Transmission Networks and Population Turnover of Echovirus 30

Leitch, E. Carol McWilliam; Bendig, Justin; Cabrerizo, María; Cardosa, Jane; Hyypiä, Timo; Ivanova, Olga E.; Kelly, Alison; Kroes, Aloys C.M.; Lukashev, Alexander N.; Macadam, Andrew; McMinn, Peter C.; Roivainen, Merja; Trallero, Gloria; Evans, David J.; Simmonds, Peter

doi:10.1128/jvi.02109-08

Cited by 97 publications

(98 citation statements)

References 61 publications

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“…In each virus, recombination breakpoints concentrate in the 2A region, although further sites occur in P2 and P3 genes and in the 5=-UTR (1,3,16,30,33,49,67). In contrast, phylogenies of the more divergent capsid-encoding genes VP1, VP2, and VP3 are congruent with each other (and correspond to their serotypic classification) (31,42,49), leading to the idea that sequence diversification in structural gene regions is largely uncoupled from that of nonstructural genes (31,32,37,55). The contribution of recombination to the evolution and molecular epidemiology of EV71 and its relationship to diversification of capsid-encoding genes is the focus of the current study.…”

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confidence: 91%

“…3Dpol classification provides the means to identify and quantify recombination events within data sets through identification of incongruences between phylogenetically supported clades in different genome regions, as used in previous analyses of EV-B serotypes (37,38). 3Dpol gene sequences of the 15 RFs of EV71 and CVA16 indeed imperfectly mapped onto the phylogeny of the VP1 region and revealed several phylogeny violations indicative of recombination ( Fig.…”

Section: Phylogeny Of Ev71 Vp1 and 3dpol Genome Regionsmentioning

confidence: 99%

“…The identification of recombination events was assisted through the assignment of 3Dpol sequences of EV71 isolates to individual recombinant forms, as developed for the analysis of EV species B viruses (37,38). The study provides convincing evidence for recombination events in the founding of most subgenogroup lineages over an evolutionary time scale comparable to that observed within EV-B serotypes.…”

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confidence: 99%

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The Association of Recombination Events in the Founding and Emergence of Subgenogroup Evolutionary Lineages of Human Enterovirus 71

Leitch

Cabrerizo

Cardosa

et al. 2012

J Virol

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109

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Enterovirus 71 (EV71) is responsible for frequent large-scale outbreaks of hand, foot, and mouth disease worldwide and represent a major etiological agent of severe, sometimes fatal neurological disease. EV71 variants have been classified into three genogroups (GgA, GgB, and GgC), and the latter two are further subdivided into subgenogroups B1 to B5 and C1 to C5. To investigate the dual roles of recombination and evolution in the epidemiology and transmission of EV71 worldwide, we performed a largescale genetic analysis of isolates (n ‫؍‬ 308) collected from 19 countries worldwide over a 40-year period. A series of recombination events occurred over this period, which have been identified through incongruities in sequence grouping between the VP1 and 3Dpol regions. Eleven 3Dpol clades were identified, each specific to EV71 and associated with specific subgenogroups but interspersed phylogenetically with clades of coxsackievirus A16 and other EV species A serotypes. The likelihood of recombination increased with VP1 sequence divergence; mean half-lives for EV71 recombinant forms (RFs) of 6 and 9 years for GgB and GgC overlapped with those observed for the EV-B serotypes, echovirus 9 (E9), E30, and E11, respectively (1.3 to 9.8 years). Furthermore, within genogroups, sporadic recombination events occurred, such as the linkage of two B4 variants to RF-W instead of RF-A and of two C4 variants to RF-H. Intriguingly, recombination events occurred as a founding event of most subgenogroups immediately preceding their lineage expansion and global emergence. The possibility that recombination contributed to their subsequent spread through improved fitness requires further biological and immunological characterization.

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confidence: 91%

Section: Phylogeny Of Ev71 Vp1 and 3dpol Genome Regionsmentioning

confidence: 99%

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confidence: 99%

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The Association of Recombination Events in the Founding and Emergence of Subgenogroup Evolutionary Lineages of Human Enterovirus 71

Leitch

Cabrerizo

Cardosa

et al. 2012

J Virol

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109

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“…2. Published VP1 substitution rates for coxsackievirus B5 (CVB5), echovirus 9 (E9), echovirus 11 (E11), echovirus 30 (E30), HAV, and HPeV were obtained via BEAST analyses similar to those used in this study (15,23,34,(46)(47)(48); those for EV71, FMDV-A, and FMDV-O were obtained via analyses performed in TipDate (58), a precursor to BEAST (29); and the remaining rates were estimated via linear regression (3,4,44,50,66,70,71). These mean rates of enterovirus VP1 evolution range from 3.40 ϫ 10 Ϫ3 to 1.19 ϫ 10 Ϫ2 nucleotide substitutions per site per year (ns/s/y), and mean VP1 rates for nonenteroviruses range from 9.76 ϫ 10 Ϫ4 to 2.79 ϫ 10 Ϫ3 ns/s/y.…”

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confidence: 99%

Genus-Specific Substitution Rate Variability among Picornaviruses

Hicks

Duffy

2011

J Virol

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Picornaviruses have some of the highest nucleotide substitution rates among viruses, but there have been no comparisons of evolutionary rates within this broad family. We combined our own Bayesian coalescent analyses of VP1 regions from four picornaviruses with 22 published VP1 rates to produce the first within-family meta-analysis of viral evolutionary rates. Similarly, we compared our rate estimates for the RNA polymerase 3D pol gene from five viruses to four published 3D pol rates. Both a structural and a nonstructural gene show that enteroviruses are evolving, on average, a half order of magnitude faster than members of other genera within the Picornaviridae family.Members of the Picornaviridae family are the most common cause of human viral infections in developed countries (28,39). Human picornaviruses produce symptoms ranging from mild respiratory illness to hemorrhagic conjunctivitis, myocarditis, acute flaccid paralysis, and neonatal organ failure (19,27,28,33,40,41). Veterinary picornaviruses, such as foot-and-mouth disease virus (FMDV), encephalomyocarditis virus (EMCV), and porcine teschovirus (PTV), can have devastating effects on livestock (5,8,21).Although picornaviruses such as poliovirus (PV) are known to evolve more rapidly than other viruses with single-stranded RNA (ssRNA) genomes (9, 29), little research has been conducted to investigate how they evolve more rapidly than other viruses with similarly error-prone RNA-dependent RNA polymerases (29, 57) or if certain picornaviruses evolve more rapidly than others. Understanding the evolutionary potentials and constraints of these important pathogens is imperative for the development of durable vaccines and effective treatment plans for individual pathogens (42). As even small, 3-fold differences in RNA virus mutation rates can have dramatic consequences, such as driving a population into lethal mutagenesis (7), similar differences in long-term evolutionary rates could indicate significantly dissimilar evolutionary potentials.While viral evolutionary rates were previously calculated only by linear regression, modern simulation software such as BEAST (11) allows for the estimation of more complex models of viral evolution. These Bayesian coalescent programs can produce both estimated mean rates of evolution and 95% credibility intervals (CIs) that provide a measure of the variability around mean rates. Instead of comparing single-point estimates, now nonoverlapping CIs provide the strongest evidence that genes or organisms are evolving at different rates (11). Many substitution rate estimates have been published for picornaviruses, especially for the antigenically significant VP1 gene, which encodes the most external of the picornavirus structural proteins and interacts with cellular receptors (37,49). Based on sequence availability in GenBank, four novel analyses were conducted, measuring the rate of evolution of the VP1 gene for two enteroviruses and producing the first rate estimates for the type species of the genera Cardiovirus and Teschoviru...

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“…Studies of E30 meningitis outbreaks have shown that point mutations give rise to substantial genetic diversity in VP1. Substitutions in VP1 region occurred predominantly at synonymous sites, with VP1 showing a rapid substitution rate of 8.3/8.4 × 10 -3 substitutions per site per year, and recombination frequency was tightly correlated with VP1 divergence [116,117]. The predicted rates of evolution in the VP1 region for E9 and E11 were 5.8 × 10 -3 and 4.8 × 10 -3 substitutions per site per year, respectively [118].…”

Section: Mutation Of Enterovirusesmentioning

confidence: 99%