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.

Emergence of human G2P[4] rotaviruses containing animal derived gene segments in the post-vaccine era

“…Rotaviruses containing a bovine-like NSP4 gene have been detected in other countries with rotavirus vaccination programs, such as Brazil, Australia, the USA and several countries in Sub-Saharan Africa10121527, but also in countries were no rotavirus vaccines are universally used like the Democratic republic of the Congo, Italy, Russia and Thailand111416. It is yet unknown for how long these bovine NSP4 gene segments have been circulating in the human rotavirus population and to elucidate this, detailed large scale analyses with time-stamped animal and human DS-1-like NSP4 genes are needed.…”

“…The analysis of complete DS-1-like genomes isolated in Brazil, Italy and the USA revealed the co-circulation of multiple lineages for several gene segments, some of which are likely of animal origin101112. In addition, the circulation of animal-human reassortant viruses possessing an animal NSP4 gene segment has been increasingly reported13141516. Animal-human reassortant viruses have the potential to change viral fitness and promote viral transmission, especially in an immune naïve population.…”

Detection of the first G6P[14] human rotavirus strain in an infant with diarrhoea in Ghana

“…Both vaccines demonstrated broad protection against the most common RVA genotypes [18]. However, their efficacy is low especially on the African continent with diverse pool of strain types [19, 20]. G6P[14] strain detected in this study shares neither G- nor P-genotype with either of the two current vaccines.…”

Multiplexed one-step RT-PCR VP7 and VP4 genotyping assays for rotaviruses using updated primers

“…The described VP7 and VP4 typing assays have been shown to consistently and correctly genotype RVA strains belonging in published lineages and sub-lineages of the six common G- and five common P-genotypes (Esona et al, 2013; Esteban et al, 2010; Le et al, 2011; Magagula et al, 2014; Martella et al, 2011; Mascarenhas et al, 2010; Nyaga et al, 2014; Stupka et al, 2009, 2012). The advantages of these two gel-based multiplexed one-step genotyping RT-PCR protocols are: (1) they do not require specialized equipment; (2) laboratory personnel need only basic skills to follow the protocols; (3) improved differentiation of samples with mixed genotypes; (4) this approach involves less handling of samples, is less labor-intensive, and less prone to sample cross-contamination; and (5) other commercially available one-step RT-PCR kits such as the MyTaq™ one-step RT-PCR kit (Bioline) and the SuperScript ® III one-step RT-PCR System with Platinum ® Taq High Fidelity DNA Polymerase (Life Technologies) can be used in place of the Qiagen one-step RT-PCR kit (Qiagen).…”

“…Four hundred of these sequences were representatives of known lineages and sub-lineages of the five common VP4 genotypes (Donato et al, 2012; Magagula et al, 2014; Nakagomi et al, 2012; Nyaga et al, 2014), while 1400 were representatives of known lineages and sub-lineages of the six common VP7 genotypes (Donato et al, 2012; Esona et al, 2013; Magagula et al, 2014; Nakagomi et al, 2012; Nyaga et al, 2014; Stupka et al, 2009, 2012). The consensus sequences obtained from multiple alignments of the six most common RVA VP7 genotypes (G1, G2, G3, G4, G9 and G12) and five most common VP4 genotypes (P[4], P[6], P[8], P[9] and P[10]) were used to design oligonucleotide primers for specificVP7 and VP4 genotypes, respectively.…”