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. Objective To characterise HRV molecular epidemiology in primary school in a rural location of Kenya. Methods Between May 2017 to April 2018, over three 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 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%) 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 one school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, 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 characterised by the considerable genotype diversity.

Rhinovirus remains prevalent in school teenagers during fight against COVID‐19 pandemic

“…An investigation of 452 children with acute respiratory infection reported that acute respiratory infection in children was mainly infected by HRV (11.28%), and most of the HRV infection occurred was in winter 7 . Respiratory virus surveillance studies showed that the positive rate of HRV was 16.4%–35.1% 8–13 . During the COVID‐19 pandemic, the government had taken all possible means to stop the pandemic, and successfully stopped the COVID‐19 pandemic in Guangzhou, and the common respiratory infectious diseases, such as influenza and pneumonia as well 3 .…”

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

“…RV detection rates decrease with increasing age as adults have had multiple and widespread exposures to RV types [ 14 ]. Other social groups are vital in RV transmission [ 6 , 40 , 41 ] and it would be useful to evaluate RV transmission patterns and prevalence within these groups.…”

“…The study was conducted at the Kilifi County Hospital (KCH) as part of long-term surveillance initially aimed at understanding the epidemiology and disease burden of respiratory syncytial virus–associated pneumonia cases [ 25 ] and expanded to a range of respiratory viruses from 2007 onward [ 6 , 26–30 ]. KCH, located on the coast of Kenya, is a referral hospital serving the wider Kilifi County, which has a population of 1453787 and covers an area of approximately 12254 km 2 .…”

“…RV infections result in a wide range of clinical outcomes spanning from asymptomatic and mild illness in the upper airways to severe illness in the lower airways [ 3 , 4 ]. The infections occur in all ages, with severe presentation more likely in children under the age of 5 years [ 5 , 6 ], the elderly [ 7 ], and immunocompromised persons [ 8 ]. Despite the clinical significance of RV infections, there is little information on the long-term trends and diversity of circulating RV types.…”

Human Rhinoviruses Prevailed Among Children in the Setting of Wearing Face Masks in Shanghai, 2020

“…In Zhao's paper, the predominant genotypes included A78, A12, A89, A61, B70, C2, C6, C24 and C16, none of which were the main genotypes in our study. Moreover, we summarized the genotypes in papers focusing on various countries and concluded that the prevailing genotypes changed greatly with time and place [12][13][14]. But what these papers have in common was that HRV-As and HRV-Cs were the most frequently detected species and usually prevailed alternatively and seasonally.…”