Whole genome in-silico analysis of south african G1P[8] rotavirus strains before and after vaccine introduction over a period of 14 years

Peter N. Mwangi, Milton T. Mogotsi, Mapaseka L. Seheri, M. Jeffrey Mphahlele, Ina Peenze, Mathew D. Esona, Benjamin Kumwenda, A. Duncan Steele, Carl D. Kirkwood, Valantine N. Ndze, Francis E. Dennis, Khuzwayo C. Jere, Martin M. Nyaga*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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 preand 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.

Original languageEnglish
Article number609
Pages (from-to)1-20
Number of pages20
JournalVaccines
Volume8
Issue number4
DOIs
Publication statusPublished - Dec 2020

Keywords

  • Evolution
  • Lineages
  • Rotavirus strains
  • Wa-like constellation
  • Whole-genome

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