Time-calibrated phylogenomics of the classical swine fever viruses: genome-wide bayesian coalescent approach

PLoS One. 2015 Mar 27;10(3):e0121578. doi: 10.1371/journal.pone.0121578. eCollection 2015.

Abstract

The phylogeny of classical swine fever virus (CSFV), the causative agent of classical swine fever (CSF), has been investigated extensively. However, no evolutionary research has been performed using the whole CSFV genome. In this study, we used 37 published genome sequences to investigate the time-calibrated phylogenomics of CSFV. In phylogenomic trees based on Bayesian inference (BI) and Maximum likelihood (ML), the 37 isolates were categorized into five genetic types (1.1, 1.2, 2.1, 2.3, and 3.4). Subgenotype 1.1 is divided into 3 groups and 1 unclassified isolate, 2.1 into 4 groups, 2.3 into 2 groups and 1 unclassified isolate, and subgenotype 1.2 and 3.4 consisted of one isolate each. We did not observe an apparent temporal or geographical relationship between isolates. Of the 14 genomic regions, NS4B showed the most powerful phylogenetic signal. Results of this evolutionary study using Bayesian coalescent approach indicate that CSFV has evolved at a rate of 13×.010-4 substitutions per site per year. The most recent common ancestor of CSFV appeared 2770.2 years ago, which was about 8000 years after pig domestication. The effective population size of CSFV underwent a slow increase until the 1950s, after which it has remained constant.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bayes Theorem
  • Classical Swine Fever / virology
  • Classical Swine Fever Virus / classification*
  • Classical Swine Fever Virus / genetics*
  • Genome, Viral
  • Mutation
  • Phylogeny
  • RNA, Viral / analysis*
  • Selection, Genetic
  • Sequence Analysis, RNA / methods*
  • Swine

Substances

  • RNA, Viral

Grant support

This study was supported by a grant (PJ009032) from the Next Generation BioGreen21 Program, Rural Development Administration, Republic of Korea. Seoae Cho is CEO of C&K Genomics Inc. C&K Genomics Inc. provided support in the form of salary for author SC, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section.