Echovirus plays a major role in natural recombination in the coxsackievirus B group

Isolation and characterization of a novel clade of coxsackievirus B2 associated with hand, foot, and mouth disease in Southwest China

Coxsackievirus B2 (CVB2) is an enterovirus B (EV-B) species and can cause aseptic meningitis, myocarditis and hand, foot, and mouth disease (HFMD). We characterized a novel CVB2 (YN31V3) associated with HFMD in Yunnan, Southwest China in 2019. Although YN31V3 and other Mainland China epidemic strains mainly belonged to genotype C, YN31V3 formed an independent branch. The genome sequence of the strain YN31V3 from this study showed 12.91% nucleotide difference to its closest strain RW41-2/YN/CHN/2012. Recombination analyses showed that the newly isolated YN31V3 was probably a recombinant, which was closely related to CVB2 strains in the genomic P1 region and other EV-B strains in the P2 and P3 regions, respectively. YN31V3 strain had a temperature-sensitive phenotype. Challenge of suckling BALB/c mice with YN31V3 could cause symptoms of disease and severe pathological lesions. This article is protected by copyright. All rights reserved.

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

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.

Two Natural Recombination gave rise to the Coxsackievirus B3 GV that triggered outbreaks in China in 2006 - 2012

Coxsackievirus B3 serotype GV caused the epidemic of Coxsackievirus B3 infection in China from 2006 to 2012. To study the evolution and recombination of Coxsackievirus B3 serotype GV, we performed recombination and phylogenetic analysis of 499 complete genomes of Enterovirus B available in GenBank, dated April 2019. Results indicated that most of the strains of Coxsackievirus B3 GV in P1 region were derived from a Coxsackievirus B3 GVI parent, and in P2-3 region from EchoV E25 strain, with nucleotide identities of 97.2% and 94.7%, respectively. Other strains of Coxsackievirus B3 GV-C1 in P1-P2 regions were derived from Coxsackievirus B3 GV-C3, whereas those in P3 regions were from CVB5. These naturally occurring recombination events were confirmed by phylogenetic analysis. This study indicates that two naturally occurring recombination gave rise to the coxsackievirus B3 GV that triggered outbreaks in China in 2006 - 2012.

Genetic characterization of a novel recombinant echovirus 30 strain causing a regional epidemic of aseptic meningitis in Hokkaido, Japan, 2017

A regional epidemic of aseptic meningitis caused by echovirus 30 (E30) occurred in Hokkaido, Japan, during the period of August-December 2017. To investigate their phylogenetic relationship to other human enteroviruses, we determined the complete genomic nucleotide sequences of isolates from this outbreak. Phylogenetic analysis of the viral capsid protein 1 gene showed that the strains were most closely related to E30 strains detected in Germany, France, and Russia in 2013. In contrast, the region encoding the viral protease and the RNA-dependent RNA polymerase had a close phylogenetic relationship to non-E30 enteroviruses detected in the United Kingdom and Switzerland in 2015-2017, suggesting that a recombination event had occurred.

Discovery of a virus of the species Enterovirus F in goats

Here, we report two novel enteroviruses, designated as SD-S67 and SD-S68, isolated from a goat farm. Their complete genome sequences were determined and found to be 7455 and 7465 nucleotides in length, respectively. Molecular characterization revealed that SD-S67 is closely related to bovine enterovirus strain 261 and that SD-S68 to caprine enterovirus strain CEV-JL14. Phylogenetic analysis showed that SD-S67 clustered with members of the species Enterovirus F, and that SD-S68 clustered with enteroviruses of goats and sheep. Recombination analysis showed that SD-S67 is likely to have undergone several recombination events in the process of its evolution. To the best of our knowledge, this is the first report of an enterovirus F isolate from a goat and of a coinfection with enteroviruses of different species in the same goat herd.