Spatio-temporal distribution of rhinovirus types in Kenya: A retrospective analysis, 2014

Rhinoviruses (RVs) are one of the most commonly detected viruses in people with acute respiratory illness (ARI). Despite their significant disease burden, RV epidemiology at national levels is underexplored. The circulation patterns of RV types throughout a population and the role of virus genotype in this distribution are ill-defined. We generated 803 VP4/VP2 gene sequences from rhinovirus-positive samples collected from ARI patients, including both in-patient and outpatient cases, between 1 ^st January and 31 ^st December 2014 from eleven surveillance sites across Kenya and used phylogenetics to characterise virus introductions and spread. RVs were detected throughout the year, with the highest detection rates observed from January to March and June to July. We detected a total of 114 of the 169 currently classified types. Our analysis revealed numerous virus introductions into Kenya characterized by local expansion and extinction, and extensive spatial mixing of types within the country due to the widespread transmission of the virus after an introduction. This work demonstrates that in a single year, the circulation of rhinovirus in Kenya was characterized by substantial genetic diversity, multiple introductions, and extensive geographical spread.