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Published on: August 18, 2023
Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya
Clayton O Onyango1, Stephen R Welch, Patrick K Munywoki
1KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. conyango@kilifi.kemri-wellcome.org
Insights
This study tracked human rhinovirus (HRV) in Kenyan children over three years. HRV-A and HRV-C were most common, with diverse strains circulating, but no species linked to disease severity.
Area of Science:
- Virology
- Epidemiology
- Pediatrics
Background:
- Human rhinovirus (HRV) is a common cause of respiratory illness in children.
- Understanding HRV species distribution and genetic diversity is crucial for public health, especially in resource-limited settings.
- Previous molecular epidemiological data for HRV in coastal Kenya was lacking.
Purpose of the Study:
- To conduct a 3-year pediatric surveillance of human rhinovirus (HRV) in Kilifi, Kenya.
- To determine the species distribution (HRV-A, HRV-B, HRV-C) of circulating HRV strains.
- To analyze HRV genetic diversity and its association with respiratory illness severity.
Main Methods:
- Collected nasopharyngeal samples from pediatric patients with and without respiratory infections over three years.
- Screened samples using real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR).
- Classified HRV species and analyzed genetic diversity via nucleotide sequencing of the VP4/VP2 junction.
Main Results:
- Identified 441 HRV positive cases, classifying 332 to species: 47% HRV-A, 5% HRV-B, 48% HRV-C.
- Observed no clear seasonal patterns or significant differences in species distribution between inpatient and outpatient groups.
- Found considerable HRV strain diversity, with HRV-A and HRV-C showing distinct circulating clusters, many unique to HRV-C.
Conclusions:
- HRV species distribution in coastal Kenya aligns with global patterns.
- Significant genetic diversity exists within circulating HRV strains, particularly HRV-A and HRV-C.
- This study did not find an association between specific HRV species and lower respiratory tract infection severity in hospitalized children.
Abstract:
This study reports pediatric surveillance over 3 years for human rhinovirus (HRV) at the District Hospital of Kilifi, coastal Kenya. Nasopharyngeal samples were collected from children presenting at outpatient clinic with no signs of acute respiratory infection, or with signs of upper respiratory tract infection, and from children admitted to the hospital with lower respiratory tract infection. Samples were screened by real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) and classified further to species by nucleotide sequencing of the VP4/VP2 junction. Of 441 HRV positives by real-time RT-PCR, 332 were classified to species, with 47% (155) being HRV-A, 5% (18) HRV-B, and 48% (159) HRV-C. There was no clear seasonal pattern of occurrence for any species. The species were present in similar proportions in the inpatient and outpatient sample sets, and no significant association between species distribution and the severity of lower respiratory tract infection in the inpatients could be determined. HRV sequence analysis revealed multiple but separate clusters in circulation particularly for HRV-A and HRV-C. Most HRV-C clusters were distinct from reference sequences downloaded from GenBank. In contrast, most HRV-A and HRV-B sequences clustered with either known serotypes or strains from elsewhere within Africa and other regions of the world. This first molecular epidemiological study of HRV in the region defines species distribution in accord with reports from elsewhere in the world, shows considerable strain diversity and does not identify an association between any species and disease severity.
