Episodic adaptive diversification of classical swine fever virus RNA-dependent RNA polymerase NS5B.
Classical swine fever virus (CSFV) is the pathogen that causes a highly infectious disease of pigs and has led to disastrous losses to pig farms and related industries. The RNA-dependent RNA polymerase (RdRp) NS5B is a central component of the replicase complex (RC) in some single-stranded RNA viruses, including CSFV. On the basis of genetic variation, the CSFV RdRps could be clearly divided into 2 major groups and a minor group, which is consistent with the phylogenetic relationships and virulence diversification of the CSFV isolates. However, the adaptive signature underlying such an evolutionary profile of the polymerase and the virus is still an interesting open question. We analyzed the evolutionary trajectory of the CSFV RdRps over different timescales to evaluate the potential adaptation. We found that adaptive selection has driven the diversification of the RdRps between, but not within, CSFV major groups. Further, the major adaptive divergence-related sites are located in the surfaces relevant to the interaction with other component(s) of RC and the entrance and exit of the template-binding channel. These results might shed some light on the nature of the RdRp in virulence diversification of CSFV groups.
a College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China.
Yan
Y
Li
b College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, People's Republic of China.
Zexiao
Z
Yang
D000818:Animals; D006691:Classical Swine Fever / Q000821:virology*; D006692:Classical Swine Fever Virus / Q000737:chemistry / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D013552:Swine; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase
ARN polymérase dépendante de l’ARN; Classical swine fever virus; RNA-dependent RNA polymerase; adaptation épisodique; diversification inter-groupe; episodic adaptation; intergroup diversification; virus classique de la grippe porcine