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Genomic analysis of a recombinant coxsackievirus A19 identified in Xinxiang, China, in 2019

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Abstract

Coxsackievirus A19 (CV-A19) is an enterovirus belonging to the species Enterovirus C, and the prototype strain 8663 was isolated from a patient with Guillain-Barré syndrome in Japan. In this study, we determined the complete genome sequence of a CV-A19 isolate identified in a stool sample from a child with hand, foot, and mouth disease in Xinxiang, Henan, China, in 2019 and named it CV-A19 strain 2019103106/XX/CHN/2019 – 2019103106 for short. The genome of this virus consists of 7409 nucleotides, including a 6624-nucleotide open reading frame encoding a potential polyprotein precursor of 2207 amino acids. Compared with strain 8663, strain 2019103106 showed 85.1% nucleotide sequence identity in the complete genome and 85.6% identity in the VP1 coding region, reflecting their genetic divergence. Phylogenetic analysis of strain 2019103106 and other representative EV-C strains with sequences available in the GenBank database showed that CV-A19 strains could be grouped into two clusters based on the complete or 214-nucleotide partial VP1 coding regions, and 2019103106 belonged to cluster 1, with the closest relationship to CV-A19 strain SWG82 from Shandong, China. Phylogenetic trees based on the P2 and P3 coding regions highlighted the divergence between strains 2019103106 and 8663, implying that strain 2019103106 had undergone recombination. Further recombination analysis suggested that strains V18A-like CV-A1 and BBD26-like CV-A19 probably recombined to yield strain 2019103106. The present study points out the genetic diversity of CV-A19. It expands our understanding of the evolution of the CV-A19 genome, but more genome sequences of epidemic strains are needed to explain the phylogeny and evolutionary history of CV-A19 comprehensively.

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The complete genome sequence of the CV-A19 strain 2019103106/XX/CHN/2019, described in this study, was deposited in the GenBank database under accession number MT175706.

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Acknowledgements

The authors are grateful to Dr. Dong Liu and Prof. Hui Hu for their help with revision.

Funding

This research was funded by the Key Scientific and Technological Research Projects of Henan Province (grant no. 212102310335 and 222102310641).

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Authors and Affiliations

  1. School of Public Health, Xinxiang Medical University, Xinxiang, 453003, China

    Liang Yi, Li Zhang, Linlin Feng, Qian Zhao, Pengwei Xu, Yinbiao Wang, Ling Tao & Weidong Wu

  2. Xinxiang Center for Disease Control and Prevention, Xinxiang, 453000, China

    Xubo Luan

Authors
  1. Liang Yi
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  2. Li Zhang
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  3. Linlin Feng
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  4. Xubo Luan
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  7. Yinbiao Wang
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  8. Ling Tao
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Contributions

Conceptualization, Ling Tao; resources, Xubo Luan; methodology, Li Zhang, Ling Tao, Pengwei Xu, and Yinbiao Wang; software, Liang Yi, Li Zhang, and Ling Tao; investigation, Liang Yi, Linlin Feng, Xubo Luan, and Ling Tao; validation, Qian Zhao and Pengwei Xu; formal analysis, Li Zhang and Yinbiao Wang; data curation, Liang Yi, Linlin Feng, and Ling Tao; writing—original draft preparation, Liang Yi, Ling Tao, and Li Zhang; writing—review and editing, Qian Zhao, Pengwei Xu, Yinbiao Wang, and Weidong Wu; visualization, Ling Tao and Li Zhang; supervision, Ling Tao and Weidong Wu; project administration, Yinbiao Wang, Ling Tao, and Weidong Wu; funding acquisition, Yinbiao Wang and Ling Tao. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Ling Tao.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This study was approved by the Ethics Committee of Xinxiang Medical University (permission no.: XYLL-2018-B015, date of approval: March 2019). The human materials used in this study were stool samples collected from children with HFMD by Xinxiang Center for Disease Control and Prevention. The routine monitoring procedures used to test the samples were performed following the approved guidelines and without accessing the other medical data of the HFMD cases except for those in the National Notifiable Disease Report System (NNDRS), so the requirement for informed consent was waived.

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Yi, L., Zhang, L., Feng, L. et al. Genomic analysis of a recombinant coxsackievirus A19 identified in Xinxiang, China, in 2019. Arch Virol 167, 1405–1420 (2022). https://doi.org/10.1007/s00705-022-05433-7

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