Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance.

John Mwita Morobe,Patrick K Munywoki,Joyce U Nyiro,Samuel Brand,C.N Agoti,Elijah Gicheru,Everlyn Kamau,D.J Nokes,Grieven P Otieno,Fredrick Eyase

doi:10.12688/wellcomeopenres.14836.2

Abstract

Background: Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections, resulting in a significant public health burden. The virus circulates as many different types (168), each generating strong homologous, but weak heterotypic, immunity. The influence of these features on transmission patterns of HRV in the community is understudied. Methods: Nasopharyngeal swabs were collected from patients with symptoms of acute respiratory infection (ARI) at nine out-patient facilities across a Health and Demographic Surveillance System between December 2015 and November 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region of the positive samples sequenced. Phylogenetic analysis was used to determine the HRV types. Classification models and G-test statistic were used to investigate HRV type spatial distribution. Demographic characteristics and clinical features of ARI were also compared. Results: Of 5,744 NPS samples collected, HRV was detected in 1057 (18.4%), of which 817 (77.3%) were successfully sequenced. HRV species A, B and C were identified in 360 (44.1%), 67 (8.2%) and 390 (47.7%) samples, respectively. In total, 87 types were determined: 39, 10 and 38 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of persistence. Spatially, identical types occurred over a wide distance at similar times, but there was statistically significant evidence for clustering of types between health facilities in close proximity or linked by major road networks. Conclusion: This study records a high prevalence of HRV in out-patient presentations exhibiting high type diversity. Patterns of occurrence suggest frequent and independent community invasion of different types. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread or multiple invasions of the same type, but evidence of similar types amongst close health facilities, or along road systems, indicate type partitioning structured by local spread.

Highlights

Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections (URTIs) referred to as the common cold[1,2,3,4]
This study investigated the human rhinovirus (HRV) infection, diversity and type distribution in individuals presenting with acute respiratory illnesses (ARI) symptoms for outpatient care at nine spatially structured health facilities in rural coastal Kenya over 12 months period
All three HRV species co-circulated with HRV-A and HRV-C co-predominant

Summary

Introduction

Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections (URTIs) referred to as the common cold[1,2,3,4]. HRV transmission, infection patterns and diversity have been rarely studied in low-income settings despite bearing the majority burden of acute respiratory illnesses (ARI). HRVs fall under the genus Enterovirus (HEVs) in the family Picornaviridae[11]. Their genome occurs as a positive-sense, single-stranded RNA molecule of approximately 7.2 kb flanked by a 5’ untranslated region (UTR) and 3’ poly-A tail. 5. The authors note that their genotyping process is “as previously described”. The authors note that their genotyping process is “as previously described” It is quite different including not being nested RT-PCR (which can enhance sensitivity). Could they provide more detail – perhaps consider adding their method in complete detail to https://www.protocols.io/ and referencing to that in this paper

Methods

Results

Conclusion