Epidemiology and Seasonality of Endemic Human Coronaviruses in South African and Zambian Children: A Case-Control Pneumonia Study.

Azwifarwi Mathunjwa,Daniel E Park,Geoffrey Kwenda,Shabir A Madhi,Vicky L Baillie,David P Moore,Donald M Thea,Lawrence Mwananyanda

doi:10.3390/v13081513

Abstract

Endemic human coronaviruses (HCoV) are capable of causing a range of diseases from the common cold to pneumonia. We evaluated the epidemiology and seasonality of endemic HCoVs in children hospitalized with clinical pneumonia and among community controls living in countries with a high HIV burden, namely South Africa and Zambia, between August 2011 to October 2013. Nasopharyngeal/oropharyngeal swabs were collected from all cases and controls and tested for endemic HCoV species and 12 other respiratory viruses using a multiplex real-time PCR assay. We found that the likelihood of detecting endemic HCoV species was higher among asymptomatic controls than cases (11% vs. 7.2%; 95% CI: 1.2–2.0). This was however only observed among children > 6 months and was mainly driven by the Betacoronavirus endemic species (HCoV-OC43 and –HKU1). Endemic HCoV species were detected through the year; however, in Zambia, the endemic Betacoronavirus species tended to peak during the winter months (May–August). There was no association between HIV status and endemic HCoV detection.

Highlights

Coronaviruses (CoVs) from the family Coronaviridae (Order Nidovirales) are enveloped, single-stranded, zoonotic RNA viruses [1]
Community controls were more likely to have human coronaviruses (HCoVs) detected in their NP/OP samples compared to cases (10.5% vs. 7.2%; 95% confidence interval (CI): 1.17–1.96); this association was only evident in the asymptomatic controls (11% vs. 7.2%; 95% CI: 1.2–2.0) (Table 1); regardless of site of enrolment (Table S1 in Supplementary Material)
This association was seen in human immunodeficiency virus type-1 (HIV)-uninfected (HIV−) participants (10% vs. 7% for controls vs. cases) as well as in children living with HIV (HIV+; 10% vs. 7% for controls vs. cases)

Summary

Introduction

Coronaviruses (CoVs) from the family Coronaviridae (Order Nidovirales) are enveloped, single-stranded, zoonotic RNA viruses [1]. There are four genera of CoVs, two of which— Alphacoronaviruses and Betacoronaviruses—are capable of infecting humans causing a variety of symptoms, ranging from gastrointestinal to cardiac and respiratory disease. Four endemic human coronaviruses (HCoVs) are commonly detected in humans, namely HCoV-229E, -HKU1, -NL63 and -OC43 [3]. East respiratory syndrome CoV (MERS-CoV) in 2012 and the 2019 novel CoV (SARS-CoV-2) is currently causing a global pandemic with symptoms ranging from mild respiratory and gastrointestinal disease to severe pneumonia and death. Endemic HCoVs are most commonly detected as co-infections with other respiratory viruses [2,3,4,5] or in immunocompromised children with underlying chronic disease [3,4]. Limited information is available on the interactions between HCoVs and human immunodeficiency virus type-1 (HIV), and severity of disease

Methods

Results

Conclusion