Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya

Abstract

Background: Human rhinovirus (HRV) is the most common cause of the common cold but may also lead to more severe respiratory illness in vulnerable populations. The epidemiology and genetic diversity of HRV within a school setting have not been described. Objective: To characterise HRV molecular epidemiology among children attending primary school in rural coastal Kenya. Methods: Between May 2017 to April 2018, over three school terms, we collected 1859 nasopharyngeal swab (NPS) samples from pupils and teachers with symptoms of acute respiratory infection in a public primary school in rural coastal Kenya. The samples were tested for HRV using real-time RT-PCR. HRV positive samples were sequenced in the VP4/VP2 coding region for species and genotype classification. Results: A total of 307 NPS (16.4%) from 164 individuals were HRV positive, and 253 (82.4%) were successfully sequenced. The proportion of HRV in the lower primary classes was higher (19.8%) than upper primary classes (12.2%), p-value <0.001. HRV-A was the most common species (134/253, 53.0%), followed by HRV-C (73/253, 28.9%) then HRV-B (46/253, 18.2%). Phylogenetic analysis identified 47 HRV genotypes. The most common genotypes were A2 and B70. Numerous (up to 22 in one school term) genotypes circulated simultaneously and no genotype was detected in all three school terms. Conclusion: HRV was frequently detected among school-going children with mild ARI symptoms, and particularly in the younger age groups (<5-year-olds). Multiple HRV introductions were observed characterized by the considerable genotype diversity.

The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses Among Paediatric Cases in Sydney, Australia

“…This significant difference was also apparent (p < 0.01) in one of two Bayesian phylogeny-trait association test statistics (PS not AI) of the VP4/VP2 capsid gene (Supplementary Tables 4 and 5). More recent studies have also shown differences in the rates of RV infection by species among early and late childhood (Bochkov, Evans et al 2018, Luka, Kamau et al 2020). Together with our results, this reinforces the potential for age-specific infectivity by RV species, particularly RV-C at younger age groups.…”

Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018

“…HRV positives underwent VP4/2 sequencing to characterize the diversity, spatial and temporal occurrence of HRV in the two settings. Comparison of the HRV diversity within the school in Junju and the health dispensary located in Junju revealed 12 common types, and the most frequent common type was HRV-A101 (n=5 in each setting) 9 , 11 .…”

“…This diversity presents a challenge in developing a sequencing protocol that works well across the different HRV types 10 . Most HRV molecular epidemiology studies utilize partial genome sequences, which offer lower resolution in identifying epidemiologically linked infections 11 .…”

Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018

“…This diversity presents a challenge in developing a sequencing protocol that works well across the different HRV types 10 . Most HRV molecular epidemiology studies utilize partial genome sequences, which offer lower resolution in identifying epidemiologically linked infections 11 .…”