Evolutionary histories of coxsackievirus B5 and swine vesicular disease virus reconstructed by phylodynamic and sequence variation analyses.

Coxsackievirus (CV)-B5 is a common human enterovirus reported worldwide; swine vesicular disease virus (SVDV) is a porcine variant of CV-B5. To clarify the transmission dynamics and molecular basis of host switching between CV-B5 and SVDV, we analysed and compared the VP1 and partial 3Dpol gene regions of these two viruses. Spatiotemporal dynamics of viral transmission were estimated using a Bayesian statistical inference framework. The detected selection events were used to analyse the key molecules associated with host switching. Analyses of VP1 sequences revealed six CV-B5 genotypes (A1-A4 and B1-B2) and three SVDV genotypes (I-III). Analyses of partial 3Dpol revealed five clusters (A-E). The genotypes evolved sequentially over different periods, albeit with some overlap. The major hub of CV-B5 transmission was in China whereas the major hubs of SVDV transmission were in Italy. Network analysis based on deduced amino acid sequences showed a diverse extension of the VP1 structural protein, whereas most sequences were clustered into two haplotypes in the partial 3Dpol region. Residue 178 of VP1 showed four epistatic interactions with residues known to play essential roles in viral host tropism, cell entry, and viral decoating.

Phylodynamic Characterization of an Ocular-Tropism Coxsackievirus A24 Variant.

Recent phylodynamic studies have focused on using tree topology patterns to elucidate interactions among the epidemiological, evolutionary, and demographic characteristics of infectious agents. However, because studies of viral phylodynamics tend to focus on epidemic outbreaks, tree topology signatures of tissue-tropism pathogens might not be clearly identified. Therefore, this study used a novel Bayesian evolutionary approach to analyze the A24 variant of coxsackievirus (CV-A24v), an ocular-tropism agent of acute hemorrhagic conjunctivitis. Analyses of the 915-nucleotide VP1 and 690-nt 3Dpol regions of 21 strains isolated in Taiwan and worldwide during 1985-2010 revealed a clear chronological trend in both the VP1 and 3Dpol phylogenetic trees: the emergence of a single dominant cluster in each outbreak. The VP1 sequences included three genotypes: GI (prototype), GIII (isolated 1985-1999), and GIV (isolated after 2000); no VP1 sequences from GII strains have been deposited in GenBank. Another five genotypes identified in the 3Dpol region had support values >0.9. Geographic and demographic transitions among CV-A24v clusters were clearly identified by Bayes algorithm. The transmission route was mapped from India to China and then to Taiwan, and each prevalent viral population declined before new clusters emerged. Notably, the VP1 and 3Dpol genes had high nucleotide sequence similarities (94.1% and 95.2%, respectively). The lack of co-circulating lineages and narrow tissue tropism affected the CV-A24v gene pool.

Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2.

BACKGROUND: 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. 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 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013. RESULTS: Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (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 3D(pol) genes. The similarities of VP1 and 3D(pol) 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. CONCLUSIONS: Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.

Comparison of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 test v1.0 with v2.0 in HIV-1 viral load quantification.

Roche modified the COBAS AmpliPrep/COBAS TaqMan human immunodeficiency virus type 1 (HIV-1) test version 1.0 (CAP/CTM v1.0), resulting in the COBAS AmpliPrep/COBAS TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0). The aim of this study was to evaluate the performance of the CAP/CTM v2.0 and to compare this performance with that of the CAP/CTM v1.0. The study was conducted in a small local study group in Kaohsiung Medical University Hospital, Kaohsiung, Taiwan. A total of 86 plasma samples from HIV-1-seropositive patients were tested using the two assays. The correlation and concordance of results between the two assays were calculated. The CAP/CTM v2.0 generated higher values than did the CAP/CTM v1.0, and five samples (5.8%) yielded a difference of > 1 log10 copies/mL. In addition, our data show that CAP/CTM v1.0 and CAP/CTM v2.0 yielded relatively consistent values for 23 samples with low viral loads (< 200 copies/mL). Furthermore, when viral loads were in a medium range (2-5 log10 copies/mL), the results of the two assays were more compatible. This study shows a good correlation between CAP/CTM v1.0 and v2.0 in HIV-1 viral load measurement. Further attention must be paid to those cases in which measured viral loads present larger differences between the two assays.

Molecular epidemiology of Coxsackievirus B3.

Molecular epidemiological characteristics are needed to understand the impact of Coxsackievirus B3 (CV-B3) infection, since no CV-B3 genotyping literature is available. Twenty-nine CV-B3 Taiwan strains obtained from 1992 to 2005 were analyzed. A phylogenetic tree was constructed based on the 290 nucleotide sequence of the VP1 gene of Taiwan isolates and in 91 other CV-B3 GenBank sequences. Five genotypes (GI-GV) were depicted. The GI, GII, and GIII were dominant in America and Europe, whereas GIV and GV were prevalent in Asia. In Taiwan, a transient outbreak of GIV occurred in 2000, while GV has been the main genotype circulating since 1992. Patient age ranged from 0.1 to 81 months (median, 4.3 months). The male:female ratio was 1.9:1. More than 60% (17/29) of cases involved children younger than 1 year. Half of them contracted respiratory tract infection (12/24). Nine of the 24 (37.5%) cases with available medical records had central nervous system (CNS) involvement. Eight of the nine patients were younger than 3 months. The CV-B3 has evolved and circulated for the past 60 years. Although the nucleotide sequence of the VP1 is highly variably, amino acids were relatively conserved within the same genotype of CV-B3. CNS infections were not associated with a specific strain or genotype. The CV-B3 poses a significant health threat to children younger than 1 year, especially those younger than 3 months old.

Coxsackievirus B4 in southern Taiwan: molecular epidemiology.

BACKGROUND: Enterovirus outbreaks caused by Coxsackievirus B4 (CB4) in Taiwan in 2004 and 2008. OBJECTIVE: To retrospectively analyze the molecular epidemiology and pathogenicity of CB4 in Taiwan. STUDY DESIGN: This study analyzed twenty-three CB4 strains isolated in Taiwan during 1993-2004. Sequence variations data were obtained using 420 bp of VP4/VP2 region and 331 bp of 3' VP1 region. Phylogenetic dendrograms were constructed with other CB4 sequences in Genebank. The clinical manifestations of CB4 infection were examined by retrospectively reviewing medical records of infected patients. RESULTS: Three CB4 genotypes were identified: genotypes II, IVb and VIII. Genotype VIII, a new and geographically distinct cluster, has been isolated in South Korea, China and Taiwan. This genotype was isolated in twelve of twenty-three CB4 patients treated in Taiwan during 1997-2004. Eight of twenty-three strains belonging to genotype II, now the major genotype worldwide, were first identified in Taiwan in 2000. Three isolates (identified 1993-1994) analyzed in this study belonged to genotype IVb. In this retrospective follow-up study of sixteen patients with CB4 infection, the median patient age at the time of infection diagnosis was 4-year-old (range, 18 days to 10-year-old), and male-female ratio was 1:1. None of the sixteen patients suffered IDDM or myocarditis after their B4 infection episodes; four had Attention Deficit Hyperactivity Disorder (ADHD) and/or tic disorders (TDs) at follow-up. CONCLUSIONS: Genotypes II and VIII of CB4 have co-circulated in Taiwan since 2000. Controlled studies are needed to evaluate a possible association between ADHD and TDs with CB4 infection.