Investigating Origins and Spread of Human Rhinovirus in Kilifi, Rural Coastal Kenya by Analysis of Molecular Sequence Data

Abstract

Human rhinovirus (HRV) is recognised as the leading cause of upper respiratory tract infections, resulting in a significant socio-economic and public health burden. Understanding of HRV transmission in communities living in low-income settings as well as their spatial-temporal patterns is currently limited. This study characterized HRV types in circulation, their origins, spread and persistence within the Kilifi Health and Demographic Surveillance System (KHDSS), Coastal Kenya. Nasopharyngeal swab (NPS) samples were collected from patients aged >7days presenting with symptoms of acute respiratory infection (ARI) at ten health facilities across a Health and Demographic Surveillance System between December 2015 and May 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region (~ 400 bp) of the positive samples sequenced by Sanger method. Phylogenetic analysis was used to determine the HRV types and their genetic diversity. Of 2,150 NPS samples collected, HRV was detected in 423 of which, 306 were successfully sequenced in the VP4/VP2 genome region. HRV species A, B and C were identified in 151, 15 and 140 samples, respectively. In total, 56 HRV types were determined: 33, 4 and 19 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of occurrence (ranging from 1-5 months) and of peak occurrence most commonly in March to May. Spatially, identical HRV types occurred over a wide distance at similar times. This study records a high prevalence of HRV in outpatient presentations exhibiting remarkably high type diversity in this low-income setting. Patterns of occurrence suggest frequent and independent invasion of different HRV types into the KHDSS. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread of types or multiple invasion of the same HRV type.