Rotaviruses are primary etiological agents of gastroenteritis in young children. In Kenya, G1P8 monovalent vaccine (Rotarix) was introduced effective July 2014, for mandatory vaccination of all newborns at 6 and 10 weeks of age. Since then, no studies have been done to identify the rotavirus genotypes circulating in Nairobi County, Kenya, following the vaccine introduction, hence the post vaccine genotype distribution is not known.
This study aimed at determining the post-vaccine occurrence of rotavirus genotypes in children <5 in Nairobi County, Kenya.
Stool samples were collected from children presenting with diarrhea where vaccination status was card-confirmed. We analyzed fecal samples for rotavirus antigen using a commercial enzyme immunoassay (EIA) kit, followed by characterization by PAGE, RT-PCR and nested PCR-genotyping targeting the most medically important genotypes.
The strains observed included G1P[8] (38.8%), G9P[8] (20.4%), G2P[4] (12.2%), G3[P4] (6.1%), G2P[6] (4.1%), and G9P[6] at 4.1%. Mixed genotype constellations G3P[4][8] were also detected at 4.1%. Remarkably, we observed an increased prevalence of G2 genotypes, revealing a change in genetic diversity of rotavirus strains. While the dominance of G1P[8] decreased after vaccination, we observed an upsurge in G2P[4] (12.2%) and G9P[8] (20.4%). Additionally, G3[P4] (6.1%) and G2P[6] (4.1%) prevalence increased along the three years of study.
The results inform the need for robust longitudinal surveillance and epidemiologic studies to assess long-term interaction between rotavirus vaccine and strain ecology.

Copyright © 2020. Published by Elsevier Ltd.