Trends and Intensity of Human Rhinovirus Invasions in Kilifi, Coastal Kenya Over a Twelve-Year Period, 2007-2018

ABSTRACT Background: Human rhinovirus (HRV) is an ubiquitous pathogen and the principal etiologic agent of common cold. Despite the high frequency of HRV infections, data describing its long-term epidemiological patterns in a single population remain limited. Methods: We analysed 1,070 VP4/VP2 genomic region sequences obtained from samples collected between 2007-2018 from hospitalised paediatric patients (< 60 months) with acute respiratory disease in Kilifi County Hospital on the Kenya Coast. Results: Of 7,231 children enrolled, HRV was detected in 1,497 (20.7%) andVP4/VP2 sequences were recovered from 1,070 samples (71.5%). A total of 144 different HRV types were identified (67 HRV-A, 18 HRV-B and 59 HRV-C) and at any time-point, several types co-circulated with alternating predominance. Within types multiple genetically divergent variants were observed. Ongoing HRV infections appeared to be a combination of (i) persistent types (observed up to seven consecutive months), (ii) reintroduced genetically distinct variants and (iii) new invasions (average of 8 new types, annually). Conclusion: Sustained HRV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than prolonged circulation of locally established strains.