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

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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.

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Authors and Affiliations

  1. Instituto de Ciências Biológicas, Federal University of Pará, Avenida Augusto Corrêa, 1, CEP 66075-000, Belém, Pará, Brazil

    Fabiola Villanova & Élcio Leal

  2. Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences, Beijing, 100094, China

    Shangjin Cui

  3. College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China

    Xia Ai

  4. State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang, Harbin, 150001, China

    Shangjin Cui

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  1. Fabiola Villanova
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  3. Xia Ai
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  4. Élcio Leal
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Correspondence to Élcio Leal.

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This article does not contain any studies with human participants or animals performed by any of the authors. E.L. was supported by the Fundação de Amparo e Desenvolvimento da Pesquisa (FADESP) and Pró-Reitoria de Pesquisa e Pós-Graduação (PROPESP) (grant no. 11/2015). S.C. was funded by the National Natural Science Foundation of China (Grants No. 31001069, No. 31172349, and No. 31172341). The authors declare that they have no conflict of interest.

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Villanova, F., Cui, S., Ai, X. et al. Analysis of full-length genomes of porcine teschovirus (PTV) and the effect of purifying selection on phylogenetic trees. Arch Virol 161, 1199–1208 (2016). https://doi.org/10.1007/s00705-015-2744-0

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