Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

Abstract

Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the pre-vaccine period. Therefore, Rotarix® did not appear to have an impact on the amino acid differences in the antigenic regions of South African post-vaccine G1P[8] strains. However, continued whole-genome surveillance of RVA strains to decipher genetic changes in the post-vaccine period remains imperative.

Comparative whole genome analysis reveals re-emergence of typical human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi

“…Previous studies have shown that the VP5* and VP8* outer capsid proteins play a significant role in inducing neutralising antibodies against rotaviruses (Ludert et al 2002;Park et al 2021;Ruggeri and Greenberg 1991;Zhao et al 2015). The VP5* protein of the Malawian G3P[8] strains were 100% conserved when compared to that of Rotarix vaccine, consistent with previous studies that have reported that the VP5* is a highly conserved protein (Rasebotsa et al 2020;Mwangi et al 2020). However, we identified E150D nonsynonymous substitutions within the VP8*-1 antigenic region and S125N, S131R and N135D substitutions within VP8*-3 antigenic region when we compared the VP4 (VP8*sub-unit) segments of our G3P [8] strains to that of the strain used in the Rotarix rotavirus vaccine.…”

“…However, we identified E150D nonsynonymous substitutions within the VP8*-1 antigenic region and S125N, S131R and N135D substitutions within VP8*-3 antigenic region when we compared the VP4 (VP8*sub-unit) segments of our G3P[8] strains to that of the strain used in the Rotarix rotavirus vaccine. These substitutions have been associated with lineage III strains that are currently predominant in eastern and southern African countries where the Rotarix vaccine is used (Rasebotsa et al 2020; Mwangi et al 2020; Maringa et al 2021). We speculate that the structural changes we observed in the VP8*-1 and VP8*-3 antigenic regions could reduce the binding of the vaccine-induced antibodies thereby reducing the vaccine effectiveness.…”

“…A 1% 0.5 X Tris borate ethylenediaminetetraacetic acid (TBE) agarose gel (Sigma-Aldrich, Dorset, UK) stained with SYBR green (Sigma-Aldrich, Dorset, UK) electrophoresis was used to check the integrity of the extracted dsRNA and was visualised on a BioDoc transilluminator. Complementary DNA (cDNA) was synthesised using the Maxima H Minus Double-Stranded cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA) and purification was done using the MSB ® Spin PCRapace (Stratec) Purification Kit as previously described (Mwangi et al 2020; Rasebotsa et al 2020).…”

“…The fragment size and quality of libraries were assessed on Agilent 2100 BioAnalyzer ® (Agilent Technologies, Waldbronn, Germany). Paired end nucleotide sequences were then generated on a MiSeq ® sequencer (Illumina, San Diego, CA, USA) at the University of the Free State-Next Generation Sequencing (UFS-NGS) Unit, Bloemfontein, South Africa as previously described (Mwangi et al 2020; Rasebotsa et al 2020).…”

Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003–2017

“…The extracted viral dsRNA was subjected to cDNA synthesis using the Maxima H Minus Double Stranded Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, USA), as described previously [ 41 ]. The DNA libraries were prepared utilizing the NexteraXT DNA Library Preparation Kit (Illumina, San Diego, CA, USA) as per the manufacturer’s instructions.…”