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

Abstract

Background: Rhinoviruses (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.

Methods: Here, 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.

Results: Of 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).

Conclusions: Sustained 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.

Keywords: coastal Kenya; invasion; long-term surveillance; persistence; rhinovirus.

Figure 1.

Monthly distribution of rhinovirus (RV) cases identified from surveillance of acute respiratory illness (ARI) in children aged <60 months admitted to the Kilifi County Hospital, Kenya, 2007–2018. Also included on the secondary y-axis are the proportion (% positivity) of the samples from the inpatients with ARI who were RV positive.

Figure 2.

A, Annual proportion of rhinovirus (RV) species across the 12-year study period. B, Total number (blue bars) and new number (purple bars) of RV types detected annually over the period 2007–2018. Also shown is the cumulative number of the different RV types observed during the study period (black line). C, Overall frequency of detection in months or the number of months each RV type was detected. The types are ordered alphabetically.

Figure 3.

Quarterly proportions of rhinovirus (RV) types detected organized at the species level; shown here are the temporal trends of the 5 most prevalent types per species while the rest are indicated as “other”. A, Quarterly proportion of RV-A types. B, Quarterly proportion of RV-B types. C, Quarterly proportion of RV-C types.

Figure 4.

A, Nucleotide variability across the sequenced VP4/VP2 region for rhinovirus types RV-A49 and RV-C2. For each type, the viruses were compared to the earliest sampled sequence. Vertical colored bars show the nucleotide differences: Red is a change to T, orange is a change to A, purple is a change to C, and blue is a change to G. B, Distribution of pairwise nucleotide difference for the VP4/VP2 region of types RV-A49 and C2. Abbreviations: RV, rhinovirus; SNP, single-nucleotide polymorphism.

Figure 5.

Bayesian phylogenetic trees showing the VP4/VP2 region of the rhinovirus (RV) types A49, C2, C38, and C11. Variant names are next to the phylogenetic clusters, eg, v1 representing variant 1 for a specific type. Node support is indicated by (∗) for posterior probabilities >0.9.