The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Houriiyah Tegally; James E. San; Matthew Cotten; Monika Moir; Bryan Tegomoh; Gerald Mboowa; Darren P. Martin; Cheryl Baxter; Arnold W. Lambisia; Amadou Diallo; Daniel G. Amoako; Moussa M. Diagne; Abay Sisay; Abdel Rahman N. Zekri; Abdou Salam Gueye; Abdoul K. Sangare; Abdoul Salam Ouedraogo; Abdourahmane Sow; Abdualmoniem O. Musa; Abdul K. Sesay; Abe G. Abias; Adem I. Elzagheid; Adamou Lagare; Adedotun Sulaiman Kemi; Aden Elmi Abar; Adeniji A. Johnson; Adeola Fowotade; Adeyemi O. Oluwapelumi; Adrienne A. Amuri; Agnes Juru; Ahmed Kandeil; Ahmed Mostafa; Ahmed Rebai; Ahmed Sayed; Kazeem Akano; Aladje Balde; Alan Christoffels; Alexander J. Trotter; Allan Campbell; Alpha K. Keita; Amadou Kone; Amal Bouzid; Amal Souissi; Ambrose Agweyu; Amel Naguib; Ana V. Gutierrez; Anatole Nkeshimana; Andrew J. Page; Anges Yadouleton; Cat Anscombe

doi:10.1126/science.abq5358

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Houriiyah Tegally, James E. San, Matthew Cotten, Monika Moir, Bryan Tegomoh, Gerald Mboowa, Darren P. Martin, Cheryl Baxter, Arnold W. Lambisia, Amadou Diallo, Daniel G. Amoako, Moussa M. Diagne, Abay Sisay, Abdel Rahman N. Zekri, Abdou Salam Gueye, Abdoul K. Sangare, Abdoul Salam Ouedraogo, Abdourahmane Sow, Abdualmoniem O. Musa, Abdul K. SesayAbe G. Abias, Adem I. Elzagheid, Adamou Lagare, Adedotun Sulaiman Kemi, Aden Elmi Abar, Adeniji A. Johnson, Adeola Fowotade, Adeyemi O. Oluwapelumi, Adrienne A. Amuri, Agnes Juru, Ahmed Kandeil, Ahmed Mostafa, Ahmed Rebai, Ahmed Sayed, Kazeem Akano, Aladje Balde, Alan Christoffels, Alexander J. Trotter, Allan Campbell, Alpha K. Keita, Amadou Kone, Amal Bouzid, Amal Souissi, Ambrose Agweyu, Amel Naguib, Ana V. Gutierrez, Anatole Nkeshimana, Andrew J. Page, Anges Yadouleton, Cat Anscombe

Clinical Sciences

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

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Abstract

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Original language	English
Article number	eabq5358
Pages (from-to)	eabq5358
Journal	Science
Volume	378
Issue number	6615
DOIs	https://doi.org/10.1126/science.abq5358
Publication status	Published - 7 Oct 2022

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Tegally, H., San, J. E., Cotten, M., Moir, M., Tegomoh, B., Mboowa, G., Martin, D. P., Baxter, C., Lambisia, A. W., Diallo, A., Amoako, D. G., Diagne, M. M., Sisay, A., Zekri, A. R. N., Gueye, A. S., Sangare, A. K., Ouedraogo, A. S., Sow, A., Musa, A. O., ... Anscombe, C. (2022). The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science, 378(6615), eabq5358. Article eabq5358. https://doi.org/10.1126/science.abq5358

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title = "The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.",

abstract = "Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.",

author = "Houriiyah Tegally and San, \{James E.\} and Matthew Cotten and Monika Moir and Bryan Tegomoh and Gerald Mboowa and Martin, \{Darren P.\} and Cheryl Baxter and Lambisia, \{Arnold W.\} and Amadou Diallo and Amoako, \{Daniel G.\} and Diagne, \{Moussa M.\} and Abay Sisay and Zekri, \{Abdel Rahman N.\} and Gueye, \{Abdou Salam\} and Sangare, \{Abdoul K.\} and Ouedraogo, \{Abdoul Salam\} and Abdourahmane Sow and Musa, \{Abdualmoniem O.\} and Sesay, \{Abdul K.\} and Abias, \{Abe G.\} and Elzagheid, \{Adem I.\} and Adamou Lagare and Kemi, \{Adedotun Sulaiman\} and Abar, \{Aden Elmi\} and Johnson, \{Adeniji A.\} and Adeola Fowotade and Oluwapelumi, \{Adeyemi O.\} and Amuri, \{Adrienne A.\} and Agnes Juru and Ahmed Kandeil and Ahmed Mostafa and Ahmed Rebai and Ahmed Sayed and Kazeem Akano and Aladje Balde and Alan Christoffels and Trotter, \{Alexander J.\} and Allan Campbell and Keita, \{Alpha K.\} and Amadou Kone and Amal Bouzid and Amal Souissi and Ambrose Agweyu and Amel Naguib and Gutierrez, \{Ana V.\} and Anatole Nkeshimana and Page, \{Andrew J.\} and Anges Yadouleton and Cat Anscombe",

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day = "7",

doi = "10.1126/science.abq5358",

language = "English",

volume = "378",

pages = "eabq5358",

journal = "Science",

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number = "6615",

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Tegally, H, San, JE, Cotten, M, Moir, M, Tegomoh, B, Mboowa, G, Martin, DP, Baxter, C, Lambisia, AW, Diallo, A, Amoako, DG, Diagne, MM, Sisay, A, Zekri, ARN, Gueye, AS, Sangare, AK, Ouedraogo, AS, Sow, A, Musa, AO, Sesay, AK, Abias, AG, Elzagheid, AI, Lagare, A, Kemi, AS, Abar, AE, Johnson, AA, Fowotade, A, Oluwapelumi, AO, Amuri, AA, Juru, A, Kandeil, A, Mostafa, A, Rebai, A, Sayed, A, Akano, K, Balde, A, Christoffels, A, Trotter, AJ, Campbell, A, Keita, AK, Kone, A, Bouzid, A, Souissi, A, Agweyu, A, Naguib, A, Gutierrez, AV, Nkeshimana, A, Page, AJ, Yadouleton, A & Anscombe, C 2022, 'The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.', Science, vol. 378, no. 6615, eabq5358, pp. eabq5358. https://doi.org/10.1126/science.abq5358

TY - JOUR

T1 - The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

AU - Tegally, Houriiyah

AU - San, James E.

AU - Cotten, Matthew

AU - Moir, Monika

AU - Tegomoh, Bryan

AU - Mboowa, Gerald

AU - Martin, Darren P.

AU - Baxter, Cheryl

AU - Lambisia, Arnold W.

AU - Diallo, Amadou

AU - Amoako, Daniel G.

AU - Diagne, Moussa M.

AU - Sisay, Abay

AU - Zekri, Abdel Rahman N.

AU - Gueye, Abdou Salam

AU - Sangare, Abdoul K.

AU - Ouedraogo, Abdoul Salam

AU - Sow, Abdourahmane

AU - Musa, Abdualmoniem O.

AU - Sesay, Abdul K.

AU - Abias, Abe G.

AU - Elzagheid, Adem I.

AU - Lagare, Adamou

AU - Kemi, Adedotun Sulaiman

AU - Abar, Aden Elmi

AU - Johnson, Adeniji A.

AU - Fowotade, Adeola

AU - Oluwapelumi, Adeyemi O.

AU - Amuri, Adrienne A.

AU - Juru, Agnes

AU - Kandeil, Ahmed

AU - Mostafa, Ahmed

AU - Rebai, Ahmed

AU - Sayed, Ahmed

AU - Akano, Kazeem

AU - Balde, Aladje

AU - Christoffels, Alan

AU - Trotter, Alexander J.

AU - Campbell, Allan

AU - Keita, Alpha K.

AU - Kone, Amadou

AU - Bouzid, Amal

AU - Souissi, Amal

AU - Agweyu, Ambrose

AU - Naguib, Amel

AU - Gutierrez, Ana V.

AU - Nkeshimana, Anatole

AU - Page, Andrew J.

AU - Yadouleton, Anges

AU - Anscombe, Cat

PY - 2022/10/7

Y1 - 2022/10/7

N2 - Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

AB - Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

U2 - 10.1126/science.abq5358

DO - 10.1126/science.abq5358

M3 - Article

SN - 0036-8075

VL - 378

SP - eabq5358

JO - Science

JF - Science

IS - 6615

M1 - eabq5358

ER -

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

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