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
Affiliations
Peter N. Mwangi
Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
Milton T. Mogotsi
Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
Mapaseka L. Seheri
Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South Africa
M. Jeffrey Mphahlele
Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South Africa
Ina Peenze
Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South Africa
Mathew D. Esona
Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South Africa
Benjamin Kumwenda
College of Medicine, Department of Biomedical Sciences, Faculty of Biomedical Sciences and Health Professions, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi
A. Duncan Steele
Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, P.O. Box 23350, Seattle, WA 98109, USA
Carl D. Kirkwood
Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, P.O. Box 23350, Seattle, WA 98109, USA
Valantine N. Ndze
Faculty of Health Sciences, University of Buea, P.O. Box 63, Buea, Cameroon
Francis E. Dennis
Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG581, Legon, Ghana
Khuzwayo C. Jere
Center for Global Vaccine Research, Institute of Infection, Liverpool L697BE, UK
Martin M. Nyaga
Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
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.
