Epidemiology of Human Seasonal Coronaviruses Among People With Mild and Severe Acute Respiratory Illness in Blantyre, Malawi, 2011-2017

Dory Kovacs; Ivan Mambule; Jonathan M Read; Anmol Kiran; Moses Chilombe; Thandiwe Bvumbwe; Stephen Aston; Mavis Menyere; Mazuba Masina; Moses Kamzati; Thokozani Namale Ganiza; Danielle Iuliano; Meredith McMorrow; Naor Bar-Zeev; Dean Everett; Neil French; Antonia Ho

doi:10.1093/infdis/jiad587

Epidemiology of Human Seasonal Coronaviruses Among People With Mild and Severe Acute Respiratory Illness in Blantyre, Malawi, 2011-2017

J Infect Dis. 2024 Feb 14:jiad587. doi: 10.1093/infdis/jiad587. Online ahead of print.

Authors

Dory Kovacs¹, Ivan Mambule^{2

3}, Jonathan M Read⁴, Anmol Kiran², Moses Chilombe^{2

5}, Thandiwe Bvumbwe^{2

6}, Stephen Aston^{2

7}, Mavis Menyere², Mazuba Masina², Moses Kamzati², Thokozani Namale Ganiza², Danielle Iuliano⁸, Meredith McMorrow⁸, Naor Bar-Zeev⁹, Dean Everett^{10

11}, Neil French^{2

12}, Antonia Ho^{2

13}

Affiliations

¹ School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom.
² Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.
³ Research Department, Joint Clinical Research Centre, Kampala, Uganda.
⁴ Centre for Health Information Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, United Kingdom.
⁵ Malaria Alert Centre, Kamuzu University of Health Sciences, Blantyre, Malawi.
⁶ Blantyre Malaria Project, Blantyre, Malawi.
⁷ Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
⁸ National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia.
⁹ International Vaccine Access Center, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States.
¹⁰ Department of Pathology and Infectious Diseases, College of Medicine and Health Sciences, Abu Dhabi, United Arab Emirates.
¹¹ Infection Research Unit, Khalifa University, Abu Dhabi, United Arab Emirates.
¹² Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
¹³ Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom.

PMID: 38365443
DOI: 10.1093/infdis/jiad587

Abstract

Background: The aim of this study was to characterize the epidemiology of human seasonal coronaviruses (HCoVs) in southern Malawi.

Methods: We tested for HCoVs 229E, OC43, NL63, and HKU1 using real-time polymerase chain reaction (PCR) on upper respiratory specimens from asymptomatic controls and individuals of all ages recruited through severe acute respiratory illness (SARI) surveillance at Queen Elizabeth Central Hospital, Blantyre, and a prospective influenza-like illness (ILI) observational study between 2011 and 2017. We modeled the probability of having a positive PCR for each HCoV using negative binomial models, and calculated pathogen-attributable fractions (PAFs).

Results: Overall, 8.8% (539/6107) of specimens were positive for ≥1 HCoV. OC43 was the most frequently detected HCoV (3.1% [191/6107]). NL63 was more frequently detected in ILI patients (adjusted incidence rate ratio [aIRR], 9.60 [95% confidence interval {CI}, 3.25-28.30]), while 229E (aIRR, 8.99 [95% CI, 1.81-44.70]) was more frequent in SARI patients than asymptomatic controls. In adults, 229E and OC43 were associated with SARI (PAF, 86.5% and 89.4%, respectively), while NL63 was associated with ILI (PAF, 85.1%). The prevalence of HCoVs was similar between children with SARI and controls. All HCoVs had bimodal peaks but distinct seasonality.

Conclusions: OC43 was the most prevalent HCoV in acute respiratory illness of all ages. Individual HCoVs had distinct seasonality that differed from temperate settings.

Keywords: Malawi; human; pathogen-attributable fraction; seasonal coronavirus; severe acute respiratory illness.

Abstract

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