Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations]
Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014. Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selec...
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| Format: | Article |
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Wellcome
2018-11-01
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| Series: | Wellcome Open Research |
| Online Access: | https://wellcomeopenresearch.org/articles/3-150/v1 |
| _version_ | 1818495954250104832 |
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| author | Betty E. Owor Mike J. Mwanga Regina Njeru Robert Mugo Mwanajuma Ngama Grieven P. Otieno D.J. Nokes C.N. Agoti |
| author_facet | Betty E. Owor Mike J. Mwanga Regina Njeru Robert Mugo Mwanajuma Ngama Grieven P. Otieno D.J. Nokes C.N. Agoti |
| author_sort | Betty E. Owor |
| collection | DOAJ |
| description | Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014. Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%). Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period. Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks. These data will be useful in interpreting genotype patterns observed in the region during the vaccine era. |
| first_indexed | 2024-12-10T18:27:19Z |
| format | Article |
| id | doaj.art-134423b022b54121b672e853eca0674b |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-12-10T18:27:19Z |
| publishDate | 2018-11-01 |
| publisher | Wellcome |
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| spelling | doaj.art-134423b022b54121b672e853eca0674b2022-12-22T01:38:02ZengWellcomeWellcome Open Research2398-502X2018-11-01310.12688/wellcomeopenres.14908.116252Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations]Betty E. Owor0Mike J. Mwanga1Regina Njeru2Robert Mugo3Mwanajuma Ngama4Grieven P. Otieno5D.J. Nokes6C.N. Agoti7Epidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaEpidemiology and Demography, KEMRI Wellcome Trust Research Program, Kilifi, Kilifi, 80108, KenyaBackground: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014. Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%). Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period. Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks. These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.https://wellcomeopenresearch.org/articles/3-150/v1 |
| spellingShingle | Betty E. Owor Mike J. Mwanga Regina Njeru Robert Mugo Mwanajuma Ngama Grieven P. Otieno D.J. Nokes C.N. Agoti Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations] Wellcome Open Research |
| title | Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_full | Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_fullStr | Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_short | Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013 [version 1; peer review: 2 approved, 1 approved with reservations] |
| title_sort | molecular characterization of rotavirus group a strains circulating prior to vaccine introduction in rural coastal kenya 2002 2013 version 1 peer review 2 approved 1 approved with reservations |
| url | https://wellcomeopenresearch.org/articles/3-150/v1 |
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