title: VP6 capsid protein of chicken rotavirus strain CH2: sequence, phylogeny and in silico antigenic analyses.
abstract: The inner capsid protein VP6 of group A rotavirus possesses group and subgroup epitope specificities. Avian rotaviruses have a unique VP6 that is antigenically different from its mammalian counterpart. The lack of information on the VP6 protein of chicken rotavirus strain, CH2, at the genetic and antigenic level was a major motivation for this work. Sequencing of the complete cDNA of the VP6 gene of CH2, revealed a nucleotide (amino acid) identity that varied from 78.3 to 98.5% (86.4-98.2%) when compared with other avian rotaviruses. Regardless of its host origin dissimilarity, CH2 VP6 showed a close sequence homology (97.4-98.2%) with turkey and pigeon rotaviruses. Homology-based modeling of the CH2 VP6 from the corresponding crystal structure of the bovine rotavirus, RF strain, demonstrated that the hypervariable region (residue 228-240) does have a critical role in strain specific antigenic characteristics of avian and mammalian rotaviruses. A predicted conformational epitope encompasses experimentally characterized group and subgroup epitopes suggesting that it is a major antibody binding site on the VP6 protein. The VP6 structure modeling and conformational epitope prediction together with enzyme immuno assay of SG MAbs placed CH2 in SGI/II. The study may be helpful in designing peptides for group A rotavirus diagnostic assays and to achieve heterotypic protection against rotavirus serotypes.
authors.affiliation: Rotavirus Department, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India.
authors.forename: Manika
authors.initials: M
authors.lastname: Buragohain
authors.forename: Sarah S
authors.initials: SS
authors.lastname: Cherian
authors.forename: G
authors.initials: G
authors.lastname: Prabhakar
authors.forename: Shobha D
authors.initials: SD
authors.lastname: Chitambar
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000956:Antigens, Viral / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D002460:Cell Line; D002645:Chickens / Q000821:virology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology*; D012401:Rotavirus / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000276:immunology; D012400:Rotavirus Infections / Q000662:veterinary* / Q000821:virology; D016415:Sequence Alignment
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins