Analysis of full-length genomes of porcine teschovirus (PTV) and the effect of purifying selection on phylogenetic trees

Abstract

To study the outcome of natural selection using phylogenetic trees, we analyzed full-length genome sequences of porcine teschovirus (PTV). PTV belongs to the family Picornaviridae and has a positive-stranded RNA genome, the replication of which is carried out by the error-prone viral RNA-dependent RNA polymerase. The viral RNA encodes a single polyprotein that is cleaved into structural (i.e., L, VP4, VP2, VP3 and VP1) and nonstructural proteins (i.e., 2A, 2B, 2C, 3A, 3B, and 3C). A high degree of genetic diversity was found based on the pairwise nucleotide distances and on the mean ratio of the number of nonsynonymous (dN) and synonymous (dS) substitutions (dN/dS) in the structural genes. Conversely, the diversity of the nonstructural genes was lower. The differences in genetic diversity between the structural and nonstructural genomic regions were likely due to strong purifying selection; consequently, the estimates of phylogenies were also discordant among these genes. In particular, maximum-likelihood and Bayesian methods generated short-branched trees when loci that are under strong purifying selection were used. These findings indicate that even in an RNA virus with an intrinsically high mutation rate, a strong purifying selection will curb genetic diversity and should be considered an important source of bias in future studies based on phylogenetic methods.

Epidemiology and molecular characterization ofPorcine teschovirusin Hunan, China

“…Notably, some PTVs showed phylogenetic incompatibility among different structural protein regions, which was significantly correlated with the multiple, complex recombination events in the evolutionary history (data not shown). A previous study demonstrated a signature of strong purifying selection in PTVs, suggesting that most amino acid mutations were the result of genetic drift (Villanova et al, 2016). In the present study, selection pressure analyses in all 72 non-recombinant PTVs revealed only two sites under positive selection by means of three methods, at codon 2 (L 2 ) and codon 120 (VP4 34 ); sites 23 and 29 in the leader protein were detected to be positively selected by two methods; and the other six amino acid substitutions were identified to be positively selected by at least one method.…”

“…Porcine teschovirus (PTV) in the genus Teschovirus within the family Picornaviridae is a non‐enveloped virus with a single‐stranded RNA genome of positive polarity (ICTV, ). PTV has a genome of about 7.1 kb containing a single long open reading frame (ORF) on the viral RNA that is processed to form 12 individual mature proteins, comprising a leader (L) protein followed by the viral capsid proteins, four structural proteins (VP1–4), and seven non‐structural proteins (2A–C, 3A–D) (Cano‐Gómez & Jiménez‐Clavero, ; Villanova, Cui, Ai, & Leal, ).…”

“…Genetic diversity among different PTVs has been demonstrated based on phylogenetic analysis (Boros et al., ; Cano‐Gómez et al., ). Several studies have shown that purifying selection and natural homologous recombination are responsible for the significant genetic diversity between structural and non‐structural genes, driving the evolution of PTV (Villanova et al., ; Wang et al., ). However, given the limited genomic information of PTVs, this hypothesis requires more data for verification and clarification of the mechanisms driving evolution and genetic diversity among isolates to best understand its transmission, distribution patterns, and establish appropriate control and prevention strategies.…”

Regional adaptations and parallel mutations in Feline panleukopenia virus strains from China revealed by nearly-full length genome analysis

“…These sequences were selected basically by the absence of recombination. Recombinant strains need to be removed because recombination is a significant bias to the inferences of trees based on maximum likelihood or Bayesian approaches [31]. The presence of positive selection was also measured in the alignments of VP2 in order to contemplate the effect of positive selection on the topology of the trees.…”

“…The diversity of carnivore protoparvoviruses has been described in many studies and seems to be represented by a great variety of strains and recombinant forms [27,[30][31][32]. Conversely, there are few studies describing the heterogeneity of FPLV strains and its relevance to the maintenance of these viruses in distinct hosts [13].…”