Molecular characterization of echovirus 9 strains isolated from hand-foot-and-mouth disease in Kunming, Yunnan Province, China

Ming Zhang,Zhaoqing Yang,Wei Guo,Guohong Bao,Shaohui Ma,Changzeng Feng,Danhan Xu,Hao Sun

doi:10.1038/s41598-022-06309-1

Abstract

Echovirus 9 (E9) belongs to the species Enterovirus B. So far, 12 whole genome sequences of E9 are available in GenBank. In this study, we determined the whole genomic sequences of five E9 strains isolated from the stools of patients with hand-foot-and-mouth disease in Kunming, Yunnan Province, China, in 2019. Their nucleotide and amino acid sequences shared 80.8–80.9% and 96.4–96.8% identity with the prototype Hill strain, respectively, and shared 99.3–99.9% and 99.1–99.8% mutual identity, respectively. Recombination analyses revealed that intertype recombination had occurred in the 2C and 3D regions of the five Yunnan E9 strains with coxsackieviruses B5 and B4, respectively. This study augmented the whole genome sequences of E9 in the GenBank database and extended the molecular characterization of this virus in China.

Highlights

EVs are commonly associated with asymptomatic or mild infections, such as fever, irritation, and hand-footand-mouth disease (HFMD), some patients may develop severe diseases, including aseptic meningitis and acute flaccid paralysis
The five isolates shared 78.3%–78.5% nucleotide identity and 85.7%–86.4% amino acid identity with the whole VP1 sequence of the Echovirus 9 (E9) prototype Hill strain, which was isolated from a healthy child in Cincinnati in 195321, and 80.8%–94.8% nucleotide and 88.1%–99.6% amino acid identity with other E9 strains
The results indicated that several potential recombination events have occurred between the E9 strains, including the Yunnan isolates, and other EV-B strains in the non-capsid coding regions, and that these E9 isolates may be the different recombinant strains

Summary

Introduction

EVs are commonly associated with asymptomatic or mild infections, such as fever, irritation, and hand-footand-mouth disease (HFMD), some patients may develop severe diseases, including aseptic meningitis and acute flaccid paralysis. EVs are the main causative pathogen of aseptic m eningitis[3,4,5]. Previous studies have reported that E9 was main causative pathogen of aseptic meningitis and HFMD in Yunnan, China, in 2009–201013,14. Twelve whole genome sequences of E9 are currently available in GenBank, which were isolated from children with aseptic meningitis or HFMD, healthy children, and children with other diseases. The whole genomic sequences of five E9 strains recovered from children aged 0.9–4.5 years with HFMD in Kunming, Yunnan Province, China, in 2019 were determined to clarify the molecular characteristics of E9 in China and to increase the number of genome sequences of E9 in the GenBank database

Methods

Results

Conclusion