A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study

Cat 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 Gordon; Kondwani Jambo; Jennifer Cornick; Nick Feasey; Kayla Barnes; Benjamin Morton; Philip M. 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; Leonard Mvaya; Marc Henrion; James Chirombo; Clemens Masesa

doi:10.1186/s12879-022-07941-y

A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study

Cat 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 Gordon
, Kondwani Jambo
, Jennifer Cornick

Nick Feasey, Kayla Barnes, Benjamin Morton, Philip M. 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, Leonard Mvaya, Marc Henrion, James Chirombo, Clemens Masesa

Research output: Contribution to journal › Article › peer-review

13 Citations (Scopus)

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.

Original language	English
Article number	79
Pages (from-to)	e79
Journal	BMC Infectious Diseases
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s12879-022-07941-y
Publication status	Published - 7 Feb 2023

Keywords

Africa
COVID
Delta
ISARIC
LMIC
Malawi
Mortality
SARS-CoV-2

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12879 2022 Article 7941Final published version, 993 KBLicence: CC BY

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Anscombe, C., Lissauer, S., Thole, H., Rylance, J., Dula, D., Menyere, M., Kutambe, B., van der Veer, C., Phiri, T., Banda, N. P., Mndolo, K. S., Mponda, K., Phiri, C., Mallewa, J., Nyirenda, M., Katha, G., Mwandumba, H., Gordon, S., Jambo, K., ... Masesa, C. (2023). A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study. BMC Infectious Diseases, 23(1), e79. Article 79. https://doi.org/10.1186/s12879-022-07941-y

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title = "A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study",

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{\texttrademark} 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.",

keywords = "Africa, COVID, Delta, ISARIC, LMIC, Malawi, Mortality, SARS-CoV-2",

author = "Cat Anscombe and Samantha Lissauer and Herbert Thole and Jamie Rylance and Dingase Dula and Mavis Menyere and Belson Kutambe and \{van der Veer\}, Charlotte and Tamara Phiri and Banda, \{Ndaziona P.\} and Mndolo, \{Kwazizira S.\} and Kelvin Mponda and Chimota Phiri and Jane Mallewa and Mulinda Nyirenda and Grace Katha and Henry Mwandumba and Stephen Gordon and Kondwani Jambo and Jennifer Cornick and Nick Feasey and Kayla Barnes and Benjamin Morton and Ashton, \{Philip M.\} and Wezzie Kalua and Peter Mandala and Barbara Katutula and Rosaleen Ng{\textquoteright}oma and Steven Lanken and Jacob Phulusa and Mercy Mkandawire and Sylvester Kaimba and Sharon Nthala and Edna Nsomba and Lucy Keyala and Beatrice Chinoko and Markus Gmeiner and Vella Kaudzu and Bridget Freyne and Swarthout, \{Todd D.\} and \{Iroh Tam\}, Pui-Ying and Simon Sichone and Ajisa Ahmadu and Grace Stima and Mazuba Masina and Oscar Kanjewa and Leonard Mvaya and Marc Henrion and James Chirombo and Clemens Masesa",

year = "2023",

month = feb,

day = "7",

doi = "10.1186/s12879-022-07941-y",

language = "English",

volume = "23",

pages = "e79",

journal = "BMC Infectious Diseases",

issn = "1471-2334",

publisher = "BioMed Central Ltd",

number = "1",

}

Anscombe, C, Lissauer, S, Thole, H, Rylance, J, Dula, D, Menyere, M, Kutambe, B, van der Veer, C, Phiri, T, Banda, NP, Mndolo, KS, Mponda, K, Phiri, C, Mallewa, J, Nyirenda, M, Katha, G, Mwandumba, H , Gordon, S , Jambo, K, Cornick, J, Feasey, N , Barnes, K , Morton, B, Ashton, PM, Kalua, W, Mandala, P, Katutula, B, Ng’oma, R, Lanken, S, Phulusa, J, Mkandawire, M, Kaimba, S, Nthala, S, Nsomba, E, Keyala, L, Chinoko, B, Gmeiner, M, Kaudzu, V, Freyne, B, Swarthout, TD, Iroh Tam, P-Y, Sichone, S, Ahmadu, A, Stima, G, Masina, M, Kanjewa, O, Mvaya, L, Henrion, M , Chirombo, J & Masesa, C 2023, 'A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study', BMC Infectious Diseases, vol. 23, no. 1, 79, pp. e79. https://doi.org/10.1186/s12879-022-07941-y

TY - JOUR

T1 - A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study

AU - Anscombe, Cat

AU - Lissauer, Samantha

AU - Thole, Herbert

AU - Rylance, Jamie

AU - Dula, Dingase

AU - Menyere, Mavis

AU - Kutambe, Belson

AU - van der Veer, Charlotte

AU - Phiri, Tamara

AU - Banda, Ndaziona P.

AU - Mndolo, Kwazizira S.

AU - Mponda, Kelvin

AU - Phiri, Chimota

AU - Mallewa, Jane

AU - Nyirenda, Mulinda

AU - Katha, Grace

AU - Mwandumba, Henry

AU - Gordon, Stephen

AU - Jambo, Kondwani

AU - Cornick, Jennifer

AU - Feasey, Nick

AU - Barnes, Kayla

AU - Morton, Benjamin

AU - Ashton, Philip M.

AU - Kalua, Wezzie

AU - Mandala, Peter

AU - Katutula, Barbara

AU - Ng’oma, Rosaleen

AU - Lanken, Steven

AU - Phulusa, Jacob

AU - Mkandawire, Mercy

AU - Kaimba, Sylvester

AU - Nthala, Sharon

AU - Nsomba, Edna

AU - Keyala, Lucy

AU - Chinoko, Beatrice

AU - Gmeiner, Markus

AU - Kaudzu, Vella

AU - Freyne, Bridget

AU - Swarthout, Todd D.

AU - Iroh Tam, Pui-Ying

AU - Sichone, Simon

AU - Ahmadu, Ajisa

AU - Stima, Grace

AU - Masina, Mazuba

AU - Kanjewa, Oscar

AU - Mvaya, Leonard

AU - Henrion, Marc

AU - Chirombo, James

AU - Masesa, Clemens

PY - 2023/2/7

Y1 - 2023/2/7

N2 - 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.

AB - 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.

KW - Africa

KW - COVID

KW - Delta

KW - ISARIC

KW - LMIC

KW - Malawi

KW - Mortality

KW - SARS-CoV-2

U2 - 10.1186/s12879-022-07941-y

DO - 10.1186/s12879-022-07941-y

M3 - Article

SN - 1471-2334

VL - 23

SP - e79

JO - BMC Infectious Diseases

JF - BMC Infectious Diseases

IS - 1

M1 - 79

ER -

A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study

Abstract

Keywords

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