Nucleotide sequence polymorphism in circoviruses

Abstract

Analysis of nucleotide diversity within six species of circovirus showed consistently stronger purifying selection at nonsynonymous sites in the rep gene than on those in the cap gene. In addition, synonymous nucleotide diversity in the rep gene was significantly lower than that in the cap gene, suggesting functional constraint even at synonymous sites in rep, which was associated in all six species with strongly negative AT-skew. Of the six virus species examined, four species showed evidence of ongoing purifying selection at nonsynonymous polymorphic sites in the rep gene, indicating the presence of slightly deterious nonsynonymous variants in these populations. The rep gene of porcine circovirus 2 (PCV2) was unique, however, in showing a strong excess of rare nonsynonymous polymorphisms. The excess of rare nonsynonymous polymorphisms suggests a prolonged population bottleneck in PCV2, allowing slightly deleterious mutations to accumulate, followed by a population expansion during which selection to remove these variants has increased in effectiveness. Such a population history is consistent with the epidemiological evidence of a recent worldwide spread of PCV2.

Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2

“…The dN/dS ratios for cap, rep, and rep-ORF3 were relatively low (dN/dS ϭ 0.230, 0.193, and 0.173, respectively), indicating that most sites within these regions are under strong purifying selection. This is in accord with previous analyses of dN/dS in PCV2, where purifying selection was found in both rep and cap (26,54). Including the region of rep that overlaps with ORF3 did not increase the strength of purifying selection measured for the rep gene.…”

Molecular analysis and associated pathology of beak and feather disease virus isolated in Italy from young Congo African grey parrots (Psittacus erithacus) with an “atypical peracute form” of the disease

“…We observed that the viral sequences of strains that produce the peracute illness clustered closely with the strains responsible for the chronic disease, thus suggesting the absence of a specific BFDV genetic variant accountable for a specific form of PBFD, as formerly hypothesized (Ypelaar et al, 1999;Bassami et al, 2001;Heath et al, 2004;Raue et al, 2004;Hughes & Piontkivska, 2008). On the basis of this observation, we have hypothesized that the clinical and pathological differences between aPF and CF of the disease could be strictly related to the age and host immune system status, rather than genomic differences between viral strains.…”

Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses

“…3) but also in the divergence of codon usages (Table 3). Many reports have indicated that synonymous substitutions can affect mRNA splicing, stability, structure and protein folding (Hughes & Piontkivska, 2008;Palermo et al, 2009). Using mRNA structure prediction software (http://www.…”