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Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

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Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
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Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South Africa
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South African Medical Research Council, Pretoria 0001, South Africa
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College of Medicine, Department of Biomedical Sciences, Faculty of Biomedical Sciences and Health Professions, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi
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Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, P.O. Box 23350, Seattle, WA 98109, USA
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Faculty of Health Sciences, University of Buea, P.O. Box 63, Buea, Cameroon
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Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG581, Legon, Ghana
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Center for Global Vaccine Research, Institute of Infection, Liverpool L697BE, UK
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Veterinary and Ecological Sciences, University of Liverpool, Liverpool L697BE, UK
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Malawi-Liverpool-Wellcome Trust Clinical Research Program, Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre 312225, Malawi
*
Author to whom correspondence should be addressed.
Vaccines 2020, 8(4), 609; https://doi.org/10.3390/vaccines8040609
Received: 7 September 2020 / Revised: 8 October 2020 / Accepted: 13 October 2020 / Published: 14 October 2020
(This article belongs to the Section Vaccines against Infectious Diseases)
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. View Full-Text
Keywords: evolution; rotavirus strains; Wa-like constellation; whole-genome; lineages evolution; rotavirus strains; Wa-like constellation; whole-genome; lineages
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MDPI and ACS Style

Mwangi, P.N.; Mogotsi, M.T.; Seheri, M.L.; Mphahlele, M.J.; Peenze, I.; Esona, M.D.; Kumwenda, B.; Steele, A.D.; Kirkwood, C.D.; Ndze, V.N.; Dennis, F.E.; Jere, K.C.; Nyaga, M.M. Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years. Vaccines 2020, 8, 609. https://doi.org/10.3390/vaccines8040609

AMA Style

Mwangi PN, Mogotsi MT, Seheri ML, Mphahlele MJ, Peenze I, Esona MD, Kumwenda B, Steele AD, Kirkwood CD, Ndze VN, Dennis FE, Jere KC, Nyaga MM. Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years. Vaccines. 2020; 8(4):609. https://doi.org/10.3390/vaccines8040609

Chicago/Turabian Style

Mwangi, Peter N., Milton T. Mogotsi, Mapaseka L. Seheri, M. J. Mphahlele, Ina Peenze, Mathew D. Esona, Benjamin Kumwenda, A. D. Steele, Carl D. Kirkwood, Valantine N. Ndze, Francis E. Dennis, Khuzwayo C. Jere, and Martin M. Nyaga 2020. "Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years" Vaccines 8, no. 4: 609. https://doi.org/10.3390/vaccines8040609

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