Abstract

Recombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.

Highlights

  • As a neurotropic virus, Enterovirus A71 (EV-A71) remains an important pathogen of severe and fatal hand, foot and mouth disease (HFMD)[1,2]

  • Our previous study found that a new subgenotype C6 of EV-A71 emerged in mainland China, which might derive from subgenotypes C4 and C2 EV-A71 ­strains[25]

  • We provided strong evidence to demonstrate that DL71 exactly formed a new branch distinct from the known subgenotypes by calculating the genetic distance and constructing the phylogenetic trees based on the genome and individual gene sequences. 9 recombination events, 2 parental strains and the breakpoints locations of DL71 were detected by recombination detection program software version 4.101 (RDP4) and Similarity Plot (SimPlot)

Read more

Summary

Introduction

Enterovirus A71 (EV-A71) remains an important pathogen of severe and fatal hand, foot and mouth disease (HFMD)[1,2]. 13.7 million HFMD cases (including 3322 deaths) were reported in mainland China during 2008–20154. Genotype A includes the sole prototype strain (BrCr) isolated in 1­ 9697 and several strains reemerged in mainland China during 2008–20108. Subgenotype C4 has been the unique predominant genetic lineage in mainland China since ­199825. Co-circulation of EV-A71 belonging to various genotypes/subgenotypes may increase the possibility of recombination. Clarifying the genetic variation and evolutionary relationship of new variants is important for disease prevention and vaccines development

Methods
Results
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call