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

doi:10.3390/vaccines8040609

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains Before and After Vaccine Introduction Over A Period of 14 Years

Vaccines (Basel). 2020 Oct 14;8(4):609. doi: 10.3390/vaccines8040609.

Authors

Affiliations

¹ Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
² Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South Africa;.
³ South African Medical Research Council, Pretoria 0001, South Africa.
⁴ College of Medicine, Department of Biomedical Sciences, Faculty of Biomedical Sciences and Health Professions, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi.
⁵ Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, P.O Box 23350, Seattle, WA 98109, USA.
⁶ Faculty of Health Sciences, University of Buea, P.O Box 63, Buea, Cameroon.
⁷ Noguchi Memorial Institute for Medical Research, University of Ghana, P.O Box LG581, Legon, Ghana.
⁸ Center for Global Vaccine Research, Institute of Infection, Liverpool L697BE, UK.
⁹ Veterinary and Ecological Sciences, University of Liverpool, Liverpool L697BE, UK.
¹⁰ Malawi-Liverpool-Wellcome Trust Clinical Research Program/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre 312225, Malawi.

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.

Keywords: Wa-like constellation; evolution; lineages; rotavirus strains; whole-genome.

Grants and funding

201945/Z/16/Z/WT_/Wellcome Trust/United Kingdom