Whole-genome analyses of rotavirus strains circulating pre- and post- Rotateq™ vaccine introduction in Rwanda
Rasebotsa, Sebotsana Paula
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Children living in developing countries are constantly faced with the burden of diarrheal infections that account for over 1.6 million death cases globally. Rotavirus group A (RVA) has been identified as one of the viruses implicated in most viral-induced diarrhoeal infections in children less than five years worldwide. In Rwanda, over 3500 RVA related mortality cases were reported yearly prior to the implementation of the RotaTeq® vaccine in 2012 to overcome this burden, which led to a significant decrease in rotavirus infections. Africa has a huge diversity of rotavirus strains compared to other developed continents especially Europe and North America, thus requiring a deeper understanding of this phenomenon. This study aimed at characterizing all the 11-segments of RVA strains circulating in Rwanda pre- and post-vaccine introduction as part of the World Health Organization (WHO) supported African rotavirus pilot surveillance program. The study was based on 158 rotavirus positive samples that were collected from children presenting symptoms associated with rotavirus infection between 2011 and 2016. The rotavirus double-stranded ribonucleic acid (dsRNA) was extracted from the viral particles and converted into complementary deoxyribonucleic acid (cDNA) prior to library preparation for whole-genome sequencing with an Illumina MiSeq platform. Several bioinformatics tools were utilized to construct phylogenetic trees and the proteins structures. From the sequenced samples, 36 samples were identified as G1P strains, and five samples were reassortant strains. Ten G1P strains were identified pre-vaccine introduction while 26 were identified post-vaccine introduction. Thirty-five of the G1P strains expressed pure Wa-like genome constellations, while one of the strains that was identified in 2012 exhibited a genome constellation typical of a RotaTeq® vaccine strain. On the other hand, the five reassortant strains were identified post-vaccine introduction between 2013-2015. Whole-genome analysis revealed that the G4P, G9P and one G12P reassortant strains exhibited both the Wa-like and the DS-1-like genome constellations while two G12P strains had all the three genogroup constellations. Furthermore, the phylogenetic analysis of most of the G1P strains revealed that they segregated according to their vaccination status; strains identified pre-vaccine introduction clustered together while post-vaccine strains also formed a separate cluster. The five reassortant strains were closely related to human RVA strains in all the gene segments and RotaTeq® vaccine strains in the VP1, VP2, NSP2, NSP4, and NSP5 gene segments. Analysis of the neutralization epitopes and cytotoxic T-lymphocytes (CTL) of the G1P strains revealed multiple amino acid substitutions, with some changes influencing the change in polarity thus deemed to be radical in nature. A similar trend was also observed in the reassortant strains, with 27 amino acid substitutions in the VP7 epitope region and only three substitutions in the VP4 epitope region. Changes observed in these epitope regions have the potential of generating vaccine-escape mutants that may undermine the effectiveness of the rotavirus vaccine with time. Whole-genome sequencing has proven to provide information that could have been missed when looking only at the outer capsid proteins. It is thus important to continue conducting rotavirus whole-genome studies to unpack the hidden information behind the huge diversity of rotavirus strains in African countries such as Rwanda.