A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study
Catherine Anscombe, Samantha Lissauer, Herbert Thole, Jamie Rylance, Dingase Dula, Mavis Menyere, Belson Kutambe, Charlotte van der Veer, Tamara Phiri, Ndaziona Peter Kwanjo Banda, Kwazizira S. Mndolo, Kelvin Mponda, Chimota Phiri, Jane Mallewa, Mulinda Nyirenda, Grace Katha, Henry C. Mwandumba, Stephen B. Gordon, Kondwani Jambo, Jennifer Cornick, Nicholas Feasey, Kayla G. Barnes, Ben Morton, Philip Ashton, Wezzie Kalua, Peter Mandala, Barbara Katutula, Rosaleen Ng’oma, Steven Lanken, Jacob Phulusa, Mercy Mkandawire, Sylvester Kaimba, Sharon Nthala, Edna Nsomba, Lucy Keyala, Beatrice Chinoko, Markus Gmeiner, Vella Kaudzu, Bridget Freyne, Todd D. Swarthout, Pui‐Ying Iroh Tam, Simon Sichone, Ajisa Ahmadu, Grace Stima, Mazuba Masina, Oscar Kanjewa, Vita Nyasulu, End Chinyama, Allan Zuza, Brigitte Denis, Evance Storey, Nedson Bondera, Danford Matchado, Adams Chande, Arthur Chingota, Chimenya Ntwea, Langford Mkandawire, Chimwemwe Mhango, Agness Lakudzala, Mphatso Chaponda, Percy Mwenechanya, Leonard Mvaya, Dumizulu Tembo, Marc Henrion, James Chirombo, Paul Kambiya, Clemens Masesa, Joel Gondwe
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 MinION™ 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.