Whole genome analysis of multiple rotavirus strains from a single stool specimen using sequence-independent amplification and 454® pyrosequencing reveals evidence of intergenotype genome segment recombination
Jere, Khuzwayo C.
Van Dijk, Alberdina A.
O'Neill, Hester G.
Page, Nicola A.
MetadataShow full item record
Infection of a single host cell with two or more different rotavirus strains creates conditions favourable for evolutionary mechanisms like reassortment and recombination that can generate novel strains. Despite numerous reports describing mixed rotavirus infections, whole genome characterisation of rotavirus strains in a mixed infection case has not been reported. Double-stranded RNA, exhibiting a long electropherotype pattern only, was extracted from a single human stool specimen (RVA/Human-wt/ZAF/2371WC/2008/G9P). Both short and long electropherotype profiles were however detected in the sequence-independent amplified cDNA derived from the dsRNA, suggesting infection with more than one rotavirus strain. 454® pyrosequencing of the amplified cDNA revealed co-infection of at least four strains. Both genotype 1 (Wa-like) and genotype 2 (DS-1-like) were assigned to the consensus sequences obtained from the nine genome segments encoding NSP1–NSP5, VP1–VP3 and VP6. Genotypes assigned to the genome segments encoding VP4 were P (DS-1-like), P (ST3-like) and P (Wa-like) genotypes. Since four distinct genotypes [G2 (DS-1-like), G8, G9 (Wa-like) and G12] were assigned to the four consensus nucleotide sequences obtained for genome segment 9 (VP7), it was concluded that at least four distinct rotaviruses were present in the stool. Intergenotype genome recombination events were observed in genome segments encoding NSP2, NSP4 and VP6. The close similarities of some of the genome segments encoding NSP2, VP6 and VP7 to artiodactyl rotaviruses suggest that some of the infecting strains shared common ancestry with animal strains, or that interspecies transmission occurred previously. The sequence-independent genome amplification technology coupled with 454® pyrosequencing used in this study enabled the characterisation of the whole genomes of multiple rotavirus strains in a single stool specimen that was previously assigned single genotypes, i.e. G9P, by sequence-dependent RT-PCR.
Showing items related by title, author, creator and subject.
Determination of the whole-genome consensus sequence of the prototype DS-1 rotavirus using sequence-independent genome amplification and 454® pyrosequencing Mlera, Luwanika; Jere, Khuzwayo C.; Van Dijk, Alberdina A.; O'Neill, Hester G. (Elsevier, 2011)The prototype DS-1 rotavirus strain, is characterised by a short electropherotype and G2P serotype specificity. Following sequence-independent genome amplification and 454® pyrosequencing of genomic cDNA, differences ...
Characterisation of Xanthomonas campestris pv. campestris isolates from South Africa using genomic DNA fingerprinting and pathogenicity tests Bezuidenhout, Cornelius Carlos; Chidamba, Lizyben (Springer, 2012)The genetic diversity of Xanthomonas campestris pv. campestris isolates from South Africa was evaluated using 28 isolates obtained from the Johannesburg Fresh Produce Market. Samples were collected from cabbage supplies ...
Molecular analysis of the mitochondrial genome in South African patients with suspected mitochondrial disorders Van Brummelen, Anna Catharina (North-West University, 2003)Human mitochondrial DNA (mtDNA) contains 37 genes, which encode 13 proteins (all subunits of the respiratory chain), 22 transfer ribonucleic acids (tRNA), and two ribosomal RNAs. The mtDNA mutation rate is approximately ...