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Volume 8, Issue 4

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

Abstract

The transient upsurge of G2P[4] group A rotavirus (RVA) after Rotarix vaccine introduction in several countries has been a matter of concern. To gain insight into the diversity and evolution of G2P[4] strains in South Africa pre- and post-RVA vaccination introduction, whole-genome sequencing was performed for RVA positive faecal specimens collected between 2003 and 2017 and samples previously sequenced were obtained from GenBank (=103; 56 pre- and 47 post-vaccine). Pre-vaccine G2 sequences predominantly clustered within sub-lineage IVa-1. In contrast, post-vaccine G2 sequences clustered mainly within sub-lineage IVa-3, whereby a radical amino acid (AA) substitution, S15F, was observed between the two sub-lineages. Pre-vaccine P[4] sequences predominantly segregated within sub-lineage IVa while post-vaccine sequences clustered mostly within sub-lineage IVb, with a radical AA substitution R162G. Both S15F and R162G occurred outside recognised antigenic sites. The AA residue at position 15 is found within the signal sequence domain of Viral Protein 7 (VP7) involved in translocation of VP7 into endoplasmic reticulum during infection process. The 162 AA residue lies within the hemagglutination domain of Viral Protein 4 (VP4) engaged in interaction with sialic acid-containing structure during attachment to the target cell. Free energy change analysis on VP7 indicated accumulation of stable point mutations in both antigenic and non-antigenic regions. The segregation of South African G2P[4] strains into pre- and post-vaccination sub-lineages is likely due to erstwhile hypothesized stepwise lineage/sub-lineage evolution of G2P[4] strains rather than RVA vaccine introduction. Our findings reinforce the need for continuous whole-genome RVA surveillance and investigation of contribution of AA substitutions in understanding the dynamic G2P[4] epidemiology.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): G2P[4] group A rotavirus strains , rotavirus , sub-lineages and whole-genome analysis
Funding
This study was supported by the:
  • National Research Foundation (Award (NRF-120814))
    • Principle Award Recipient: MartinM Nyaga
  • Poliomyelitis Research Foundation (Award (PRF-19/16))
    • Principle Award Recipient: MartinM Nyaga
  • South African Medical Research Council (Award Self-Initiated Research grant (SIR),)
    • Principle Award Recipient: MartinM Nyaga
  • Bill and Melinda Gates Foundation (Award BMGF-OPP1180423_2017)
    • Principle Award Recipient: MartinM Nyaga
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003–2017
M Gen 8, 000809 (2022); https://doi.org/10.1099/mgen.0.000809
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