| ObjectiveIn order to reveal the epidemiological and molecular genetic characteristics of Echovirus 6(E6)in China’s mainland,based on the E6 isolates from hand-foot-mouth cases in China’s mainland from 2009 to 2018,and the sequence analysis of E6 downloaded from GenBank,discussed the molecular variation and changes of E6.To provide basic data for the monitoring and prevention of hand,foot and mouth disease and vaccine development in China.MethodsSearched E6 strain in 2009-2018 from the National Poliomyelitis Laboratory Specimen Database and used Real-time reverse transcription-polymerase chain reaction(Real-time RT-PCR)to detect samples and virus isolation was carried out for the samples with positive E6 nucleic acid.The target gene(VP1)and the whole genome of E6 are amplified by Reverse transcription-polymerase chain reaction(RT-PCR)method and the sequenced.Combined with the E6 VP1 region and the whole genome representative sequence downloaded from GenBank.The global E6 database was constructed by using Sequencer 5.0,Mega 5.05,Simplot3.5.1 and other bioinformatics software to construct a global E6 database.Results(1)After comparison and screening,88 global E6 representative sequences were obtained.According to the published enterovirus genotyping standards,divided E6 into five genotypes A to F used ML to construct a phylogenetic tree.Except for HEB15-54497H,JX15-110 and GZ13-6,the 24 isolates belonged to the C genotype,and the others belonged to the F genotype.(2)Obtained an MCMC tree based on 84 globally distributed E6 full-length VP1 sequences using the BEAST software.The results show that the earliest ancestor of E6(TMRCA)can be traced back to 1863(95%HPD:130-185 years ago).Bayesian Skyline analysis shows that E6 fluctuated slightly during 2007-2009(especially around 2009)in China.(3)By sorting out 708 sequences downloaded from GenBank and 24 strains of E6 in our laboratory,the number of E6 reported gradually increased after 2008,especially from 2008 to 2013,reaching 45.86%.At the same time,356 Chinese sequences were counted from the above sorted sequence,including 17 of 31 provinces.After analysis,nearly half of them were separated from sewage,followed by aseptic meningitis/meningitis and acute flaccid paralysis.(4)The phylogenetic tree analysis of the entire E6 gene component segment in this study suggested that there are at least three recombination modes.The representative sequences of E6 were selected for different recombination modes and they all recombined with the EV-B group epidemic strains.Conclusions(1)Since 1988,the C,E,and F genotypes are popular E6 strains in China.The F genotype was currently the most popular genotype in China and severe,fatal cases are distributed.Different genotypes are widely distributed in regions and case types,and there was no significant difference between the geographical distributions of each genotype.(2)The origin time of genotype E is very close to genotype F,and they may evolve into two different branches within a period of time.Bayesian skyline analysis results show that the population tended to expand on a small scale of E6 in 2009.After that,the effective population has remained at a stable level,and the change in virus mutation has always been at a low level.(3)The high detection rate of E6 in environmental monitoring indicates that the virus continues to exist and evolve in the environment.(4)In this study,E6 recombined with the epidemic strains in the EV-B group between the P2 and P3 regions and the recombination of fatal cases was more complicated than other cases.Figure[19]table[13]reference[93]... |
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