Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

Mike J Mwanga, Betty E Owor, John B Ochieng, Mwanajuma H Ngama, Billy Ogwel, Clayton Onyango, Jane Juma, Regina Njeru, Elijah Gicheru, Grieven P Otieno, Sammy Khagayi, Charles N Agoti, Godfrey M Bigogo, Richard Omore, O Yaw Addo, Seheri Mapaseka, Jacqueline E Tate, Umesh D Parashar, Elizabeth Hunsperger, Jennifer R VeraniRobert F Breiman, D James Nokes

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


BACKGROUND: Kenya introduced the monovalent G1P [8] 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 [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (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 [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-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.

Original languageEnglish
Pages (from-to)504
JournalBMC Infectious Diseases
Issue number1
Publication statusPublished - 13 Jul 2020


  • Child
  • Child, Preschool
  • Enzyme-Linked Immunosorbent Assay
  • Feces/virology
  • Female
  • Gastroenteritis/etiology
  • Genotype
  • Humans
  • Immunization Schedule
  • Infant
  • Kenya/epidemiology
  • Male
  • Phylogeny
  • Prevalence
  • Rotavirus/genetics
  • Rotavirus Infections/epidemiology
  • Rotavirus Vaccines/adverse effects
  • Vaccination
  • Vaccines, Attenuated/adverse effects


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