Molecular Epidemiology and Evolution of Coxsackievirus A14
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 (CV...
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MDPI AG
2023-11-01
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| Online Access: | https://www.mdpi.com/1999-4915/15/12/2323 |
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| author | Liheng Yu Qin Guo Haiyan Wei Yingying Liu Wenbin Tong Shuangli Zhu Tianjiao Ji Qian Yang Dongyan Wang Jinbo Xiao Huanhuan Lu Ying Liu Jichen Li Wenhui Wang Yun He Yong Zhang Dongmei Yan |
| author_facet | Liheng Yu Qin Guo Haiyan Wei Yingying Liu Wenbin Tong Shuangli Zhu Tianjiao Ji Qian Yang Dongyan Wang Jinbo Xiao Huanhuan Lu Ying Liu Jichen Li Wenhui Wang Yun He Yong Zhang Dongmei Yan |
| author_sort | Liheng Yu |
| collection | DOAJ |
| description | 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<sup>−3</sup> substitutions/site/year (95% HPD: 4.03–6.89 × 10<sup>−3</sup>) 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. |
| first_indexed | 2024-03-08T20:17:28Z |
| format | Article |
| id | doaj.art-b79529ff0fcc46d5b0d70c64f387ee62 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-08T20:17:28Z |
| publishDate | 2023-11-01 |
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| spelling | doaj.art-b79529ff0fcc46d5b0d70c64f387ee622023-12-22T14:49:05ZengMDPI AGViruses1999-49152023-11-011512232310.3390/v15122323Molecular Epidemiology and Evolution of Coxsackievirus A14Liheng Yu0Qin Guo1Haiyan Wei2Yingying Liu3Wenbin Tong4Shuangli Zhu5Tianjiao Ji6Qian Yang7Dongyan Wang8Jinbo Xiao9Huanhuan Lu10Ying Liu11Jichen Li12Wenhui Wang13Yun He14Yong Zhang15Dongmei Yan16National 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, ChinaNational 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, ChinaHenan Center for Disease Control and Prevention, Zhengzhou 450003, ChinaHebei Center for Disease Control and Prevention, Shijiazhuang 050024, ChinaSichuan Center for Disease Control and Prevention, Chengdu 610044, ChinaNational 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, ChinaNational 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, ChinaNational 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, ChinaNational 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, ChinaNational 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, ChinaNational 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, ChinaNational 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, ChinaNational 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, ChinaShandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271016, ChinaShandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271016, ChinaNational 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, ChinaNational 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, ChinaAs 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<sup>−3</sup> substitutions/site/year (95% HPD: 4.03–6.89 × 10<sup>−3</sup>) 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.https://www.mdpi.com/1999-4915/15/12/2323coxsackievirus A14phylodynamic analysisrecombination |
| spellingShingle | Liheng Yu Qin Guo Haiyan Wei Yingying Liu Wenbin Tong Shuangli Zhu Tianjiao Ji Qian Yang Dongyan Wang Jinbo Xiao Huanhuan Lu Ying Liu Jichen Li Wenhui Wang Yun He Yong Zhang Dongmei Yan Molecular Epidemiology and Evolution of Coxsackievirus A14 Viruses coxsackievirus A14 phylodynamic analysis recombination |
| title | Molecular Epidemiology and Evolution of Coxsackievirus A14 |
| title_full | Molecular Epidemiology and Evolution of Coxsackievirus A14 |
| title_fullStr | Molecular Epidemiology and Evolution of Coxsackievirus A14 |
| title_full_unstemmed | Molecular Epidemiology and Evolution of Coxsackievirus A14 |
| title_short | Molecular Epidemiology and Evolution of Coxsackievirus A14 |
| title_sort | molecular epidemiology and evolution of coxsackievirus a14 |
| topic | coxsackievirus A14 phylodynamic analysis recombination |
| url | https://www.mdpi.com/1999-4915/15/12/2323 |
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