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

Huang, He; Chen, Yao-Shen; Chen, Jeff Yi‐Fu; Lu, Po‐Liang; Lin, Yen-Ting; Chen, Bao-Chen; Chou, Li-Chiu; Wang, Chufeng; Su, Hui-Ju; Huang, Yi-Chien; Shi, Yipeng; Chen, Hsiu-Lin; Sanno-Duanda, Bintou; Huang, Tsi-Shu; Lin, Kuei-Hsiang; Tyan, Yu‐Chang; Chu, Pei‐Yu

doi:10.1186/s12859-015-0738-2

Cited by 8 publications

(12 citation statements)

References 39 publications

(43 reference statements)

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“…Sampled viral strains were amplified in confluent rhabdomyosarcoma cells. The procedures for RNA purification, RT-PCR, and sequencing were performed as described previously 41 , 42 . Briefly, viral RNA was extracted from 200 μl of viral culture supernatant using the QIAmp viral RNA purification kit (Qiagen, Chatsworth, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

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

Huang

Chu²,

Pan

et al. 2018

Sci Rep

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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.

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Section: Methodsmentioning

confidence: 99%

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

Huang

Chu²,

Pan

et al. 2018

Sci Rep

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“…The RNA extraction, RT-PCR and sequencing procedures were performed as described previously [ 9 ] except for the use of PCR primers ( Table 1 ). Primer set designed for the 3D pol region of CV-B2, a serotype belongs to species EV-B, in our previous study was used for amplification in this study [ 10 ]. Briefly, viral RNA was extracted using a QIAmp viral RNA purification kit (Qiagen, Chatsworth, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

Phylodynamic Characterization of an Ocular-Tropism Coxsackievirus A24 Variant

Yen

Chu²,

et al. 2016

PLoS ONE

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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.

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“…Bayesian phylogenetic methods also have a capacity for estimating a historical population size using the Bayesian skyline plot . There was a fair correlation between inferred population size fluctuations and the registered outbreaks, and much smaller suggestive fluctuations among the “endemic” types CV‐B1 and CV‐B2 (see below), which do not feature pronounced expansion‐extinction cycles, than in EV‐A71, which has caused epidemics worldwide . So far, the Bayesian skyline plot seems a sensible additional tool for enterovirus phylogenetic studies, but the level of bias that can be introduced by a much higher sampling of viral sequences during outbreaks remains to be evaluated.…”

Section: Bayesian Phylogenetic Analysis: Novel Possibilities and Limimentioning

confidence: 99%

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

Lukashev

Vakulenko

Turbabina

et al. 2018

Reviews in Medical Virology

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Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.

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

Cited by 8 publications

References 39 publications

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

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

Phylodynamic Characterization of an Ocular-Tropism Coxsackievirus A24 Variant

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

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