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.

Transmission and Demographic Dynamics of Coxsackievirus B1.

The infectious activity of coxsackievirus B1 (CV-B1) in Taiwan was high from 2008 to 2010, following an alarming increase in severe neonate disease in the United States (US). To examine the relationship between CV-B1 strains isolated in Taiwan and those from other parts of the world, we performed a phylodynamic study using VP1 and partial 3Dpol (414 nt) sequences from 22 strains of CV-B1 isolated in Taiwan (1989-2010) and compared them to sequences from strains isolated worldwide. Phylogenetic trees were constructed by neighbor-joining, maximum likelihood, and Bayesian Monte Carlo Markov Chain methods. Four genotypes (GI-IV) in the VP1 region of CV-B1 and three genotypes (GA-C) in the 3Dpol region of enterovirus B were identified and had high support values. The phylogenetic analysis indicates that the GI and GIII strains in VP1 were geographically distributed in Taiwan (1993-1994) and in India (2007-2009). On the other hand, the GII and GIV strains appear to have a wider spatiotemporal distribution and ladder-like topology A stair-like phylogeny was observed in the VP1 region indicating that the phylogeny of the virus may be affected by different selection pressures in the specified regions. Further, most of the GI and GII strains in the VP1 tree were clustered together in GA in the 3D tree, while the GIV strains diverged into GB and GC. Taken together, these data provide important insights into the population dynamics of CV-B1 and indicate that incongruencies in specific gene regions may contribute to spatiotemporal patterns of epidemicity for this virus.

The development of a beacon-based real-time PCR for cytomegalovirus and its application in immunocompromised patients.

BACKGROUND: Because of the high cost of commercially available quantitative PCR kits, we developed a beacon- based real-time PCR (B-rt-PCR) for Cytomegalovirus (CMV) viral load determination. METHODS: A total of 197 samples from 60 immunocompromised patients, who were bone marrow transplantation recipients or had hematological malignancies, were tested using B-rt-PCR, COBAS Amplicor CMV Monitor test (Amplicor CMV test), and conventional CMV PCR. The correlation results among these 3 assays were calculated. RESULTS: In these 197 samples, the CMV viral load determined by B-rt-PCR for positive specimens ranged from 19.8 to 4148.7 copies/10(5) peripheral blood mononuclear cells (PBMCs). When any positive result of B-rt-PCR, the Amplicor CMV test, or conventional PCR was considered as "CMV positive" for the 56 specimens tested by all three methods, we found that the positive and negative predictive values, respectively, were 100% and 98.6% for B-rt-PCR, 100% and 46.2% for the Amplicor CMV test, and 100% and 89.4% for conventional PCR. These three methods had good specificity (all 100%). However, the sensitivity rate of B-rt-PCR (96.3%) was higher compared to the Amplicor CMV test (46.2%) and conventional PCR (89.4%). CONCLUSIONS: The B-rt-PCR is evaluated to be a sensitive method for CMV detection in immunocompromised patients.

Spatiotemporal phylogenetic analysis and molecular characterization of coxsackievirus A4.

Coxsackievirus A4 outbreaks occurred in Taiwan in 2004 and 2006. The spatiotemporal transmission of this error-prone RNA virus involves a continuous interaction between rapid sequence variation and natural selection. To elucidate the molecular characteristics of CV-A4 and the spatiotemporal dynamic changes in CV-A4 transmission, worldwide sequences of the 3' VP1 region (420 nt) obtained from GenBank were analyzed together with sequences isolated in Taiwan from 2002 to 2009. Sequences were characterized in terms of recombination, variability, and selection. Phylogenetic trees were constructed using neighbor-joining, maximum likelihood and Monte Carlo Markov Chain methods. Spatiotemporal dynamics of CV-A4 transmission were further estimated by a Bayesian statistical inference framework. No recombination was detected in the 420 nt region. The estimated evolution rate of CV-A4 was 8.65 × 10(-3) substitutions/site/year, and a purifying selection (d(N)/d(S)=0.032) was noted over the 3' VP1 region. All trees had similar topology: two genotypes (GI and GII), each including two subgenotypes (A and B), with the prototype and a Kenyan strain in separate branches. The results revealed that the virus first appeared in USA in 1950. Since 1998, it has evolved into the Kenya, GI-A (Asia) and GII-A (Asia and Europe) strains. Since 2004, GI-B and GII-B have evolved continuously and have remained prevalent. The co-existence of several positive selection lineages of GI-B in 2006 indicates that the subgenotype might have survived lineage extinction. This study revealed rapid lineage turnover of CV-A4 and the replacement of previously circulating strains by a new dominant variant. Therefore, continuous surveillance for further CV-A4 transmission is essential.

Molecular epidemiology of Echovirus 30 in Taiwan, 1988-2008.

To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).

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.