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Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

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Owor, Betty E., Mwanga, Mike J., Njeru, Regina, Mugo, Robert, Ngama, Mwanajuma, Otieno, Grieven P., Nokes, D. James and Agoti, C.N. (2018) Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013. Wellcome Open Research, 3 . 150. doi:doi:10.12688/wellcomeopenres.14908.1

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Abstract

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

Item Type: Journal Article
Subjects: Q Science > QR Microbiology > QR355 Virology
R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Rotaviruses -- Vaccination -- Kenya
Journal or Publication Title: Wellcome Open Research
Publisher: F1000Research
ISSN: 2398-502X
Official Date: 2018
Dates:
DateEvent
2018UNSPECIFIED
Date of first compliant deposit: 7 May 2019
Volume: 3
Article Number: 150
DOI: doi:10.12688/wellcomeopenres.14908.1
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
RIPEKGAVI Alliancehttp://dx.doi.org/10.13039/100001125
UNSPECIFIEDEmory Universityhttp://dx.doi.org/10.13039/100006939
UNSPECIFIEDCenters for Disease Control and Preventionhttp://dx.doi.org/10.13039/100000030
UNSPECIFIEDKenya Medical Research Institutehttp://viaf.org/viaf/151310353
203077 Wellcome Trusthttp://dx.doi.org/10.13039/100010269
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
UNSPECIFIEDCentre for Geographic Medicine Research-Coast, KilifiUNSPECIFIED

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