Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda

Abstract

Rwanda was the first low-income African country to introduce RotaTeq vaccine into its Expanded Programme on Immunization in May 2012. To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre-and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped with conventional RT-PCR based methods and whole genome sequenced using the Illumina MiSeq platform. From a pool of samples sequenced (n = 158), 36 were identified as G1P[8] strains (10 pre-vaccine and 26 post-vaccine), of which 35 exhibited a typical Wa-like genome constellation. However, one post vaccine strain, RVA/Human-wt/RWA/UFS-NGS:MRC-DPRU442/2012/ G1P[8], exhibited a RotaTeq vaccine strain constellation of G1-P[8]-I2-R2-C2-M2-A3-N2-T6-E2-H3, with most of the gene segments having a close relationship with a vaccine derived reassortant strain, previously reported in USA in 2010 and Australia in 2012. The study strains segregated into two lineages, each containing a paraphyletic pre-and post-vaccine introduction sub-lineages. In addition, the study strains demonstrated close relationship amongst each other when compared with globally selected group A rotavirus (RVA) G1P[8] reference strains. For VP7 neutralization epitopes, amino acid substitutions observed at positions T91A/V, S195D and M217T in relation to the RotaTeq vaccine were radical in nature and resulted in a change in polarity from a polar to non-polar molecule, while for the VP4, amino acid differences at position D195G was radical in nature and resulted in a change in polarity from a polar to non-polar molecule. The polarity change at position T91A/V of the neutralizing antigens might play a role in generating vaccine-escape mutants, while substitutions at positions S195D and M217T may be due to natural fluctuation of the RVA. Surveillance of RVA at whole genome level will enhance further assessment of vaccine impact on circulating strains, the frequency of reassortment events under natural conditions and epidemiological fitness generated by such events. Group A rotavirus is a significant viral etiological agents of acute gastroenteritis (AGE) resulting in approximately 125,000 deaths annually in children under 5 years worldwide 1. Rwanda rolled out the RotaTeq (Merck and Co., Whitehouse Station, NJ, USA) vaccine into her Expanded Program on Immunization in May 2012 and the vaccination coverage rate has been consistently high over the years > 95% since 2013, resulting in significant

Epidemiology of major entero-pathogenic viruses and genetic characterization of Group A rotaviruses among children (≤5 years) with acute gastroenteritis in eastern India, 2018–2020

“…G1 rotavirus strains circulating endemically between 2011 and 2016 were found to harbour most of these substitutions (Mullick et al, 2014; Nayak et al, 2019). For three lineage I strain clustering differentially, substitution of threonine by isoleucine at position 87 was observed in this study similar to certain G1P[8] strains circulating in Rwanda in 2015 (Rasebotsa et al, 2020). Though there is no proper evidence of compromised vaccine efficacy as a result of amino acid substitutions at the aforementioned epitopes, few studies have highlighted that pre‐existing antibodies that block amino acid residues 94, 213 and 217 of G1 type of rotaviruses are protective in case of re‐infection with a more virulent rotavirus strain (Green & Kapikian, 1992; O'Ryan et al, 1994).…”

Detection and Molecular Characterization of Rotavirus Infections in Children and Adults with Gastroenteritis from Vojvodina, Serbia

“…Aside from that, another amino acid difference was located on the surface of the protein structure at position 195 (Asn/Asp to Gly). The amino acid changes identified at positions N113D, S131R and N135D in this study are previously described by a few search groups from Rwanda [ 42 ] and Zambia [ 43 ]. They resulted in polarity changes and play a role in RV’s escape from host immunity.…”

“…Compared with the VP7 G1 component of RotaTeq™ vaccine, all of Serbian G1 strains had an amino acid substitution at position 97 (Asp to Glu) and 147 (Ser to Asn) which refer to differences in the electrostatic charge distribution. These variations are known neutralization escape mutation sites and have been described among G1 strains around the world [ 42 , 43 ]. Additionally, few single-point mutations occurred in the other two G1 strains in the study.…”

High Prevalence of Coinfecting Enteropathogens in Suspected Rotavirus Vaccine Breakthrough Cases

“…Since rotavirus genotype diversity changes temporally, and its segmented genome makes it prone to reassortments, unusual genotype constellations can emerge and escape vaccine-induced immunity ( 65 ). Especially following the mass introduction of rotavirus vaccines, selection of vaccine escape mutants has been a concerning issue ( 66 – 68 ). Our investigation of rotavirus genotypes in the suspected breakthrough infections revealed a pattern similar to that in previous observations, with common detection of Wa and DS-1-like genotype constellations and a lack of evidence of possible vaccine escape mutants ( 6 ).…”