A Comparison of Four Epidemic Waves of COVID-19 in Malawi; an Observational Cohort Study

Overview

Journal medRxiv

Date 2022 Jul 21

PMID 35860218

Authors

Catherine Anscombe

Samantha Lissauer

Herbert Thole

Jamie Rylance

Dingase Dula

Mavis Menyere

Belson Kutambe

Charlotte van der Veer

Tamara Phiri

Ndaziona P Banda

Kwazizira S Mndolo

Kelvin Mponda

Chimota Phiri

Jane Mallewa

Mulinda Nyirenda

Grace Katha

Henry Mwandumba

Stephen B Gordon

Kondwani C Jambo

Jennifer Cornick

Nicholas Feasey

Kayla G Barnes

Ben Morton

Philip M Ashton

Affiliations

Soon will be listed here.

Abstract

Background: Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome.

Methods: We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinIONâ"¢ in Blantyre.

Results: We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection.

Conclusions: Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.

Summary: We used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.

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