BACKGROUND: Kenya introduced the monovalent G1P  Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction.
METHODS: Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.
RESULTS: We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P  (45.8%), G8P  (15.8%), G9P  (13.2%), G2P  (7.0%) and G3P  (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P  (52.1%), G2P  (20.7%) and G3P  (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P  (7.0 to 20.7%, P < .001) and G3P  (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P  (15.8 to 0.4%, P < .001) and G9P  (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P , revealed circulation of strains of lineages G1-I, G1-II and P -1, P -III and P -IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.
CONCLUSION: Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.
- Child, Preschool
- Enzyme-Linked Immunosorbent Assay
- Immunization Schedule
- Rotavirus Infections/epidemiology
- Rotavirus Vaccines/adverse effects
- Vaccines, Attenuated/adverse effects