The evolution of foot-and-mouth disease virus: Impacts of recombination and selection

Lewis-Rogers, Nicole; McClellan, David A.; Crandall, Keith A.

doi:10.1016/j.meegid.2008.07.009

Cited by 47 publications

(41 citation statements)

References 61 publications

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“…Our results indicated that five FMDV serotypes, O, A, Asia 1, C, and SAT 3, were each monophyletic but the remaining two serotypes SAT 1 and SAT 2 were not so clearly differentiated. This configuration is consistent with a previous study based on coding sequences of the genome excluding the 3B gene (Lewis-Rogers et al, 2008). Tully and Fares (2008), however, have claimed that both SAT 1 and SAT 2, as well as above five serotypes, were also monophyletic on the basis of 1D gene sequences.…”

Section: Discussionsupporting

confidence: 92%

“…However, genomelevel analysis of global FMDVs including all seven FMDV serotypes has not been well described. Only three studies have focused on aspects of complete genome analysis of FMDV sequences (Carrillo et al, 2005;Cooke and Westover, 2008;Lewis-Rogers et al, 2008). Carrillo et al (2005) pioneered work in this field by determining 103 complete genomic sequences from FMDV isolates representing all seven serotypes, and then comparing them with the sequences of 30 published FMDVs using neighbor-joining, split decomposition, and puzzling methods.…”

Section: Introductionmentioning

confidence: 99%

“…Each of five serotypes (O, Asia 1, C, A, and SAT 1+2+3) appeared as independent clades and serotype C and Asia 1 had a sister group relationship to each other. Furthermore, Lewis-Rogers et al (2008) also analyzed 159 sequences of coding genome excluding 3B gene using Bayesian inference and maximum likelihood, and suggested that each of five serotypes (O, Asia 1, C, A, and SAT 3) were monophyletic and serotypes O and Asia 1 were most closely related to each other. However, the lack of bootstrap values in these studies did not allow the robustness of the phylogenetic relationships to be interpreted.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomics and Molecular Evolution of Foot-and-Mouth Disease Virus

Yoon

Park

King

et al. 2011

Molecules and Cells

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Phylogenomics and Molecular Evolution of Foot-and-Mouth Disease Virus

Yoon

Park

King

et al. 2011

Molecules and Cells

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“…Evolutionary forces such as selection and recombination are known to affect phylogenetic inferences (Schierup and Hein, 2000;Moya et al, 2004;Lewis-Rogers et al, 2008) and could bias evolutionary estimates. Recombination within some regions of the FMDV genome contributing to genetic heterogeneity has been reported in previous studies involving both the NSP coding regions Lee et al, 2009 andLi et al, 2007;Mohapatra et al, 2008) and the capsid coding regions (Haydon et al, 2004;Tosh et al, 2002b).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa

Wekesa

Sangula²,

Belsham

et al. 2014

Infection, Genetics and Evolution

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Serotype A is the most genetically and antigenically diverse of the foot-and-mouth disease virus (FMDV) serotypes. Records of its occurrence in Kenya date back to 1952 and the antigenic diversity of the outbreak viruses in this region is reflected by the current use of two different vaccine strains (K5/1980 and K35/1980) and previous use of two other strains (K18/66 and K179/71). This study aimed at enhancing the understanding of the patterns of genetic variation of serotype A FMDV in Kenya. The complete VP1 coding region sequences of 38 field isolates, identified as serotype A FMDV, collected between 1964 and 2013 were determined. Coalescent-based methods were used to infer times of divergence of the virus strains and the evolutionary rates alongside 27 other serotype A FMDV sequences from Genbank and the World Reference Laboratory (WRL). This study represents the first comprehensive genetic analysis of serotype A FMDVs from Kenya. The study detected four previously defined genotypes/clusters (termed G-I, G-III, G-VII and G-VIII), within the Africa topotype, together with a fifth lineage that has apparently emerged from within G-I; these different lineages have each had a countrywide distribution. Genotypes G-III and G-VIII that were first isolated in 1964 are now apparently extinct; G-VII was last recorded in 2005, while G-I (including the new lineage) is currently in widespread circulation. High genetic diversity, widespread distribution and transboundary spread of serotype A FMDVs across the region of eastern Africa was apparent. Continuous surveillance for the virus, coupled to genetic and antigenic characterization is recommended for improved regional control strategies.Danish International Development Agency (DANIDA); Livestock-Wildlife Diseases in East Africa Project (LWDEA); Trans-boundary Animal Diseases in East Africa (TADEA) project: (DFC no. 10-006KU)

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“…This difference might be due to the fact that serotypes Asia 1, A, C, and O are clearly distinct from serotypes SAT 1-3 in their evolutionary characteristics (Lewis-Rogers et al, 2008). Researchers introduced two additional AUGs into FMDV Region-La, and found that the ribosomes never registered the additional AUGs and still had a tendency to initiate translation from the original second AUG (Belsham, 1992).…”

Section: Resultsmentioning

confidence: 99%

Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The mechanism of alternative AUG usage in footand-mouth disease virus is not completely understood. Using simple computational approaches, we evaluated the contributions of overall codon bias, quantitative codon bias, and %GC of the region between the two alternative AUGs, Region-La, as well as the nucleotide bias of the sequence context flanking each AUG with respect to translation initiation efficiency. For all serotypes of this virus, we found that only a small component of the effect of RNA secondary structure on ribosome scanning was due to the low %GC of RegionLa. In addition, we found that the nucleotide bias of the context from position -4 to +6 flanking the AUG 2nd had a negative correlation with the overall codon bias, and that a strong purine bias existed in this AUG 2nd context. However, the quantitative codon bias of RegionLa was seen to be significantly lower than that of Region-Lb (the 16803-16812 (2015) sequence following AUG 2nd ) in all serotypes except SAT 1-3. Taken together, our results suggest that the low codon bias of Region-La might impair the translation initiation efficiency at the AUG 1st in all serotypes except SAT 1-3, and the specific AUG 2nd context might be used as a strong signal to initiate translation from the AUG 2nd in all serotypes.

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The evolution of foot-and-mouth disease virus: Impacts of recombination and selection

Cited by 47 publications

References 61 publications

Phylogenomics and Molecular Evolution of Foot-and-Mouth Disease Virus

Phylogenomics and Molecular Evolution of Foot-and-Mouth Disease Virus

Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa

Translation of foot-and-mouth disease virus RNA: factors influencing alternative AUG selection

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