Molecular surveillance of coxsackievirus A16 reveals the emergence of a new clade in mainland China

  • Long ChenEmail author
  • Xiang-Jie Yao
  • Shao-Jian Xu
  • Hong Yang
  • Chun-Li Wu
  • Jing Lu
  • Wen-Bo Xu
  • Hai-Long Zhang
  • Jun Meng
  • Yong Zhang
  • Ya-Qing HeEmail author
  • Ren-Li ZhangEmail author
Annotated Sequence Record


Coxsackievirus A16 (CV-A16) of the genotypes B1a and B1b have co-circulated in mainland China in the past decades. From 2013 to 2017, a total of 3,008 specimens from 3,008 patients with mild hand, foot, and mouth disease were collected in the present study. Viral RNA was tested for CV-A16 by a real-time RT-PCR method, and complete VP1 sequences and full-length genome sequences of CV-A16 strains from this study were determined by RT-PCR and sequencing. Sequences were analyzed using a series of bioinformatics programs. The detection rate for CV-A16 was 4.1%, 25.9%, 10.6%, 28.1% and 12.9% in 2013, 2014, 2015, 2016 and 2017, respectively. Overall, the detection rate for CV-A16 was 16.5% (497/3008) in this 5-year period in Shenzhen, China. One hundred forty-two (142/155, 91.6%) of the 155 genotype B1 strains in the study belonged to subgenotype B1b, and 13 (13/155, 8.4%) strains belonged to subgenotype B1a. Two strains (CVA16/Shenzhen174/CHN/2017 and CVA16/Shenzhen189/CHN/2017) could not be assigned to a known genotype. Phylogenetic analysis of these two strains and other Chinese CV-A16 strains indicated that these two CV-A16 strains clustered independently in a novel clade whose members differed by 8.4%-11.8%, 8.4%-12.1%, and 14.6%-14.8% in their nucleotide sequences from those of Chinese B1a, B1b, and genotype D strains, respectively. Phylogenetic analysis of global CV-A16 strains further indicated that the two novel CV-A16 strains from this study grouped in a previously uncharacterized clade, which was designated as the subgenogroup B3 in present study. Meanwhile, phylogenetic reconstruction revealed two other new genotypes, B1d and B4, which included a Malaysian strain and two American strains, respectively. The complete genome sequences of the two novel CV-A16 strains showed the highest nucleotide sequence identity of 92.3% to the Malaysian strain PM-15765-00 from 2000. Comparative analysis of amino acid sequences of the two novel CV-A16 strains and their relatives suggested that variations in the nonstructural proteins may play an important role in the evolution of modern CV-A16.



This work was supported by the Sanming Project of Medicine in Shenzhen (No. SZSM201611064), the Shenzhen Science and Technology Research Project (JCYJ20170306160217433), and special funds for the surveillance of HFMD from Shenzhen CDC. We are grateful to the pediatricians from the sentinel surveillance system for HFMD in Shenzhen, China.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Animal and human rights statement

This article does not contain any studies with human or animal subjects performed by any of the authors.

Supplementary material

705_2018_4112_MOESM1_ESM.docx (43 kb)
Supplementary material 1 (DOCX 43 kb)


  1. 1.
    Mao Q, Wang Y, Yao X, Bian L, Wu X, Xu M, Liang Z (2014) Coxsackievirus A16: epidemiology, diagnosis, and vaccine. Hum Vaccines Immunother 10:360–367CrossRefGoogle Scholar
  2. 2.
    Tapparel C, Siegrist F, Petty TJ, Kaiser L (2013) Picornavirus and enterovirus diversity with associated human diseases. Infect Genet Evol 14:282–293CrossRefGoogle Scholar
  3. 3.
    Huang Y, Zhou Y, Lu H, Yang H, Feng Q, Dai Y, Chen L, Yu S, Yao X, Zhang H, Jiang M, Wang Y, Han N, Hu G, He Y (2015) Characterization of severe hand, foot, and mouth disease in Shenzhen, China, 2009–2013. J Med Virol 87:1471–1479CrossRefGoogle Scholar
  4. 4.
    Chen L, Yang H, Feng QJ, Yao XJ, Zhang HL, Zhang RL, He YQ (2015) Complete genome sequence of a coxsackievirus a16 strain, isolated from a fatal case in Shenzhen, southern China, in 2014. Genome Announc 3:e00391–15CrossRefGoogle Scholar
  5. 5.
    Perera D, Yusof MA, Podin Y, Ooi MH, Thao NT, Wong KK, Zaki A, Chua KB, Malik YA, Tu PV, Tien NT, Puthavathana P, McMinn PC, Cardosa MJ (2007) Molecular phylogeny of modern coxsackievirus A16. Arch Virol 152:1201–1208CrossRefGoogle Scholar
  6. 6.
    Zhang Y, Wang D, Yan D, Zhu S, Liu J, Wang H, Zhao S, Yu D, Nan L, An J, Chen L, An H, Xu A, Xu W (2010) Molecular evidence of persistent epidemic and evolution of subgenotype B1coxsackievirus A16-associated hand, foot, and mouth disease in China. J Clin Microbiol 48:619–622CrossRefGoogle Scholar
  7. 7.
    Carrion G, Huaman JL, Silva M, Ampuero JS, Paz I, Ocaña VR, Laguna-Torres VA, Hontz RD (2016) Molecular epidemiology of coxsackievirus A16 strains from four sentinel surveillance sites in Peru. Int J Infect Dis 52:83–85CrossRefGoogle Scholar
  8. 8.
    Hassel C, Mirand A, Farkas A, Diedrich S, Huemer HP, Peigue-Lafeuille H, Archimbaud C, Henquell C, Bailly JL, HFMD French Study Network (2017) Phylogeography of coxsackievirus A16 reveals global transmission pathways and recent emergence and spread of a recombinant genogroup. J Virol 91:e00630–17CrossRefGoogle Scholar
  9. 9.
    Wang J, Teng Z, Chu W, Fang F, Cui X, Guo X, Zhang X, Thorley BR, Zhu Y (2018) The emergence and spread of one Coxsackievirus A16 Genogroup D novel recombinant strain that caused a clustering HFMD outbreak in Shanghai, China, 2016. Emerg Microbes Infect 7:131CrossRefGoogle Scholar
  10. 10.
    He YQ, Chen L, Xu WB, Yang H, Wang HZ, Zong WP, Xian HX, Chen HL, Yao XJ, Hu ZL, Luo M, Zhang HL, Ma HW, Cheng JQ, Feng QJ, Zhao DJ (2013) Emergence, circulation, and spatiotemporal phylogenetic analysis of coxsackievirus A6-and coxsackievirus A10-associated hand, foot, and mouth disease infections from 2008 to 2012 in Shenzhen, China. J Clin Microbiol 51:3560–3566CrossRefGoogle Scholar
  11. 11.
    Zong W, He Y, Yu S, Yang H, Xian H, Liao Y, Hu G (2011) Molecular phylogeny of Coxsackievirus A16 in Shenzhen, China, from 2005 to 2009. J Clin Microbiol 49:1659–1661CrossRefGoogle Scholar
  12. 12.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  13. 13.
    Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003CrossRefGoogle Scholar
  14. 14.
    Chen X, Tan X, Li J, Jin Y, Gong L, Hong M, Shi Y, Zhu S, Zhang B, Zhang S, Zhang Y, Mao N, Xu W (2013) Molecular epidemiology of coxsackievirus A16: intratype and prevalent intertype recombination identified. PLoS One 8:e82861CrossRefGoogle Scholar
  15. 15.
    Guo WP, Lin XD, Chen YP, Liu Q, Wang W, Wang CQ, Li MH, Sun XY, Shi M, Holmes EC, Zhang YZ (2015) Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China. J Clin Virol 70:29–38CrossRefGoogle Scholar
  16. 16.
    Hu YF, Yang F, Du J, Dong J, Zhang T, Wu ZQ, Xue Y, Jin Q (2011) Complete genome analysis of coxsackievirus A2, A4, A5, and A10 strains isolated from hand, foot, and mouth disease patients in China revealing frequent recombination of human enterovirus A. J Clin Microbiol 49:2426–2434CrossRefGoogle Scholar
  17. 17.
    Liu W, Wu S, Xiong Y, Li T, Wen Z, Yan M, Qin K, Liu Y, Wu J (2014) Co-circulation and genomic recombination of coxsackievirus A16 and enterovirus 71 during a large outbreak of hand, foot, and mouth disease in Central China. PLoS One 9:e96051CrossRefGoogle Scholar
  18. 18.
    Lukashev AN, Shumilina EY, Belalov IS, Ivanova OE, Eremeeva TP, Reznik VI, Trotsenko OE, Drexler JF, Drosten C (2014) Recombination strategies and evolutionary dynamics of the human enterovirus A global gene pool. J Gen Virol 95:868–873CrossRefGoogle Scholar
  19. 19.
    Chen L, Yang H, Wang C, Yao XJ, Zhang HL, Zhang RL, He YQ (2016) Genomic characteristics of coxsackievirus A8 strains associated with hand, foot, and mouth disease and herpangina. Arch Virol 161:213–217CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Major Infectious Disease Control Key Laboratory and Shenzhen Public Service Platform of Pathogenic Microorganisms RepositoryInstitute of Pathogen Biology, Shenzhen Center for Disease Control and PreventionShenzhenChina
  2. 2.District Key Laboratory for Infectious Disease Prevention and ControlLonghua Center for Disease Control and PreventionShenzhenChina
  3. 3.Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and PreventionGuangzhouChina
  4. 4.National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijingChina

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