Evolution of Picornaviridae: An examination of phylogenetic relationships and cophylogeny

Lewis-Rogers, Nicole; Crandall, Keith A.

doi:10.1016/j.ympev.2009.10.015

Cited by 24 publications

(27 citation statements)

References 59 publications

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“…It is generally acknowledged that the current sampling of the picornavirus diversity is limited and biased (29,41). This variation is illustrated spectacularly for viruses of the M-2010 data set: 82% of the least populated species account for only 18% of the viral genomes (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Their calculation is technically straightforward and fast. However, the applicability of this measure to data sets with considerable genetic divergence may be compromised by saturation effects that are linked to multiple substitutions at a site (41). Since RNA viruses are known for the extremely high mutation rates of their polymerases (19,20,67), pairwise identity percentages may indeed misrepresent the actual distances between the viruses.…”

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confidence: 99%

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Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

Lauber

Gorbalenya

2012

J Virol

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The recent advent of genome sequences as the only source available to classify many newly discovered viruses challenges the development of virus taxonomy by expert virologists who traditionally rely on extensive virus characterization. In this proof-ofprinciple study, we address this issue by presenting a computational approach (DEmARC) to classify viruses of a family into groups at hierarchical levels using a sole criterion-intervirus genetic divergence. To quantify genetic divergence, we used pairwise evolutionary distances (PEDs) estimated by maximum likelihood inference on a multiple alignment of family-wide conserved proteins. PEDs were calculated for all virus pairs, and the resulting distribution was modeled via a mixture of probability density functions. The model enables the quantitative inference of regions of distance discontinuity in the family-wide PED distribution, which define the levels of hierarchy. For each level, a limit on genetic divergence, below which two viruses join the same group, was objectively selected among a set of candidates by minimizing violations of intragroup PEDs to the limit. In a case study, we applied the procedure to hundreds of genome sequences of picornaviruses and extensively evaluated it by modulating four key parameters. It was found that the genetics-based classification largely tolerates variations in virus sampling and multiple alignment construction but is affected by the choice of protein and the measure of genetic divergence. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3905-3915, 2012), we analyze the substantial insight gained with the genetics-based classification approach by comparing it with the expert-based picornavirus taxonomy.

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Section: Resultsmentioning

confidence: 99%

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Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

Lauber

Gorbalenya

2012

J Virol

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“…The family Picornaviridae is genetically highly diverse, currently comprising 12 classified genera and several more currently proposed genera, many of which include several species, subspecies, and serotypes/genotypes (http://www.picornaviridae.com/) (18). Aichivirus (AiV), discovered in stool samples from children with diarrhea in the Aichi Prefecture of Japan, is a human pathogen that causes acute gastroenteritis and is classified as a species of the genus Kobuvirus of the family Picornaviridae (31).…”

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confidence: 99%

“…However, serological studies indicate that up to 90% of the human population has been exposed to AiV by the age of 40 years (25). Information on the origin and ongoing circulation of AiV in humans and the existence of potential animal reservoirs for human infection remains elusive (18,25,30).…”

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Characterization of a Canine Homolog of Human Aichivirus

Kapoor

Simmonds

Dubovi

et al. 2011

J Virol

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“…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).…”

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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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Evolution of Picornaviridae: An examination of phylogenetic relationships and cophylogeny

Cited by 24 publications

References 59 publications

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

Partitioning the Genetic Diversity of a Virus Family: Approach and Evaluation through a Case Study of Picornaviruses

Characterization of a Canine Homolog of Human Aichivirus

Genus-Specific Substitution Rate Variability among Picornaviruses

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