Analysis on whole genome characteristics of coxsackievirus-A6 in Changchun region
Objective To analyze the whole genomes characteristicsof Coxsackievirus A6(CV-A6)samples in Changchun City.Methods Eight stool samples of children with hand,foot and mouth disease(HFMD)from 2019 to 2022 in Chang-chun City were selected,suspension was prepared,RNA was extracted,whole-genome amplification and sequencing were performed by Illumina next-generation sequencing technology,and homology,phylogenetic evolution and recombination a-nalysis were performed by MegAlign,MEGA 11,RDP4,Simplot and other biological software.Results The whole genome length was 7423-7425 bp.The nucleotide sequence homology was 93.0％-100.0％,compared with the prototype strain Gdula(AY421764),the nucleotide homology was 80.4％-80.9％,and the homology with other domestic reference strains of CV-A6 was 93.7％-99.6％.However,the homology of C9 in the non-structural protein 3D region was the lowest 85.3％.Further recombination analysis showed that C9 may be reorganized in the 3D region.A total of 8 mutation sites were detec-ted in the 2A,2C,3A,3D and 3'UTR regions of the 8 CV-A6 endemic strains.Conclusion In this study,1 potential recombinant strain and 7 stable transmitted strains were identified.And some mutation sites were found to be related to viru-lence and clinical phenotype,which need to be further verified.
Coxsackievirus-A6(CV-A6)Genome sequencesRecombinant analysisSystematic evolutionChangchun City
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