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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

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dc.contributor.author Jere, Khuzwayo
dc.contributor.author Mlera, Luwanika
dc.contributor.author Van Dijk, Alberdina Aike
dc.contributor.author Page, Nicola A.
dc.contributor.author O'Neill, Hester Gertruida
dc.date.accessioned 2012-10-17T06:52:18Z
dc.date.available 2012-10-17T06:52:18Z
dc.date.issued 2011
dc.identifier.citation Jere, K. et al. 2011. 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. Infection, genetics and evolution, 11(8):2072-2082. [http://www.journals.elsevier.com/infection-genetics-and-evolution/] en_US
dc.identifier.issn 1567-1348
dc.identifier.issn 1567-7257 (Online)
dc.identifier.uri http://hdl.handle.net/10394/7508
dc.description.abstract 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[8]). 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[4] (DS-1-like), P[6] (ST3-like) and P[8] (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[8], by sequence-dependent RT-PCR. en_US
dc.description.uri http://dx.doi.org/10.1016/j.meegid.2011.09.023
dc.language.iso en en_US
dc.publisher Elsevier en_US
dc.subject Rotavirus en_US
dc.subject whole genome analysis en_US
dc.subject genome recombination en_US
dc.subject sequence-independent genome en_US
dc.subject amplification and 454® pyrosequencing en_US
dc.title 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 en_US
dc.type Article en_US


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