Detecting natural selection in RNA virus populations using sequence summary statistics

Bhatt, Samir; Katzourakis, Aris; Pybus, Oliver G.

doi:10.1016/j.meegid.2009.06.001

Cited by 32 publications

(49 citation statements)

References 40 publications

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“…The signatures of directional selection were sought using McDonald–Kreitman test (MK-test) [36] implemented in DnaSP v.5.10 [37] and modified MK-tests [38], [39] implemented in The standard and generalized MKT website (http://mkt.uab.es/mkt/) [38] and Adapt-A-Rate v.1.0 software [40]. The MK-test compares the ratio of fixed non-synonymous to synonymous differences between two predefined groups and the ratio of polymorphic non-synonymous to synonymous differences and assumes that under neutral evolution these ratios should be equal.…”

Section: Methodsmentioning

confidence: 99%

The Evolution of Vp1 Gene in Enterovirus C Species Sub-Group That Contains Types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

et al. 2014

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Genus Enterovirus (Family Picornaviridae,) consists of twelve species divided into genetically diverse types by their capsid protein VP1 coding sequences. Each enterovirus type can further be divided into intra-typic sub-clusters (genotypes). The aim of this study was to elucidate what leads to the emergence of novel enterovirus clades (types and genotypes). An evolutionary analysis was conducted for a sub-group of Enterovirus C species that contains types Coxsackievirus A21 (CVA-21), CVA-24, Enterovirus C95 (EV-C95), EV-C96 and EV-C99. VP1 gene datasets were collected and analysed to infer the phylogeny, rate of evolution, nucleotide and amino acid substitution patterns and signs of selection. In VP1 coding gene, high intra-typic sequence diversities and robust grouping into distinct genotypes within each type were detected. Within each type the majority of nucleotide substitutions were synonymous and the non-synonymous substitutions tended to cluster in distinct highly polymorphic sites. Signs of positive selection were detected in some of these highly polymorphic sites, while strong negative selection was indicated in most of the codons. Despite robust clustering to intra-typic genotypes, only few genotype-specific ‘signature’ amino acids were detected. In contrast, when different enterovirus types were compared, there was a clear tendency towards fixation of type-specific ‘signature’ amino acids. The results suggest that permanent fixation of type-specific amino acids is a hallmark associated with evolution of different enterovirus types, whereas neutral evolution and/or (frequency-dependent) positive selection in few highly polymorphic amino acid sites are the dominant forms of evolution when strains within an enterovirus type are compared.

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Section: Methodsmentioning

confidence: 99%

The Evolution of Vp1 Gene in Enterovirus C Species Sub-Group That Contains Types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

et al. 2014

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“…The absence of fixed differences, whose deficit usually indicates the action of purifying selection, here might also suggest that the MKT is not the most appropriate test for these data. This interpretation is supported by a simulation study that shows that the MKT exhibits unduly high type-I error rates at the large mutation rates (scaled to effective population sizes) typically found in RNA viruses such as Influenza viruses [23]. On the other hand, the Tajima test failed to reject the null hypothesis of neutral evolution for all protein-coding genes.…”

Section: Resultsmentioning

confidence: 89%

“…Alternatively, the genes with an indication that neutrality could be rejected (PB1, HA, NA, the M and NS genes) are those that underwent a rapid and recent expansion. The results of the Tajima test are therefore potentially compounded by the effect of a recent "population" expansion of these segments, which is known to inflate the type-I error rate of this test [23]. In the absence of a clear rejection of the neutral hypothesis both with population genetics and phylogenetic approaches, the emergence of the 2009 H1N1 pandemic was therefore most likely due to nonadaptive processes such as drift (e.g., [24]).…”

Section: Resultsmentioning

confidence: 99%

“…First, in terms of methodology, the use of codon models proved here to return more sensible results than the use of population genetics test of neutrality such as the MKT or the Tajima test, which both have limitations when it comes to analyzing viral data as population genetics-based tests can be sensitive to demographic changes and/or high levels of diversity, so that these tests can have low power [23,34]. However, the use of codon models in the context of a population study is also not fully satisfactory, as not all nonsynonymous substitutions can be assumed to be fixed.…”

Section: Discussionmentioning

confidence: 99%

“…The alignments were used as computed above, and divergences were corrected with the Jukes and Cantor model, which is similar in spirit to a recently proposed method [23]. The p -values were computed as a χ 2 homogeneity test on a contingency table.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host

Abdussamad

Aris‐Brosou

2011

BMC Evol Biol

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BackgroundThe emergence of the 2009 H1N1 Influenza pandemic followed a multiple reassortment event from viruses originally circulating in swines and humans, but the adaptive nature of this emergence is poorly understood.ResultsHere we base our analysis on 1180 complete genomes of H1N1 viruses sampled in North America between 2000 and 2010 in swine and human hosts. We show that while transmission to a human host might require an adaptive phase in the HA and NA antigens, the emergence of the 2009 pandemic was essentially nonadaptive. A more detailed analysis of the NA protein shows that the 2009 pandemic sequence is characterized by novel epitopes and by a particular substitution in loop 150, which is responsible for a nonadaptive structural change tightly associated with the emergence of the pandemic.ConclusionsBecause this substitution was not present in the 1918 H1N1 pandemic virus, we posit that the emergence of pandemics is due to epistatic interactions between sites distributed over different segments. Altogether, our results are consistent with population dynamics models that highlight the epistatic and nonadaptive rise of novel epitopes in viral populations, followed by their demise when the resulting virus is too virulent.

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The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola

et al. 2022

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Detecting natural selection in RNA virus populations using sequence summary statistics

Cited by 32 publications

References 40 publications

The Evolution of Vp1 Gene in Enterovirus C Species Sub-Group That Contains Types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

The Evolution of Vp1 Gene in Enterovirus C Species Sub-Group That Contains Types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host

The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola

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