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Yu L, Guo Q, Wei H, Liu Y, Tong W, Zhu S, Ji T, Yang Q, Wang D, Xiao J, Lu H, Liu Y, Li J, Wang W, He Y, Zhang Y, Yan D. Molecular Epidemiology and Evolution of Coxsackievirus A14. Viruses 2023; 15:2323. [PMID: 38140564 PMCID: PMC10748285 DOI: 10.3390/v15122323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
As the proportion of non-enterovirus 71 and non-coxsackievirus A16 which proportion of composition in the hand, foot, and mouth pathogenic spectrum gradually increases worldwide, the attention paid to other enteroviruses has increased. As a member of the species enterovirus A, coxsackievirus A14 (CVA14) has been epidemic around the world until now since it has been isolated. However, studies on CVA14 are poor and the effective population size, evolutionary dynamics, and recombination patterns of CVA14 are not well understood. In this study, 15 CVA14 strains were isolated from HFMD patients in mainland China from 2009 to 2019, and the complete sequences of CVA14 in GenBank as research objects were analyzed. CVA14 was divided into seven genotypes A-G based on an average nucleotide difference of the full-length VP1 coding region of more than 15%. Compared with the CVA14 prototype strain, the 15 CVA14 strains showed 84.0-84.7% nucleotide identity in the complete genome and 96.9-97.6% amino acid identity in the encoding region. Phylodynamic analysis based on 15 CVA14 strains and 22 full-length VP1 sequences in GenBank showed a mean substitution rate of 5.35 × 10-3 substitutions/site/year (95% HPD: 4.03-6.89 × 10-3) and the most recent common ancestor (tMRCA) of CVA14 dates back to 1942 (95% HPD: 1930-1950). The Bayesian skyline showed that the effective population size had experienced a decrease-increase-decrease fluctuation since 2004. The phylogeographic analysis indicated two and three possible migration paths in the world and mainland China, respectively. Four recombination patterns with others of species enterovirus A were observed in 15 CVA14 strains, among which coxsackievirus A2 (CVA2), coxsackievirus A4 (CVA4), coxsackievirus A6 (CVA6), coxsackievirus A8 (CVA8), and coxsackievirus A12 (CVA12) may act as recombinant donors in multiple regions. This study has filled the gap in the molecular epidemiological characteristics of CVA14, enriched the global CVA14 sequence database, and laid the epidemiological foundation for the future study of CVA14 worldwide.
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Affiliation(s)
- Liheng Yu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Qin Guo
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou 450003, China;
| | - Yingying Liu
- Hebei Center for Disease Control and Prevention, Shijiazhuang 050024, China;
| | - Wenbin Tong
- Sichuan Center for Disease Control and Prevention, Chengdu 610044, China;
| | - Shuangli Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Tianjiao Ji
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Qian Yang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Dongyan Wang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Jinbo Xiao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Huanhuan Lu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Ying Liu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Jichen Li
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Wenhui Wang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271016, China; (W.W.); (Y.H.)
| | - Yun He
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271016, China; (W.W.); (Y.H.)
| | - Yong Zhang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
| | - Dongmei Yan
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory of Medical Virology, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.Y.); (Q.G.); (S.Z.); (T.J.); (Q.Y.); (D.W.); (J.X.); (H.L.); (Y.L.); (J.L.); (Y.Z.)
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