Diversity within the VP4 gene of rotavirus P[8] strains: Implications for reverse transcription-PCR genotyping

Abstract

A degenerate version (1T1-D) of the rotavirus P[8]-specific primer (IT- 1) allowed strains previously untypeable due to the accumulation of point mutations at the primer binding site to be P typed by reverse transcription- PCR. Sequencing of the cDNA followed by sequence alignment and phylogenetic analysis identified lineages and sublineages within the rotavirus P[8] types, while the use of 1T-1 or 1T-1D primers did not yield vital clusters in any particular lineage.