The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Houriiyah Tegally, James Emmanuel San, Matthew Cotten, Monika Moir, Bryan Tegomoh, Gerald Mboowa, Darren P. Martin, Cheryl Baxter, Arnold W. Lambisia, Amadou Diallo, Daniel G. Amoako, Moussa Moïse Diagne, Abay Sisay, Abdel‐Rahman N. Zekri, Abdou Salam Guèye, Abdoul Karim Sangaré, Abdoul–Salam Ouédraogo, Abdourahmane Sow, Abdualmoniem O. Musa, Abdul Karim Sesay, Abe G. Abias, Adam Elzagheid, Adamou Lagaré, Adedotun-Sulaiman Kemi, Aden Elmi Abar, Adeniji A. Johnson, Adeola Fowotade, Oluwapelumi O. Adeyemi, Adrienne Amuri-Aziza, Agnes Juru, Ahmed Kandeil, Ahmed Mostafa, Ahmed Rebaï, Ahmed A. Sayed, Kazeem Akano, Aladje Baldé, Alan Christoffels, Alexander J. Trotter, Allan Campbell, Alpha Kabinet Kéita, A. Koné, Amal Bouzid, Amal Souissi, Ambrose Agweyu, Amel Naguib, Ana Victoria Gutiérrez, Anatole Nkeshimana, Andrew J. Page, Anges Yadouléton, Anika Vinzé, Anise N. Happi, Anissa Chouikha, Arash Iranzadeh, Arisha Maharaj, Armel L. Batchi‐Bouyou, Arshad Ismail, Augustina Angelina Sylverken, Augustine Goba, Femi Ayoade, Ayotunde E. Sijuwola, Baba M, Babatunde Lawal Salako, Bamidele Soji Oderinde, Bankole Bolajoko, Bassirou Diarra, Belinda L. Herring, Benjamin Tsofa, Bernard Lekana-Douki, Bernard Mvula, Berthe‐Marie Njanpop‐Lafourcade, Blessing T. Marondera, Bouh Abdi Khaireh, Bourèma Kouriba, Bright Adu, Brigitte Pool, Bronwyn McInnis, Cara E. Brook, Carolyn Williamson, Cassien Nduwimana, Catherine Anscombe, Catherine Pratt, Cathrine Scheepers, Chantal Akoua‐Koffi, Charles N. Agoti, Chastel M. Mapanguy, Cheikh Loucoubar, Chika Onwuamah, Chikwe Ihekweazu, Christian Malaka, Christophe N. Peyrefitte, Chukwa Grace, Chukwuma Ewean Omoruyi, Clotaire Donatien Rafaï, Collins M. Morang’a, Cyril Erameh, Daniel Lule Bugembe, Daniel J. Bridges, Daniel Mukadi‐Bamuleka, Daniel J. Park, David A. Rasmussen
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.