title: Whole-genome analyses of DS-1-like human G2P[4] and G8P[4] rotavirus strains from Eastern, Western and Southern Africa.
abstract: Group A rotaviruses (RVAs) with distinct G and P genotype combinations have been reported globally. We report the genome composition and possible origin of seven G8P[4] and five G2P[4] human RVA strains based on the genetic evolution of all 11 genome segments at the nucleotide level. Twelve RVA ELISA positive stool samples collected in the representative countries of Eastern, Southern and West Africa during the 2007-2012 surveillance seasons were subjected to sequencing using the Ion Torrent PGM and Illumina MiSeq platforms. A reference-based assembly was performed using CLC Bio's clc_ref_assemble_long program, and full-genome consensus sequences were obtained. With the exception of the neutralising antigen, VP7, all study strains exhibited the DS-1-like genome constellation (P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and clustered phylogenetically with reference strains having a DS-1-like genetic backbone. Comparison of the nucleotide and amino acid sequences with selected global cognate genome segments revealed nucleotide and amino acid sequence identities of 81.7-100 % and 90.6-100 %, respectively, with NSP4 gene segment showing the most diversity among the strains. Bayesian analyses of all gene sequences to estimate the time of divergence of the lineage indicated that divergence times ranged from 16 to 44 years, except for the NSP4 gene where the lineage seemed to arise in the more distant past at an estimated 203 years ago. However, the long-term effects of changes found within the NSP4 genome segment should be further explored, and thus we recommend continued whole-genome analyses from larger sample sets to determine the evolutionary mechanisms of the DS-1-like strains collected in Africa.
authors: South African Medical Research Council/UL Diarrhoeal Pathogens Research Unit (MRC/DPRU), Department of Virology, University of Limpopo (Medunsa Campus) and National Health Laboratory Service, PO Box 173, Medunsa, Pretoria, 0204, South Africa.
authors: Martin M
authors: MM
authors: Nyaga
authors: Karla M
authors: KM
authors: Stucker
authors: Mathew D
authors: MD
authors: Esona
authors: Khuzwayo C
authors: KC
authors: Jere
authors: Bakari
authors: B
authors: Mwinyi
authors: Annie
authors: A
authors: Shonhai
authors: Enyonam
authors: E
authors: Tsolenyanu
authors: Augustine
authors: A
authors: Mulindwa
authors: Julia N
authors: JN
authors: Chibumbya
authors: Hokororo
authors: H
authors: Adolfine
authors: Rebecca A
authors: RA
authors: Halpin
authors: Sunando
authors: S
authors: Roy
authors: Timothy B
authors: TB
authors: Stockwell
authors: Chipo
authors: C
authors: Berejena
authors: Mapaseka L
authors: ML
authors: Seheri
authors: Jason M
authors: JM
authors: Mwenda
authors: A Duncan
authors: AD
authors: Steele
authors: David E
authors: DE
authors: Wentworth
authors: M Jeffrey
authors: MJ
authors: Mphahlele
mesh_terms: D000351:Africa, Eastern; D000353:Africa, Southern; D000354:Africa, Western; D016000:Cluster Analysis; D005243:Feces / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D012401:Rotavirus / Q000235:genetics* / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000821:virology*; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012367:RNA, Viral