Molecular Epidemiology of Human Rhinovirus From 1-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 previously described. The objective of this study was to characterize HRV molecular epidemiology in a primary school in a rural location of Kenya.

Methods: Between May 2017 and April 2018, over 3 school terms, we collected 1859 nasopharyngeal swabs (NPS) from pupils and teachers with symptoms of acute respiratory infection in a public primary school in Kilifi County, coastal Kenya. The samples were tested for HRV using real-time reverse transcription polymerase chain reaction. 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 < .001). HRV-A was the most common species (134/253; 53.0%), followed by HRV-C (73/253; 28.9%) and 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 1 school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, and no genotype was detected in all 3 school terms.

Conclusions: HRV was frequently detected among school-going children with mild acute respiratory illness symptoms, particularly in the younger age groups (<5-year-olds). Multiple HRV introductions were observed that were characterized by considerable genotype diversity.

Keywords: Kenya; human rhinovirus; molecular epidemiology; school-going children; transmission.

Figure 1.

Patterns of HRV infections within the school over 1 year. A, Month-by-month HRV proportion with respective 95% confidence intervals and number of samples tested. B, Class-specific HRV proportion with respective 95% confidence intervals. The 2 bars furthest to the right are aggregated proportions of lower primary and upper primary groups. Abbreviation: HRV, human rhinovirus.

Figure 2.

Phylogenetic analysis and genotype assignment of generated HRV sequences. Species-specific maximum likelihood trees of (A) HRV-A, (B) HRV-B, and (C) HRV-C. The tip shapes are colored by the school class of the individual. The scale bars represent nucleotide substitutions per site. The black tips represent the prototype sequence of respective strain. D, A circular bar plot showing the frequencies of HRV genotypes identified. The bars are colored by HRV species and the tips are labeled by HRV type and frequency. Abbreviation: HRV, human rhinovirus.

Figure 2.

Phylogenetic analysis and genotype assignment of generated HRV sequences. Species-specific maximum likelihood trees of (A) HRV-A, (B) HRV-B, and (C) HRV-C. The tip shapes are colored by the school class of the individual. The scale bars represent nucleotide substitutions per site. The black tips represent the prototype sequence of respective strain. D, A circular bar plot showing the frequencies of HRV genotypes identified. The bars are colored by HRV species and the tips are labeled by HRV type and frequency. Abbreviation: HRV, human rhinovirus.

Figure 3.

The temporal occurrence and infection patterns of HRV. A, The temporal occurrence of all HRV genotypes across the 1-year study period. B, Individual infection patterns across the 1-year period. The individuals are ordered by date of first HRV infection. C, Number of days to a subsequent HRV case for individuals who were re-infected during the study period. All individual first infections are dated day 0. The individuals are ordered by number of HRV-positive samples, with the individual with the most positive samples appearing at the bottom. Abbreviation: HRV, human rhinovirus.

Figure 3.

The temporal occurrence and infection patterns of HRV. A, The temporal occurrence of all HRV genotypes across the 1-year study period. B, Individual infection patterns across the 1-year period. The individuals are ordered by date of first HRV infection. C, Number of days to a subsequent HRV case for individuals who were re-infected during the study period. All individual first infections are dated day 0. The individuals are ordered by number of HRV-positive samples, with the individual with the most positive samples appearing at the bottom. Abbreviation: HRV, human rhinovirus.

Figure 3.

The temporal occurrence and infection patterns of HRV. A, The temporal occurrence of all HRV genotypes across the 1-year study period. B, Individual infection patterns across the 1-year period. The individuals are ordered by date of first HRV infection. C, Number of days to a subsequent HRV case for individuals who were re-infected during the study period. All individual first infections are dated day 0. The individuals are ordered by number of HRV-positive samples, with the individual with the most positive samples appearing at the bottom. Abbreviation: HRV, human rhinovirus.

Figure 4.

Distribution of genotypes across the school. A, Heatmap showing the distribution of frequent genotypes across the school classes. The intensity of the color correlates to the frequency of samples. Color intensity has been scaled to correct for sampling bias between the lower primary and upper primary classes. B, Distribution of frequent genotypes between the upper and lower primary groups. The sizes of the circles correlate to the number of samples and the color to the respective group: either lower or upper primary. Abbreviation: HRV, human rhinovirus.

Figure 5.

Genetic diversity of HRV genotypes with a frequency of >10. From the top left: A2, A28, A36, B48-like, B70, C_pat19, C3, and C13 (bottom right). Nucleotide substitutions are demonstrated by a colored bar. A substitution to an “A” is indicated by green, “T” by red, “G” by indigo, and “C” by blue bars. The sequences are labeled by grade of individual and ordered by date of sample collection with the genotype’s index sequence at the bottom (acting as a reference). Abbreviation: HRV, human rhinovirus.

Figure 5.

Genetic diversity of HRV genotypes with a frequency of >10. From the top left: A2, A28, A36, B48-like, B70, C_pat19, C3, and C13 (bottom right). Nucleotide substitutions are demonstrated by a colored bar. A substitution to an “A” is indicated by green, “T” by red, “G” by indigo, and “C” by blue bars. The sequences are labeled by grade of individual and ordered by date of sample collection with the genotype’s index sequence at the bottom (acting as a reference). Abbreviation: HRV, human rhinovirus.