil, with detection of coxsackievirus A6","volume":"126","author":"Justino","year":"2020","journal-title":"J. Clin. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6607294","DOI":"10.1155\/2022\/6607294","article-title":"An Outbreak of Coxsackievirus A6 Infection in Adults of a Collective Unit, China, 2019","volume":"2022","author":"Gao","year":"2022","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"546","DOI":"10.2340\/00015555-2261","article-title":"Coxsackievirus A6 Polymorphic Exanthem in Israeli Children","volume":"96","author":"Marva","year":"2016","journal-title":"Acta Derm. Venereol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jcv.2018.11.003","article-title":"Severe atypical hand-foot-and-mouth disease in adults due to coxsackievirus A6: Clinical presentation and phylogenesis of CV-A6 strains","volume":"110","author":"Broccolo","year":"2019","journal-title":"J. Clin. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"634","DOI":"10.3947\/ic.2020.52.4.634","article-title":"Coxsackievirus A6-induced Hand-Foot-and-Mouth Disease Mimicking Stevens-Johnson Syndrome in an Immunocompetent Adult","volume":"52","author":"No","year":"2020","journal-title":"Infect. Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s12929-019-0573-2","article-title":"The History of Enterovirus A71 Outbreaks and Molecular Epidemiology in the Asia-Pacific Region","volume":"26","author":"Puenpa","year":"2019","journal-title":"J. Biomed. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1016\/S1473-3099(10)70194-8","article-title":"Virology, epidemiology, pathogenesis, and control of enterovirus 71","volume":"10","author":"Solomon","year":"2010","journal-title":"Lancet Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e2552","DOI":"10.1093\/cid\/ciaa1853","article-title":"Basic Reproduction Number of Enterovirus 71 and Coxsackievirus A16 and A6: Evidence From Outbreaks of Hand, Foot, and Mouth Disease in China Between 2011 and 2018","volume":"73","author":"Zhang","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1007\/s00705-021-05156-1","article-title":"Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)","volume":"166","author":"Walker","year":"2021","journal-title":"Arch. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1086\/511073","article-title":"Human enterovirus 71 disease in Sarawak, Malaysia: A prospective clinical, virological, and molecular epidemiological study","volume":"44","author":"Ooi","year":"2007","journal-title":"Clin. Infect. Dis."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Wu, W.H., Kuo, T.C., Lin, Y.T., Huang, S.W., Liu, H.F., Wang, J., and Chen, Y.M. (2013). Molecular epidemiology of enterovirus 71 infection in the central region of Taiwan from 2002 to 2012. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0083711"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Kim, H.J., Hyeon, J.Y., Hwang, S., Lee, Y.P., Lee, S.W., Yoo, J.S., Kang, B., Ahn, J.B., Jeong, Y.S., and Lee, J.W. (2016). Epidemiology and virologic investigation of human enterovirus 71 infection in the Republic of Korea from 2007 to 2012: A nationwide cross-sectional study. BMC Infect. Dis., 16.","DOI":"10.1186\/s12879-016-1755-0"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1128\/MMBR.00012-14","article-title":"Picornavirus morphogenesis","volume":"78","author":"Jiang","year":"2014","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"8741","DOI":"10.1128\/JVI.73.10.8741-8749.1999","article-title":"Evidence of recombination among enteroviruses","volume":"73","author":"Santti","year":"1999","journal-title":"J. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Muslin, C., Mac Kain, A., Bessaud, M., Blondel, B., and Delpeyroux, F. (2019). Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses, 11.","DOI":"10.3390\/v11090859"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3281","DOI":"10.1099\/vir.0.81264-0","article-title":"Recombination in circulating Human enterovirus B: Independent evolution of structural and non-structural genome regions","volume":"86","author":"Lukashev","year":"2005","journal-title":"J. Gen. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.virusres.2017.11.023","article-title":"Nonstructural Protein 2A Modulates Replication and Virulence of Enterovirus","volume":"244","author":"Li","year":"2018","journal-title":"Virus Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.jviromet.2017.06.013","article-title":"Development of single-step multiplex real-time RT-PCR assays for rapid diagnosis of enterovirus 71, coxsackievirus A6, and A16 in patients with hand, foot, and mouth disease","volume":"248","author":"Puenpa","year":"2017","journal-title":"J. Virol. Methods"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2698","DOI":"10.1128\/JCM.00542-06","article-title":"Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens","volume":"44","author":"Nix","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"W636","DOI":"10.1093\/nar\/gkz268","article-title":"The EMBL-EBI search and sequence analysis tools APIs in 2019","volume":"47","author":"Madeira","year":"2019","journal-title":"Nucleic Acids. Res."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duch\u00eane, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., K\u00fchnert, D., and De Maio, N. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol., 15.","DOI":"10.1371\/journal.pcbi.1006650"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"veaa048","DOI":"10.1093\/ve\/veaa048","article-title":"Genetic recombination in fast-spreading coxsackievirus A6 variants: A potential role in evolution and pathogenicity","volume":"6","author":"Song","year":"2020","journal-title":"Virus Evol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Tomba Ngangas, S., Bisseux, M., Jugie, G., Lambert, C., Cohen, R., Werner, A., Archimbaud, C., Henquell, C., Mirand, A., and Bailly, J.L. (2022). Coxsackievirus A6 Recombinant Subclades D3\/A and D3\/H Were Predominant in Hand-Foot-And-Mouth Disease Outbreaks in the Paediatric Population, France, 2010\u20132018. Viruses, 14.","DOI":"10.3390\/v14051078"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3225","DOI":"10.1099\/jgv.0.000619","article-title":"Molecular epidemiology and the evolution of human coxsackievirus A6","volume":"97","author":"Puenpa","year":"2016","journal-title":"J. Gen. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/1743-422X-11-157","article-title":"Circulation of Coxsackievirus A6 in hand-foot-mouth disease in Guangzhou, 2010\u20132012","volume":"11","author":"Di","year":"2014","journal-title":"Virol. J."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"10423","DOI":"10.1128\/JVI.77.19.10423-10431.2003","article-title":"Recombination in circulating enteroviruses","volume":"77","author":"Lukashev","year":"2003","journal-title":"J. Virol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1080\/22221751.2021.1906754","article-title":"Viral determinants that drive Enterovirus-A71 fitness and virulence","volume":"10","author":"Ang","year":"2021","journal-title":"Emerg. Microbes. Infect."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"641","DOI":"10.3201\/eid1904.121666","article-title":"Hand, foot, and mouth disease caused by coxsackievirus A6, Thailand, 2012","volume":"19","author":"Puenpa","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"78","DOI":"10.3201\/eid1301.020112","article-title":"Epidemic hand, foot and mouth disease caused by human enterovirus 71, Singapore","volume":"9","author":"Chan","year":"2003","journal-title":"Emerg. Infect. Dis."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/1423-0127-21-16","article-title":"Epidemiology and seroepidemiology of human enterovirus 71 among Thai populations","volume":"21","author":"Linsuwanon","year":"2014","journal-title":"J. Biomed. Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/S1473-3099(13)70264-0","article-title":"Atypical hand, foot, and mouth disease: A vesiculobullous eruption caused by Coxsackie virus A6","volume":"14","author":"Feder","year":"2014","journal-title":"Lancet Infect. Dis."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/j.jaad.2013.07.024","article-title":"Atypical hand-foot-and-mouth disease associated with coxsackievirus A6 infection","volume":"69","author":"Lott","year":"2013","journal-title":"J. Am. Acad. Dermatol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/1743-422X-10-209","article-title":"Atypical hand-foot-mouth disease in children: A hospital-based prospective cohort study","volume":"10","author":"Huang","year":"2013","journal-title":"Virol. J."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/1\/73\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:52:39Z","timestamp":1760147559000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/1\/73"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,27]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1]]}},"alternative-id":["v15010073"],"URL":"https:\/\/doi.org\/10.3390\/v15010073","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,27]]}}}