Author:
Anscombe Catherine,Lissauer Samantha,Thole Herbert,Rylance Jamie,Dula Dingase,Menyere Mavis,Kutambe Belson,van der Veer Charlotte,Phiri Tamara,Banda Ndaziona P.,Mndolo Kwazizira S.,Mponda Kelvin,Phiri Chimota,Mallewa Jane,Nyirenda Mulinda,Katha Grace,Mwandumba Henry,Gordon Stephen B.,Jambo Kondwani C.,Cornick Jennifer,Feasey Nicholas,Barnes Kayla G.,Morton Ben,Ashton Philip M.,Kalua Wezzie,Mandala Peter,Katutula Barbara,Ng’oma Rosaleen,Lanken Steven,Phulusa Jacob,Mkandawire Mercy,Kaimba Sylvester,Nthala Sharon,Nsomba Edna,Keyala Lucy,Chinoko Beatrice,Gmeiner Markus,Kaudzu Vella,Freyne Bridget,Swarthout Todd D.,Tam Pui-Ying Iroh,Sichone Simon,Ahmadu Ajisa,Stima Grace,Masina Mazuba,Kanjewa Oscar,Nyasulu Vita,Chinyama End,Zuza Allan,Denis Brigitte,Storey Evance,Bondera Nedson,Matchado Danford,Chande Adams,Chingota Arthur,Ntwea Chimenya,Mkandawire Langford,Mhango Chimwemwe,Lakudzala Agness,Chaponda Mphatso,Mwenechanya Percy,Mvaya Leonard,Tembo Dumizulu,Henrion Marc Y. R.,Chirombo James,Kambiya Paul,Masesa Clemens,Gondwe Joel,
Abstract
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.
Publisher
Springer Science and Business Media LLC
Reference34 articles.
1. Brito AF, Semenova E, Dudas G, et al. Global disparities in SARS-CoV-2 genomic surveillance. medRxiv 2021; :2021.08.21.21262393.
2. Aborode AT, Hasan MM, Jain S, et al. Impact of poor disease surveillance system on COVID-19 response in africa: time to rethink and rebuilt. Clin Epidemiol Global Health. 2021;12: 100841.
3. Wolter N, Jassat W, Walaza S, et al. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. The Lancet. 2022;399:437–46.
4. Novel 2019 coronavirus genome—SARS-CoV-2 coronavirus. 2020. Available at: https://virological.org/t/novel-2019-coronavirus-genome/319. Accessed 28 October 2021.
5. CDC. CDC’s Diagnostic Test for COVID-19 Only and Supplies. 2020. Available at: https://www.cdc.gov/coronavirus/2019-ncov/lab/virus-requests.html. Accessed 28 October 2021.