Whole-genome sequence characteristics of coxsackievirus A16 related to hand, foot and mouth disease in Jiaxing from 2021 to 2023
10.3760/cma.j.cn112309-20240819-00309
- VernacularTitle:2021—2023年嘉兴市手足口病相关柯萨奇病毒A组16型全基因组序列特征分析
- Author:
Jimei JI
1
;
Shencong LYU
1
;
Yin SONG
1
;
Yamei ZHOU
1
;
Lina LI
1
;
Ping LI
1
;
Yong YAN
1
Author Information
1. 嘉兴市疾病预防控制中心，嘉兴市病原微生物检测重点实验室，嘉兴 314050
- Publication Type:Journal Article
- Keywords:
Hand, foot and mouth disease;
Enterovirus;
Coxsackievirus A16 (CVA16);
Full genome;
Genetic recombination
- From:
Chinese Journal of Microbiology and Immunology
2025;45(7):578-586
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the genetic characteristics of coxsackievirus A16 (CVA16) related to hand, foot and mouth disease (HFMD) in Jiaxing from 2021 to 2023, and understand the biological and molecular evolutionary characteristics of CVA16 in this city.Methods:Real-time fluorescent quantitative PCR was used to detect enterovirus and its types in collected HFMD case samples. At the same time, virus isolation and cultivation were performed on positive samples using RD cells. Then high-throughput sequencing of the whole genome was performed on 23 strains of CVA16 identified from the isolated samples. Finally we obtained its whole genome sequence. DNAStar, MEGA 6.0, Simplot 3.5.1 and other bioinformatics software were used to compare and analyze the sequences, construct the phylogenetic tree of VP1 region, and realize the genotype composition. And these software were also used to analyze the homology of the whole genome nucleotide sequence and the encoded amino acids, while know well the amino acid mutation sites and gene recombination in the main regions.Results:The results showed that among the 1 836 HFMD specimens tested from 2021 to 2023, 1 432 (78.00%, 1 432/1 836) were positive for enterovirus general genes, of which 263 were positive for CVA16, accounting for 18.37% (263/1 432) of the confirmed positive cases. Twenty-three CVA16 strains were sequenced and all of them were B1 subtype, of which 6 strains belong to B1b and 17 strains belong to B1a, with B1a being dominant. B1a strains in Jiaxing showed genetic relatedness to strains isolated in Beijing, Yunnan, Guangzhou, Jiangsu and other places in 2018 to 2023, as well as strains from Vietnam, Thailand, and Australia from 2015 to 2017. B1b strains exhibited consistent amino acid mutations of L23M in the VP1 region and V217I in the VP2 region, while B1a strains exhibited amino acid mutations of S14N/D, T164K, and V251I in the VP1 region and R41H in the VP3 region. Compared with the prototype strain, the 23 strains of CVA16 in Jiaxing accumulated the largest number of amino acid mutations in the coding region, with 28 and 50 mutations in the VP1 and 3D regions, respectively. The recombination patterns of B1a and B1b strains were slightly different, with B1a type showing recombination with CVA8 in the 5′-UTR region instead of CVA4, B1a was similar to enterovirus A71 in most of P2 and P3 regions, and recombined with CVA5 in the 3D region of P3.Conclusions:The prevalent strain of CVA16 in Jiaxing may share a common trend of co-circulation and evolution with those in other provinces. The recombination mainly occurs in the 5′-UTR region and non-structural protein coding regions of P2 and P3. Continuous molecular surveillance of CVA16 is in need, and whole-genome sequencing can help understand the genetic variation, evolution, and recombination of strains.This information will provide a more robust basis for the monitoring and early warning, vaccine development, and prevention and control efforts against HFMD.
