Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007-2018.

John Mwita Morobe,Everlyn Kamau,Martha M Luka,Robinson Cheruiyot,Martin Mutunga,Nickson Murunga,Winfred Gatua,Calleb Odundo,D James Nokes,Charles N Agoti,Clement Lewa

doi:10.1093/ofid/ofab571

John Mwita Morobe, Everlyn Kamau + Show 9 more

Open Access

https://doi.org/10.1093/ofid/ofab571

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Abstract

BackgroundRhinoviruses (RVs) are ubiquitous pathogens and the principal etiological agents of common cold. Despite the high frequency of RV infections, data describing their long-term epidemiological patterns in a defined population remain limited.MethodsHere, we analyzed 1070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya coast. The samples were collected between 2007 and 2018 from hospitalized pediatric patients (<60 months of age) with acute respiratory illness.ResultsOf 7231 children enrolled, RV was detected in 1497 (20.7%) and VP4/VP2 sequences were recovered from 1070 samples (71.5%). A total of 144 different RV types were identified (67 Rhinovirus A, 18 Rhinovirus B, and 59 Rhinovirus C) and at any month, several types co-circulated with alternating predominance. Within types, multiple genetically divergent variants were observed. Ongoing RV infections through time appeared to be a combination of (1) persistent types (observed up to 7 consecutive months), (2) reintroduced genetically distinct variants, and (3) new invasions (average of 8 new types annually).ConclusionsSustained RV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than continuous transmission of locally established types/variants.

Highlights

Rhinovirus (RVs) are a highly prevalent group of viruses and are the principal cause of common cold syndrome in humans globally [1,2]
Despite the clinical significance of RV infections, there is little information on the long-term t trends and diversity of circulating RV types. rip RV belongs to the genus Enterovirus of the family Picornaviridae
The high genetic variability in the VP4/VP2 and VP1 a genomic regions of rhinoviruses have been instrumental in molecular typing [12,13] and M molecular epidemiological investigations of rhinovirus infections [14,15,16]

Summary

Methods

We analysed 1,070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya Coast. The samples were collected between 2007 and 2018 t from hospitalised paediatric patients (< 60 months) with acute respiratory illness. Within types multiple genetically nu divergent variants were observed. Ongoing RV infections through time appeared to be a a combination of (i) persistent types (observed up to seven consecutive months), (ii) reintroduced genetically distinct variants and (iii) new invasions D Conclusion: Sustained RV presence in the Kilifi community is mainly due to frequent te invasion by new types and variants rather than continuous transmission of locally p established types/variants. Acce Key words: Rhinovirus, coastal Kenya, long-term surveillance, persistence, invasion

Introduction

Findings

C24 C29 C30 C34 C48 C50 Cpat16