The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Authors: Tegally Houriiyah , San James E. , Cotten Matthew , Tegomoh Bryan , Mboowa Gerald , Martin Darren P. , Baxter Cheryl , Moir Monika , Lambisia Arnold , Diallo Amadou , Amoako Daniel G. , Diagne Moussa M. , Sisay Abay , Zekri Abdel-Rahman N. , Barakat Abdelhamid , Gueye Abdou Salam , Sangare Abdoul K. , Ouedraogo Abdoul-Salam , Sow Abdourahmane , Musa Abdualmoniem O. , Sesay Abdul K. , Lagare Adamou , Kemi Adedotun-Sulaiman , Abar Aden Elmi , Johnson Adeniji A. , Fowotade Adeola , Olubusuyi Adewumi M. , Oluwapelumi Adeyemi O. , Amuri Adrienne A. , Juru Agnes , Ramadan Ahmad Mabrouk , Kandeil Ahmed , Mostafa Ahmed , Rebai Ahmed , Sayed Ahmed , Kazeem Akano , Balde Aladje , Christoffels Alan , Trotter Alexander J. , Campbell Allan , Keita Alpha Kabinet , Kone Amadou , Bouzid Amal , Souissi Amal , Agweyu Ambrose , Gutierrez Ana V. , Page Andrew J. , Yadouleton Anges , Vinze Anika , Happi Anise N. , Chouikha Anissa , Iranzadeh Arash , Maharaj Arisha , Batchi-Bouyou Armel Landry , Ismail Arshad , Sylverken Augustina , Goba Augustine , Femi Ayoade , Sijuwola Ayotunde Elijah , Ibrahimi Azeddine , Marycelin Baba , Salako Babatunde Lawal , Oderinde Bamidele S. , Bolajoko Bankole , Dhaala Beatrice , Herring Belinda L. , Tsofa Benjamin , Mvula Bernard , Njanpop-Lafourcade Berthe-Marie , Marondera Blessing T. , Khaireh Bouh Abdi , Kouriba Bourema , Adu Bright , Pool Brigitte , McInnis Bronwyn , Brook Cara , Williamson Carolyn , Anscombe Catherine , Pratt Catherine B. , Scheepers Cathrine , Akoua-Koffi Chantal G. , Agoti Charles N. , Loucoubar Cheikh , Onwuamah Chika Kingsley , Ihekweazu Chikwe , Malaka Christian Noël , Peyrefitte Christophe , Omoruyi Chukwuma Ewean , Rafaï Clotaire Donatien , Morang’a Collins M. , Nokes D. James , Lule Daniel Bugembe , Bridges Daniel J. , Mukadi-Bamuleka Daniel , Park Danny , Baker David , Doolabh Deelan , Ssemwanga Deogratius , Tshiabuila Derek , Bassirou Diarra , Amuzu Dominic S.Y. , Goedhals Dominique , Grant Donald S. , Omuoyo Donwilliams O. , Maruapula Dorcas , Wanjohi Dorcas Waruguru , Foster-Nyarko Ebenezer , Lusamaki Eddy K. , Simulundu Edgar , Ong’era Edidah M. , Ngabana Edith N. , Abworo Edward O. , Otieno Edward , Shumba Edwin , Barasa Edwine , Ahmed El Bara , Kampira Elizabeth , Fahime Elmostafa El , Lokilo Emmanuel , Mukantwari Enatha , Cyril Erameh , Philomena Eromon , Belarbi Essia , Simon-Loriere Etienne , Anoh Etilé A. , Leendertz Fabian , Taweh Fahn M. , Wasfi Fares , Abdelmoula Fatma , Takawira Faustinos T. , Derrar Fawzi , Ajogbasile Fehintola V , Treurnicht Florette , Onikepe Folarin , Ntoumi Francine , Muyembe Francisca M. , Ngiambudulu Francisco , Zongo Ragomzingba Frank Edgard , Dratibi Fred Athanasius , Iyanu Fred-Akintunwa , Mbunsu Gabriel K. , Thilliez Gaetan , Kay Gemma L. , Akpede George O. , George Uwem E. , van Zyl Gert , Awandare Gordon A. , Schubert Grit , Maphalala Gugu P. , Ranaivoson Hafaliana C. , Lemriss Hajar , Omunakwe Hannah E , Onywera Harris , Abe Haruka , Karray Hela , Nansumba Hellen , Triki Henda , Adje Kadjo Herve Albéric , Elgahzaly Hesham , Gumbo Hlanai , mathieu Hota , Kavunga-Membo Hugo , Smeti Ibtihel , Olawoye Idowu B. , Adetifa Ifedayo , Odia Ikponmwosa , Boubaker Ilhem Boutiba-Ben , Ssewanyana Isaac , Wurie Isatta , Konstantinus Iyaloo S , Afiwa Halatoko Jacqueline Wemboo , Ayei James , Sonoo Janaki , Lekana-Douki Jean Bernard , Makangara Jean-Claude C. , Tamfum Jean-Jacques M. , Heraud Jean-Michel , Shaffer Jeffrey G. , Giandhari Jennifer , Musyoki Jennifer , Uwanibe Jessica N. , Bhiman Jinal N. , Yasuda Jiro , Morais Joana , Mends Joana Q. , Kiconco Jocelyn , Sandi John Demby , Huddleston John , Odoom John Kofi , Morobe John M. , Gyapong John O. , Kayiwa John T. , Okolie Johnson C. , Xavier Joicymara Santos , Gyamfi Jones , Kofi Bonney Joseph Humphrey , Nyandwi Joseph , Everatt Josie , Farah Jouali , Nakaseegu Joweria , Ngoi Joyce M. , Namulondo Joyce , Oguzie Judith U. , Andeko Julia C. , Lutwama Julius J. , O’Grady Justin , Siddle Katherine J , Victoir Kathleen , Adeyemi Kayode T. , Tumedi Kefentse A. , Carvalho Kevin Sanders , Mohammed Khadija Said , Musonda Kunda G. , Duedu Kwabena O. , Belyamani Lahcen , Fki-Berrajah Lamia , Singh Lavanya , Biscornet Leon , de Oliveira Martins Leonardo , Chabuka Lucious , Olubayo Luicer , Deng Lul Lojok , Ochola-Oyier Lynette Isabella , Mine Madisa , Ramuth Magalutcheemee , Mastouri Maha , ElHefnawi Mahmoud , Mbanne Maimouna , Matsheka Maitshwarelo I. , Kebabonye Malebogo , Diop Mamadou , Momoh Mambu , Lima Mendonça Maria da Luz , Venter Marietjie , Paye Marietou F , Faye Martin , Nyaga Martin M. , Mareka Mathabo , Damaris Matoke-Muhia , Mburu Maureen W. , Mpina Maximillian , Claujens Chastel Mfoutou Mapanguy , Owusu Michael , Wiley Michael R. , Tatfeng Mirabeau Youtchou , Ayekaba Mitoha Ondo’o , Abouelhoda Mohamed , Beloufa Mohamed Amine , Seadawy Mohamed G , Khalifa Mohamed K. , Dellagi Mohammed Koussai , Matobo Mooko Marethabile , Kane Mouhamed , Ouadghiri Mouna , Salou Mounerou , Mbulawa Mphaphi B. , Saibu Mudashiru Femi , Mwenda Mulenga , Kaba Muluken , Phan My V.T. , Abid Nabil , Touil Nadia , Rujeni Nadine , Ismael Nalia , Top Ndeye Marieme , Dia Ndongo , Mabunda Nédio , Hsiao Nei-yuan , Silochi Nelson Boricó , Saasa Ngonda , Bbosa Nicholas , Murunga Nickson , Gumede Nicksy , Wolter Nicole , Sitharam Nikita , Ndodo Nnaemeka , Ajayi Nnennaya A. , Tordo Noël , Mbhele Nokuzola , Razanajatovo Norosoa H , Iguosadolo Nosamiefan , Mba Nwando , Kingsley Ojide C. , Sylvanus Okogbenin , Peter Okokhere , Femi Oladiji , Testimony Olumade , Ogunsanya Olusola Akinola , Fakayode Oluwatosin , Ogah Onwe E. , Faye Ousmane , Smith-Lawrence Pamela , Ondoa Pascale , Combe Patrice , Nabisubi Patricia , Semanda Patrick , Oluniyi Paul E. , Arnaldo Paulo , Quashie Peter Kojo , Bejon Philip , Dussart Philippe , Bester Phillip A. , Mbala Placide K. , Kaleebu Pontiano , Abechi Priscilla , El-Shesheny Rabeh , Joseph Rageema , Aziz Ramy Karam , Essomba René Ghislain , Ayivor-Djanie Reuben , Njouom Richard , Phillips Richard O. , Gorman Richmond , Kingsley Robert A. , Audu Rosemary , Carr Rosina A.A. , Kabbaj Saâd El , Gargouri Saba , Masmoudi Saber , Sankhe Safietou , Mohamed Sahra Isse , Mhalla Salma , Hosch Salome , Kassim Samar Kamal , Metha Samar , Trabelsi Sameh , Lemriss Sanaâ , Agwa Sara Hassan , Mwangi Sarah Wambui , Doumbia Seydou , Makiala-Mandanda Sheila , Aryeetey Sherihane , Ahmed Shymaa S. , Ahmed Sidi Mohamed , Elhamoumi Siham , Moyo Sikhulile , Lutucuta Silvia , Gaseitsiwe Simani , Jalloh Simbirie , Andriamandimby Soafy , Oguntope Sobajo , Grayo Solène , Lekana-Douki Sonia , Prosolek Sophie , Ouangraoua Soumeya , van Wyk Stephanie , Schaffner Stephen F. , Kanyerezi Stephen , Ahuka-Mundeke Steve , Rudder Steven , Pillay Sureshnee , Nabadda Susan , Behillil Sylvie , Budiaki Sylvie L. , van der Werf Sylvie , Mashe Tapfumanei , Aanniz Tarik , Mohale Thabo , Le-Viet Thanh , Velavan Thirumalaisamy P. , Schindler Tobias , Maponga Tongai , Bedford Trevor , Anyaneji Ugochukwu J. , Chinedu Ugwu , Ramphal Upasana , Enouf Vincent , Nene Vishvanath , Gorova Vivianne , Roshdy Wael H. , Karim Wasim Abdul , Ampofo William K. , Preiser Wolfgang , Choga Wonderful T. , Ahmed Yahaya Ali , Ramphal Yajna , Bediako Yaw , Naidoo Yeshnee , Butera Yvan , de Laurent Zaydah R. , Ouma Ahmed E.O. , von Gottberg Anne , Githinji George , Moeti Matshidiso , Tomori Oyewale , Sabeti Pardis C. , Sall Amadou A. , Oyola Samuel O. , Tebeje Yenew K. , Tessema Sofonias K. , de Oliveira Tulio , Happi Christian , Lessells Richard , Nkengasong John , Wilkinson Eduan 
Published: April 2022

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.

One-Sentence Summary

Expanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.