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.
The study may help to design peptides that may be further investigated as candidate for development of diagnostic assays and heterotypic protective immunity for group A rotavirus.
Sarah Cherian, Prabhakar G, Manika Burghein, S. D. Chitambar, “In Silico Immunogenic Analysis of the VP6 Capsid protein of Avian Rotaviruses” at the International Conference on Bioinformatics, INCOB 2006, New Delhi. (Dec 18-20, 2006).
“VP6 capsid protein of chicken rotavirus strain CH2: sequence phylogeny and in silico antigenic analysis”. Buragohain M, Cherian S, Prabhakar G, Chitambar S*. Virus Res., 137(2): 173-8 (2008).
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