Journal of Shandong University (Health Sciences) ›› 2025, Vol. 63 ›› Issue (9): 92-101.doi: 10.6040/j.issn.1671-7554.0.2024.1149

• Clinical Research • Previous Articles    

Whole genome characterization analysis of Coxsackievirus A6 in Jining in 2021

WANG Shan1,2,3, LIU Wei1,3, FENG Qiang4, FAN Yingying1,3, LIU Haixia1,3, DUAN Yanhua1, WEN Hongling2, JIAO Boyan1,3   

  1. 1.Jining Center for Disease Control and Prevention, Jining 272008, Shandong, China;
    2. School of Public Health, Shandong University, Jinan 250100, Shandong, China;
    3. Jining Key Laboratory of Infectious Disease Control and Prevention, Jining 272008, Shandong, China;
    4. Jining Rencheng Center for Disease Control and Prevention, Jining 272103, Shandong, China
  • Published:2025-09-08

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Abstract: Objective To analyze the epidemiological characteristics and whole-genome features of Coxsackievirus A6(CVA6)in Jining City in 2021, providing a basis for the prevention and control of hand, foot, and mouth disease(HFMD). Methods Reverse transcription quantitative real-time PCR(RT-qPCR)was used to detect CVA6 nucleic acid in HFMD case samples collected from 11 counties and districts in Jining City in 2021. CVA6-positive samples were inoculated into human rhabdomyosarcoma cells for viral culture, and viral nucleic acid was extracted for whole-genome sequencing using next-generation sequencing technology. Bioinformatics analyses, including sequence similarity analysis, internal ribosome entry site(IRES)secondary structure modeling, phosphorylation site analysis, glycosylation site analysis, and lipidation site analysis, were conducted using MEGA 7.0.14, RNAfold, NetPhos 3.1, NetNGlyc 1.0, and GPS Lipid software. Results Nucleic acid testing showed that the positive rate of CVA6 among the confirmed HFMD cases in Jining City in 2021 was 35.79%(97/271). Whole-genome sequencing results revealed that three CVA6 strains exhibited nucleotide homology of 80.69%-80.95% and polyprotein amino acid homology of 94.83%-94.92% with the prototype strain Gdula. Bioinformatics analysis showed that all three CVA6 strains belonged to the D3a evolutionary branch but were located in different evolutionary clusters. Compared to the Gdula prototype strain, seven nucleotide mutations were observed in the 5'UTR IRES region, Q98L and G160S mutations occurred in the VP1 antigenic epitope, an S194T mutation was found in the VP1 receptor-binding site, and T308S, L342S, and K346R mutations were identified in the 3D polymerase active site. Additionally, multiple variations were observed in phosphorylation, glycosylation, and lipidation sites of the encoded proteins. Conclusion CVA6 was the predominant pathogen in HFMD cases in Jining City in 2021. It was evolving in the direction of adapting to the host. The monitoring and prevention efforts against CVA6 should be strengthened.

Key words: Hand, foot and mouth disease, Enterovirus, Coxsackievirus A6, Whole genome analysis

CLC Number: 

  • R183.4
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