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 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 from hospitalised paediatric patients (< 60 months) with acute respiratory illness. Results Of 7,231 children enrolled, RV was detected in 1,497 (20.7%) and VP4/VP2 sequences were recovered from 1,070 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 (i) persistent types (observed up to seven consecutive months), (ii) reintroduced genetically distinct variants and (iii) new invasions (average of eight new types, annually). Conclusion 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.

SARS-CoV-2 elicits non-sterilizing immunity and evades vaccine-induced immunity: implications for future vaccination strategies

“…This pattern of short-lasting immunity is similar to that of common cold viruses HCoV-NL63, HCoV-HKU1, HCoV-229E and HCoV-OC43 but different from the long-lasting immunity induced by SARS-CoV-1 and MERS [ 25 , 26 ]. Antibodies elicited after SARS-CoV-2 infection and vaccination predominantly target the receptor-binding domain, which rapidly mutates [ 27 , 28 ].…”

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

“…Spatial-temporal analysis revealed occurrence of multiple types and variants across space and time in agreement with previous studies 12, 14, 44 . The observed variations in time and duration of circulation among the rhinovirus types could be due to (i) differences in the duration of type-specific immunity, (ii) frequency of introductions or, iii) level of antigenic similarity (heterologous immunity) 34 . The concurrent and sequential circulation of RV types seen as the occurrence of multiple peaks of the same type in the same or distant locations could signify multiple introductions, antigenic variation, or infections in different population strata 34 .…”

“…The observed variations in time and duration of circulation among the rhinovirus types could be due to (i) differences in the duration of type-specific immunity, (ii) frequency of introductions or, iii) level of antigenic similarity (heterologous immunity) 34 . The concurrent and sequential circulation of RV types seen as the occurrence of multiple peaks of the same type in the same or distant locations could signify multiple introductions, antigenic variation, or infections in different population strata 34 . The heterogeneity in RV detection by month and location could be attributed to the seasonal variation in SARI or sampling methods or to regional differences in environmental and climatic factors.…”

“…Distributions of pairwise genetic distances were assessed for evaluation of intertype and intra-type divergence 11 . Intra-type 'variant' was defined based on a divergence cut-off or threshold value determined as the least frequent value between the first (same phylogenetic clade) and second (different phylogenetic clades) modes in a pairwise nucleotide difference distribution plot as previously described 34 . Viruses within the same phylogenetic clade were assumed to belong to the same variant of an RV type.…”

Molecular epidemiology of Human Rhinoviruses in children in Hong Kong, 2020-2021

“…Genotypes frequently cocirculate, and infection with one genotype elicits only low or no cross-protection (9), which poses a challenge for HRV vaccine design. Previous studies suggest that predominant genotypes are varied and often transient (5,10,11,12,13,14,15). However, the lack of HRV sequencing in most regions limits our understanding of individual epidemic patterns, including transmission and pathogenicity, and the mechanisms underlying genotype turnover and persistence.…”