Virology

Permanent URI for this community

http://hdl.handle.net/11660/12643

Browse

Browsing Virology by Title

Now showing 1 - 1 of 1
  • Thumbnail Image
    ItemOpen Access
    Whole genome analysis of Rwandan G9P [8] rotavirus strains pre- and post-RotaTeq® vaccine introduction
    (University of the Free State, 2023) Potgieter, Robyn-Lee; Nyaga, M. M.; Mwangi, P. N.
    Children under the age of five who live in developing countries, are consistently exposed to the threat posed by Group A rotaviruses (RVA), despite the introduction of vaccines. Prior to the introduction of the rotavirus vaccine, over 3500 children in Rwanda died per year due to RVA associated disease. Therefore, the RotaTeq® vaccine was implemented in May 2012 to alleviate the disease burden. This led to a significant decline in rotavirus infections and fatalities in this region. Considering the extensive diversity of rotavirus strains found in Africa, additional data is necessary to assess the impact of vaccine introduction on RVA strains that are currently circulating in Rwanda. This study aimed to perform whole genome analysis of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. This was a descriptive observational experimental study which was executed at the University of the Free State - Next Generating Sequencing (UFS-NGS) Unit at the Faculty of Health Sciences, Bloemfontein, South Africa. This study formed part of a larger project aimed at addressing the Terms of Reference (ToRs) for Technical Service Agreement (TSA) between the World Health Organisation (WHO) and the UFS-NGS Unit. This study involved 30/158 faecal samples from Rwandan children that had already been conventionally genotyped as G9P[8] (based on the outer capsid proteins), as part of routine surveillance by World Health Organization African Regional Office (WHO/AFRO). A total of 23 samples were retrieved from the period prior to vaccination, while seven samples were used from the period following vaccination. To conduct whole genome sequencing on the Illumina MiSeq® platform, double-stranded RNA (dsRNA) was isolated from the faecal samples and complementary DNA (cDNA) was synthesised from the extracted material using the Maxima Kit. Subsequently, library preparation was carried out utilising the NextEra XT Kit. Following this, a variety of bioinformatics tools were employed to analyse the study data. Whole genome analysis revealed that all 30 of the Rwandan G9P[8] study strains displayed the characteristic Wa-like constellation. Phylogenetic analysis in the form of maximum likelihood phylogenetic trees were constructed and revealed that the Rwandan study strains were clustering closely together. It was observed that three study strains from the post- vaccination study era were clustering distinctly from the rest of the G9P[8] study strains. The ranges of high similarity between nucleotides in all 11 genome segments agreed with the phylogenetic relationships that were observed. Amino acid differences were observed in the neutralisation epitope regions of the VP4 and VP7 genome segments compared to the Rwandan G9P[8] study strains and the RotaTeq® vaccine strain. These changes were mainly seen in the post- vaccine study strains and may lead to the escape of vaccine mutants, which could potentially affect the efficacy of the vaccine. The protein surfaces displayed these amino acid variations, as observed in three-dimensional (3D) protein structures. Analysis of selection pressures revealed that ten of the genome segments were subject to purifying selection, except for the VP4 genome segment, where two sites were subject to positive selection, which could influence the protein’s evolutionary dynamics. To unpack the unknown information surrounding rotavirus strain diversity, evolution, and the epidemiology of circulating RVA strains in Rwanda during the pre- and post- vaccine introduction periods, it remains important to continue performing whole genome studies in this region.