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.

Fig. 1

a–l Maximum likelihood phylogenetic trees based on the full-length coding nucleotide sequences of the rotavirus genes: a VP7 (G8), b VP7 (G2), c VP1, d VP2, e VP3, f VP4, g VP6, h NSP1, i NSP2, j NSP3, k NSP4 and l NSP5. Bootstrap values above 70 are provided for 500 replicates. The clades for each viral protein genotype are labelled in each tree. For the VP7 and VP4 trees, representative strains from different lineages were used to determine in which lineage the study strains clustered. The black squares represent the G8 study strains and the black circles indicate the G2 study strain in all trees

Fig. 1

a–l Maximum likelihood phylogenetic trees based on the full-length coding nucleotide sequences of the rotavirus genes: a VP7 (G8), b VP7 (G2), c VP1, d VP2, e VP3, f VP4, g VP6, h NSP1, i NSP2, j NSP3, k NSP4 and l NSP5. Bootstrap values above 70 are provided for 500 replicates. The clades for each viral protein genotype are labelled in each tree. For the VP7 and VP4 trees, representative strains from different lineages were used to determine in which lineage the study strains clustered. The black squares represent the G8 study strains and the black circles indicate the G2 study strain in all trees

Fig. 1

a–l Maximum likelihood phylogenetic trees based on the full-length coding nucleotide sequences of the rotavirus genes: a VP7 (G8), b VP7 (G2), c VP1, d VP2, e VP3, f VP4, g VP6, h NSP1, i NSP2, j NSP3, k NSP4 and l NSP5. Bootstrap values above 70 are provided for 500 replicates. The clades for each viral protein genotype are labelled in each tree. For the VP7 and VP4 trees, representative strains from different lineages were used to determine in which lineage the study strains clustered. The black squares represent the G8 study strains and the black circles indicate the G2 study strain in all trees