Prevalence and molecular epidemiology of rotavirus gastroenteritis among children in Nairobi’s urban informal settlements following introduction of the Rotavac® vaccine

BACKGROUND: Rotavirus is the leading cause of acute gastroenteritis among children under five years of age globally. In Kenya, rotavirus vaccination was introduced in 2014 using Rotarix® (G1P[8]), with a subsequent national transition to Rotavac® (G9P[11]) vaccine, in 2023. Evidence on post-introduction rotavirus disease burden, strain diversity, and Rotavac® vaccine effectiveness in Kenya remains limited. This study assessed the burden of rotavirus gastroenteritis and vaccine effectiveness of the rotavirus vaccine among children under five years of age in Nairobi's urban slums, after the rollout of the Rotavac® vaccine. METHODS: In this cross-sectional surveillance study, 353 stool samples were collected from children under five years of age presenting with acute gastroenteritis at selected health facilities in Mukuru informal settlement, Nairobi, between October 2023 and November 2024. The samples were analyzed using TaqMan array card PCR and multiplexed semi-nested RT-PCR. Vaccine effectiveness for overall rotavirus vaccination and Rotavac® specifically was estimated using a post-hoc test-negative case-control analysis. RESULTS: Rotavirus was detected in 19.5% (69/353; 95% CI 15.5-24.1%) of the samples. The highest detection occurred among children aged 12-23 months at 24.4% (30/123; 95% CI 17.1-33.0%), with significant differences across age groups (p = 0.023). Rotavirus prevalence was significantly lower among vaccinated children 18.4% (60/327; 95% CI 14.3-23.0%), compared with unvaccinated children 34.6% (9/26; 95% CI 17.2-55.7%) (p = 0.044). The predominant strain was G2P[4] (29.0%; 20/69), which also dominated among the vaccinated children (31.7%; 19/60), while G12P[6] was most frequent among unvaccinated children (33.3%; 3/9). Newly detected strains included G2P[8] and G12P[8], and two equine-like strains (G3P[8]eG3 and G2G3P[4]P[8]eG3). Short electropherotypes predominated. First-dose vaccine coverage was 92.6% (327/353) while the last-dose coverage was 76.2% (269/353). Estimated Rotavac® vaccine effectiveness was 74.1% (95% CI 16.3-92.0%), and overall rotavirus vaccine effectiveness was 57.6% (95% CI 18.1-99.8%). CONCLUSION: Rotavirus remains a significant cause of gastroenteritis among children in Nairobi's urban informal settlements. The circulation of diverse and emerging strains underscores the need for continued molecular surveillance to monitor vaccine performance and guide future immunization strategies.