title: Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close derivatives of the SA11-H96 strain.
abstract: Whole-genome, sequence-independent amplification and 454(®) pyrosequencing of a rotavirus SA11 cell culture sample with an unknown passage history yielded consensus sequences of twelve complete genome segments. Two distinct sequences for genome segment 8 (encoding NSP2) were present, indicating a mixed infection with two rotavirus SA11 strains. The genotypes of the viruses were G3-P[2]-I2-R2-C5-M5-A5-Nx-T5-E2-H5, where x was either 5 or 2. The strains were named RVA/Simian-tc/ZAF/SA11-N5/1958/G3P[2] and RVA/Simian-tc/ZAF/SA11-N2/1958/G3P[2]. The genotype (N2) and sequence of genome segment 8 of RVA/Simian-tc/ZAF/SA11-N2/1958/G3P[2] were identical to that of the bovine rotavirus O agent. Five novel amino acids were detected in minor population variants of three genome segments. Genome segment 1 (VP1) has a high nucleotide substitution rate, but the substitutions are synonymous. Distance matrices and Bayesian molecular clock phylogenetics showed that SA11-N2 is a reassortant containing genome segment 8 from the O agent, whereas SA11-N5 is a very close derivative of the prototype SA11-H96.
authors.affiliation: Biochemistry Division, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa.
authors.forename: Luwanika
authors.initials: L
authors.lastname: Mlera
authors.forename: Hester G
authors.initials: HG
authors.lastname: O'Neill
authors.forename: Khuzwayo C
authors.initials: KC
authors.lastname: Jere
authors.forename: Alberdina A
authors.initials: AA
authors.lastname: van Dijk
mesh_terms: D060085:Coinfection / Q000821:virology; D016384:Consensus Sequence; D014644:Genetic Variation; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics; D012401:Rotavirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012400:Rotavirus Infections / Q000821:virology*; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral