title: Analysis of the VP6 gene of human and porcine group A rotavirus strains with unusual subgroup specificities.
abstract: Full-length VP6 amino acid sequences of human and porcine rotaviruses with subgroup (SG) (I + II) and SG non-(I + II) were analyzed in comparison with those of SG I and SG II. In human rotaviruses, the strains in the same SG shared a very high degree of amino acid identity, ranging from 97.4% to 99.4% for SG I, 95.9% to 100% for SG II, and 99.4% to 100% for SG non-(I + II), while viruses in different SGs shared somewhat lower sequence identity at 90.4-93.1%. Conserved amino acids that distinguished the strains of SG I from SG II were observed at 21 positions. The viruses with SG non-(I + II) shared sequence identity with SG II as high as 97.2-99.7%, suggesting that they belonged to genogroup II. Similarly, porcine rotaviruses in the same SG shared 96.4-99.7% for SG I, 98.2-100% for SG II, 97.4-100% for SG (I + II), and 96.2-99.7% for SG non-(I + II), while strains in different SGs shared sequence identity ranging from 91.9% to 94.4%. Interestingly, the strains with SG (I + II) and SG non-(I + II) shared a high degree of sequence identity with SG I, at 96.4-100% and 94.7-99.7% respectively, suggesting that they are related to porcine SG I strains. The conserved amino acids which distinguished SG I from SG II were observed at 13 positions. The strains with SG I, SG (I + II), and SG non-(I + II) showed identical amino acid residues at these positions. Phylogenetic analysis strongly supported the findings of the sequence analysis.
authors.affiliation: Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
authors.forename: Aksara
authors.initials: A
authors.lastname: Thongprachum
authors.forename: Pattara
authors.initials: P
authors.lastname: Khamrin
authors.forename: Prayuth
authors.initials: P
authors.lastname: Saekhow
authors.forename: Chansom
authors.initials: C
authors.lastname: Pantip
authors.forename: Supatra
authors.initials: S
authors.lastname: Peerakome
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ushijima
authors.forename: Niwat
authors.initials: N
authors.lastname: Maneekarn
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000831:Animals, Newborn; D000956:Antigens, Viral / Q000235:genetics*; D036022:Capsid Proteins / Q000235:genetics*; D002648:Child; D016000:Cluster Analysis; D017124:Conserved Sequence; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012401:Rotavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000662:veterinary* / Q000821:virology; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013552:Swine; D013553:Swine Diseases / Q000821:virology*
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; C061332:VP6 protein, Rotavirus