title: Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses.
abstract: Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004-2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977-1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts.
authors.affiliation: Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Brazil.
authors.forename: Fernanda D F
authors.initials: FD
authors.lastname: Silva
authors.affiliation: Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Brazil.
authors.forename: F
authors.initials: F
authors.lastname: Gregori
authors.affiliation: Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA. Electronic address: mcdonaldsa@vtc.vt.edu.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: McDonald
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D012401:Rotavirus / Q000145:classification* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D013552:Swine; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: Amino acid changes; Genomics; Genotype 1; Group A rotavirus; Host tropism; Human; Porcine; Sub-genotypic diversity