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Last year, an inactivated EV\u2010A71 whole virus vaccine was used to prevent this disease in Yunnan, China. To obtain a viral genetic background for evaluating vaccine protection and monitor the adaptive evolution of the virus after the vaccination, a 5\u2010year molecular epidemiology survey was performed before the vaccination. Twenty\u2010six EV\u2010A71 strains were separated from 561 stool specimens of patients with serious HFMD. The whole\u2010genomic sequences of these strains were sequenced. Phylogenetic trees were constructed, and the mutation spectra were analyzed based on these viral sequences. There was no obvious mutation for the circular EV\u2010A71 strains of the same year. Pathogenic EV\u2010A71 strains may arise from a \u201csubgroup\u201d randomly each year. Whole\u2010genomic analyses showed that a hotspot nonsynonymous substitution potentially affecting the immunogenicity of vaccines was found in the 2A gene, but not in genes of the viral capsid proteins, and the genetic diversity of whole viral genomes associated with the incidence of HFMD. Therefore, it will be valuable to monitor the genome\u2010wide changes of EV\u2010A71 to detect the adaptive mutations affecting immunogenicity or perform investigations using genetic diversity as a parameter.<\/jats:p>","DOI":"10.1002\/jmv.25657","type":"journal-article","created":{"date-parts":[[2019,12,18]],"date-time":"2019-12-18T11:29:40Z","timestamp":1576668580000},"page":"1085-1092","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["A 5\u2010year molecular epidemiology survey of human enterovirus 71 before vaccine application in Yunnan Province, China"],"prefix":"10.1002","volume":"92","author":[{"given":"Hong\u2010Bo","family":"Liu","sequence":"first","affiliation":[{"name":"Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College  Kunming China"},{"name":"Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease  Kunming 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