Abstract
BackgroundStudies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3Dpol sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988–2013.ResultsFour and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3Dpol (6641–7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3Dpol genes. The similarities of VP1 and 3Dpol gene were 80.0 %–96.8 % and 74.7 %–91.9 %, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region.ConclusionsPhylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0738-2) contains supplementary material, which is available to authorized users.
Highlights
Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity
The analysis of the historical transmission routes for VP1 by using the Spread program showed that only the TaiwanSouth Korea route had a Bayes factor (BF) of 6.67
The demographic history determined by Bayesian skyline plot (BSP) showed that the coxsackievirus B2 (CV-B2) viral population had maintained a stable level with only a slight decrease since 1947, where the median Effective population size over time (Neτ) was 3.57–3.42 (Fig. 3a)
Summary
Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. A clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). Long-term surveillance of circulating EV serotypes has identified three main outbreak patterns: epidemic, endemic and sporadic [1]. Huang et al BMC Bioinformatics (2015) 16:302 infections are still reported almost annually to the Taiwan Centers for Disease Control (Additional file 1). CV-B2 has an endemic circulation pattern worldwide where it comprises 1.5 %–6.0 % of the annual reported EV rates (Additional file 2) [1, 3,4,5,6,7]. Identifying the phylodynamics of CV-B2 is essential for bridging relationships between successive prevalent serotypes and identifying EV circulation trends
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