INTRODUCTION:
Despite global rotavirus vaccination efforts, rotavirus remains a leading cause of childhood mortality from acute gastroenteritis. Kenya introduced Rotarix vaccine into her National immunization Program in 2014. However, the country switched to Rotavac vaccine in January 2023. This study investigated rotavirus vaccine effectiveness, rotavirus disease severity and burden in Mukuru urban informal settlement in Nairobi, Kenya following the country’s transition to the new vaccine.

METHODS:
We conducted an observational study recruiting children under five years of age presenting with acute diarrhea at selected health facilities within Mukuru urban informal settlement in Nairobi, from October 2023 to November 2024. Demographic, clinical and card-confirmed immunization data were collected. Detection and genotyping of rotavirus from stool samples was conducted using TaqMan array card PCR and multiplexed semi-nested RT-PCR. Vaccine effectiveness was estimated using a post-hoc test-negative case-control analysis.

RESULTS:
Out of 353 diarrheal cases, 19.5% tested positive for rotavirus. Rotavirus was highest among children aged 12-23 months (24.4%). Rotavirus prevalence was significantly lower among vaccinated children compared with unvaccinated children (p = 0.044). Severe gastroenteritis was observed in majority of the rotavirus-positive cases at 46.4%. Genotype G2P[4] predominated with a notable increase in G3P[8] and the detection of equine-like strains for the first time in this setting. Estimated Rotavac vaccine effectiveness was 74.1% and overall rotavirus vaccine effectiveness was 57.6%.

CONCLUSIONS:
Rotavirus remains a significant cause of gastroenteritis among children in urban informal settlements in Kenya despite rotavirus vaccination. The circulation of diverse and emerging strains underscores the need for continued molecular surveillance to monitor vaccine performance and guide future immunization strategies.