Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings

Josue Togo; Anou Moise Somboro; Oumar Dolo; Fatoumata Tata Traore; Ibrehima Guindo; Djeneba B. Fofana; Eve Todesco; Anne Geneviève Marcelin; Vincent Calvez; Jane Holl; Robert Leo Murphy; Christophe Rodriguez; Mamoudou Maiga; Almoustapha Issiaka Maiga

doi:10.1016/j.meegid.2024.105681

Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings

Josue Togo^*, Anou Moise Somboro, Oumar Dolo, Fatoumata Tata Traore, Ibrehima Guindo, Djeneba B. Fofana, Eve Todesco, Anne Geneviève Marcelin, Vincent Calvez, Jane Holl, Robert Leo Murphy, Christophe Rodriguez, Mamoudou Maiga, Almoustapha Issiaka Maiga

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

Abstract

SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.

Original language	English (US)
Article number	105681
Journal	Infection, Genetics and Evolution
Volume	125
DOIs	https://doi.org/10.1016/j.meegid.2024.105681
State	Published - Nov 2024

Funding

Funding for this work was provided by: Catalyser from the Institute for Global Health of Northwestern University (M.M., J.T., A.M.S., and A.I.M.,); National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health under Award Number U54EB027049 and the Fogarty International Center of the National Institutes of Health under award number Building the Next Generation of Researchers in TB/HIV Diagnostics in Mali (B-NextGen) Mali, D43TW010350. ANRS MIE (Agence Nationale de Recherche sur le SIDA, les h\u00E9patites virales et les maladies infectieuses \u00E9mergentes).

Keywords

Evolution
SARS-CoV-2
Variants dynamics
West-Africa

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics
Molecular Biology
Genetics
Microbiology (medical)
Infectious Diseases

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.meegid.2024.105681

Cite this

Togo, J., Somboro, A. M., Dolo, O., Traore, F. T., Guindo, I., Fofana, D. B., Todesco, E., Marcelin, A. G., Calvez, V., Holl, J., Murphy, R. L., Rodriguez, C., Maiga, M., & Maiga, A. I. (2024). Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings. Infection, Genetics and Evolution, 125, Article 105681. https://doi.org/10.1016/j.meegid.2024.105681

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title = "Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings",

abstract = "SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.",

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author = "Josue Togo and Somboro, {Anou Moise} and Oumar Dolo and Traore, {Fatoumata Tata} and Ibrehima Guindo and Fofana, {Djeneba B.} and Eve Todesco and Marcelin, {Anne Genevi{\`e}ve} and Vincent Calvez and Jane Holl and Murphy, {Robert Leo} and Christophe Rodriguez and Mamoudou Maiga and Maiga, {Almoustapha Issiaka}",

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year = "2024",

month = nov,

doi = "10.1016/j.meegid.2024.105681",

language = "English (US)",

volume = "125",

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Togo, J, Somboro, AM, Dolo, O, Traore, FT, Guindo, I, Fofana, DB, Todesco, E, Marcelin, AG, Calvez, V, Holl, J, Murphy, RL, Rodriguez, C, Maiga, M & Maiga, AI 2024, 'Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings', Infection, Genetics and Evolution, vol. 125, 105681. https://doi.org/10.1016/j.meegid.2024.105681

TY - JOUR

T1 - Dynamics of SARS-CoV-2 variants in West Africa

T2 - Insights into genomic surveillance in resource-constrained settings

AU - Togo, Josue

AU - Somboro, Anou Moise

AU - Dolo, Oumar

AU - Traore, Fatoumata Tata

AU - Guindo, Ibrehima

AU - Fofana, Djeneba B.

AU - Todesco, Eve

AU - Marcelin, Anne Geneviève

AU - Calvez, Vincent

AU - Holl, Jane

AU - Murphy, Robert Leo

AU - Rodriguez, Christophe

AU - Maiga, Mamoudou

AU - Maiga, Almoustapha Issiaka

PY - 2024/11

Y1 - 2024/11

N2 - SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.

AB - SARS-CoV-2 geno-surveillance has been challenging in West Africa. Despite the multiple challenges encountered, particularly in West Africa during the COVID-19 pandemic, efforts were made to circumscribe the spread of the disease and to provide methods and resources for surveillance. We aim to describe the dynamic of SARS-CoV-2 variants and highlight the efforts made in genomic surveillance in West Africa. Therefore, we proceeded to retrieve West African countries' SARS-CoV-2 data from public repository (GISAID) and then ensued to a descriptive statistical analysis. From the start of the pandemic till December 2023, we found less than a million COVID-19 cases notified within the West African region. Overall, the study population was 50.21 % Males with a median age of 37. Regarding genomic data, only 3.02 % of cases were sequenced and deposited in GISAID. Of the available sequence, we noted that most of the variants have circulated in West Africa before the official notification of the variants. Nigeria, Ghana, and Senegal provided together more than half of West Africa's originating sequences when Omicron and Delta variants were the most sequenced in West Africa.

KW - Evolution

KW - SARS-CoV-2

KW - Variants dynamics

KW - West-Africa

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U2 - 10.1016/j.meegid.2024.105681

DO - 10.1016/j.meegid.2024.105681

M3 - Review article

C2 - 39437881

AN - SCOPUS:85206881342

SN - 1567-1348

VL - 125

JO - Infection, Genetics and Evolution

JF - Infection, Genetics and Evolution

M1 - 105681

ER -

Dynamics of SARS-CoV-2 variants in West Africa: Insights into genomic surveillance in resource-constrained settings

Abstract

Funding

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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