Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years
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<sup>®</...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-10-01
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| Series: | Vaccines |
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| Online Access: | https://www.mdpi.com/2076-393X/8/4/609 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Peter N. Mwangi |
| collection | DOAJ |
| description | 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<sup>®</sup> 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<sup>®</sup> 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<sup>®</sup> 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. |
| first_indexed | 2024-03-10T15:37:24Z |
| format | Article |
| id | doaj.art-5a95a395347a4c1fbf3e854140027f9a |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-10T15:37:24Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-5a95a395347a4c1fbf3e854140027f9a2023-11-20T17:05:58ZengMDPI AGVaccines2076-393X2020-10-018460910.3390/vaccines8040609Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 YearsPeter N. Mwangi0Milton T. Mogotsi1Mapaseka L. Seheri2M. Jeffrey Mphahlele3Ina Peenze4Mathew D. Esona5Benjamin Kumwenda6A. Duncan Steele7Carl D. Kirkwood8Valantine N. Ndze9Francis E. Dennis10Khuzwayo C. Jere11Martin M. Nyaga12Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South AfricaNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South AfricaDiarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South AfricaDiarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South AfricaDiarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South AfricaDiarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, South AfricaCollege of Medicine, Department of Biomedical Sciences, Faculty of Biomedical Sciences and Health Professions, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, MalawiEnteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, P.O. Box 23350, Seattle, WA 98109, USAEnteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, P.O. Box 23350, Seattle, WA 98109, USAFaculty of Health Sciences, University of Buea, P.O. Box 63, Buea, CameroonNoguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG581, Legon, GhanaCenter for Global Vaccine Research, Institute of Infection, Liverpool L697BE, UKNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South AfricaRotavirus 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<sup>®</sup> 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<sup>®</sup> 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<sup>®</sup> 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.https://www.mdpi.com/2076-393X/8/4/609evolutionrotavirus strainsWa-like constellationwhole-genomelineages |
| spellingShingle | 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 Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years Vaccines evolution rotavirus strains Wa-like constellation whole-genome lineages |
| title | Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years |
| title_full | Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years |
| title_fullStr | Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years |
| title_full_unstemmed | Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years |
| title_short | Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years |
| title_sort | whole genome in silico analysis of south african g1p 8 rotavirus strains before and after vaccine introduction over a period of 14 years |
| topic | evolution rotavirus strains Wa-like constellation whole-genome lineages |
| url | https://www.mdpi.com/2076-393X/8/4/609 |
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