Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018
Open Access
- 26 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Archiv für die gesamte Virusforschung
- Vol. 166 (5), 1305-1312
- https://doi.org/10.1007/s00705-020-04934-7
Abstract
Echovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.Funding Information
- Key Technologies Research and Development Program (2018ZX10201002-003-003)
This publication has 42 references indexed in Scilit:
- Bayesian Phylogenetics with BEAUti and the BEAST 1.7Molecular Biology and Evolution, 2012
- Epidemics of viral meningitis caused by echovirus 6 and 30 in Korea in 2008Virology Journal, 2012
- The Persistent Circulation of Enterovirus 71 in People's Republic of China: Causing Emerging Nationwide Epidemics Since 2008PLOS ONE, 2011
- Cocirculation of Two Transmission Lineages of Echovirus 6 in Jinan, China, as Revealed by Environmental Surveillance and Sequence AnalysisApplied and Environmental Microbiology, 2011
- Molecular epidemiology of Echovirus 6 in GreeceEuropean Journal of Clinical Microbiology & Infectious Diseases, 2009
- Echovírus 6 associado à doença exantemáticaRevista da Sociedade Brasileira de Medicina Tropical, 2008
- Prospective Identification of Enteroviruses Involved in Meningitis in 2006 through Direct Genotyping in Cerebrospinal FluidJournal of Clinical Microbiology, 2008
- BEAST: Bayesian evolutionary analysis by sampling treesBMC Evolutionary Biology, 2007
- Bayesian Coalescent Inference of Past Population Dynamics from Molecular SequencesMolecular Biology and Evolution, 2005
- Rapid molecular evolution of wild type 3 poliovirus during infection in individual hostsJournal of General Virology, 1990