Group A rotaviruses circulating prior to a national immunization programme in Nigeria: Clinical manifestations, high G12P[8] frequency, intra‐genotypic divergence of VP4 and VP7

Abstract

Nigeria having approximately 50 000 Rotavirus A (RVA) deaths annually is yet to introduce RVA vaccine into routine national immunization; therefore surveillance of RVA strains circulating before vaccine introduction is essential in evaluating impact of the intervention. Stool samples and sociodemographic data of diarrhoeic children, <5 years were collected between August 2012 and December 2013. While a high prevalence of RVA infection (47.6%; 49/103) was observed by quantitative reverse transcription real time PCR, only 25% (26/103) had high RVA genome concentrations and were antigen positive. G and P types were obtained for 31 and 37 samples respectively. G12P[8] strains were predominant (30.6%; 16/31); Other genotypes found included G9, G3, G2 and P[4], P[6], P[8]. A G12 + G2/P[8] + P[6] mixed infection was detected. The P[8] genotype showed divergence with strains distributed in lineage III and IV. Compared to the vaccines, changes in antigenic sites of VP8* and VP7 were found. The finding of the G2P[6] genotype combination and emergence of G12 strains support observations in most of the recent RVA studies from Africa. P[6] is common in many African countries, in contrast to countries in Europe and the Americas. In conclusion, this study shows the circulation of other RVA genotypes compared to the common RVA genotypes in Nigeria. PCR results should be interpreted with caution to avoid significant bias from samples with low RVA genome concentrations. These findings provide important information on the detection and molecular epidemiology of RVA prior to vaccination and contribute as a baseline for future evaluations after possible vaccine introduction.

Phylogeography and Evolutionary analysis of African Rotavirus A genotype G12 reveals district genetic diversification within Lineage III

“…The evolutionary rate observed in our study hovers around the global rate previously reported for rotavirus genotype G12 in 2010 (Matthijnssis et al, 2010), this shows that the African strains have a steady mutation rate but possess the potential to diversify rapidly through molecular evolution. This can also be due to repeated outbreaks in populated communities, giving opportunity for recombination and reassortment (Gomez et al, 2014, Japhet et al, 2018. The time to most recent common ancestor T MRC, was calculated to be 16.8 years, 95% HPD (15.0 -25.54), dating back to around mid-1996.…”

Molecular Characteristics of Rotavirus Genotypes Circulating in the South of Benin, 2016-2018

“…At country level in West Africa, before vaccine introduction, Ghana reported G1P [8] (20%) as the predominant genotype [17], but others genotypes such as G6P [6] was found to be medically important in Burkina Faso [18], G12P [8] in Côte d'Ivoire [19] and G4P [8] and G12P [8] in Nigeria [20,21]. During the post vaccine period, Ghana reported G1P [8] as the fourth common genotype detected with a rate of 8.0% [17].…”

“…Commonly detected at low rates in Africa, over the past decade, G12P [8] has been isolated as a predominant genotype in some countries such as Côte d'Ivoire and Nigeria in the pre-vaccination period [19,21], and Ghana in the post-vaccination period [17]. Also, according to some studies, G12P [8] may come from a reassortment between human and pig rotavirus strains [31].…”

Molecular characteristics of rotavirus genotypes circulating in the south of Benin, 2016-2018

“…At country level in West Africa, before vaccine introduction, Ghana reported G1P [8] (20%) as the predominant genotype (18), but others genotypes such as G6P [6] was found to be medically important in Burkina Faso (19), G12P [8] in Côte d'Ivoire (20) and G4P [8] and G12P [8] in Nigeria (21,22). During the post vaccine period, Ghana reported G1P [8] as the fourth common genotype detected with a rate of 8.0% (18).…”