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

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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.
American Association for the Advancement of Science (AAAS)
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 Adam 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 Akano Kazeem 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 Anika Vinze Anise N. Happi Anissa Chouikha Arash Iranzadeh Arisha Maharaj Armel L. Batchi-Bouyou Arshad Ismail Augustina A. Sylverken Augustine Goba Ayoade Femi Ayotunde E. Sijuwola Baba Marycelin Babatunde L. Salako Bamidele S. 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 Bourema Kouriba Bright Adu Brigitte Pool Bronwyn McInnis Cara Brook Carolyn Williamson Cassien Nduwimana Catherine Anscombe Catherine B. Pratt Cathrine Scheepers Chantal G. Akoua-Koffi Charles N. Agoti Chastel M. Mapanguy Cheikh Loucoubar Chika K. Onwuamah Chikwe Ihekweazu Christian N. Malaka Christophe Peyrefitte Chukwa Grace Chukwuma E. Omoruyi Clotaire D. Rafaï Collins M. Morang’a Cyril Erameh Daniel B. Lule Daniel J. Bridges Daniel Mukadi-Bamuleka Danny Park David A. Rasmussen David Baker David J. Nokes Deogratius Ssemwanga Derek Tshiabuila Dominic S. Y. Amuzu Dominique Goedhals Donald S. Grant Donwilliams O. Omuoyo Dorcas Maruapula Dorcas W. Wanjohi Ebenezer Foster-Nyarko Eddy K. Lusamaki Edgar Simulundu Edidah M. Ong’era Edith N. Ngabana Edward O. Abworo Edward Otieno Edwin Shumba Edwine Barasa El Bara Ahmed Elhadi A. Ahmed Emmanuel Lokilo Enatha Mukantwari Eromon Philomena Essia Belarbi Etienne Simon-Loriere Etilé A. Anoh Eusebio Manuel Fabian Leendertz Fahn M. Taweh Fares Wasfi Fatma Abdelmoula Faustinos T. Takawira Fawzi Derrar Fehintola V. Ajogbasile Florette Treurnicht Folarin Onikepe Francine Ntoumi Francisca M. Muyembe Frank E. Z. Ragomzingba Fred A. Dratibi Fred-Akintunwa Iyanu Gabriel K. Mbunsu Gaetan Thilliez Gemma L. Kay George O. Akpede Gert U. van Zyl Gordon A. Awandare Grace S. Kpeli Grit Schubert Gugu P. Maphalala Hafaliana C. Ranaivoson Hannah E. Omunakwe Harris Onywera Haruka Abe Hela Karray Hellen Nansumba Henda Triki Herve Albéric Adje Kadjo Hesham Elgahzaly Hlanai Gumbo Hota Mathieu Hugo Kavunga-Membo Ibtihel Smeti Idowu B. Olawoye Ifedayo M. O. Adetifa Ikponmwosa Odia Ilhem Boutiba Ben Boubaker Iluoreh Ahmed Muhammad Isaac Ssewanyana Isatta Wurie Iyaloo S. Konstantinus Jacqueline Wemboo Afiwa Halatoko James Ayei Janaki Sonoo Jean-Claude C. Makangara Jean-Jacques M. Tamfum Jean-Michel Heraud Jeffrey G. Shaffer Jennifer Giandhari Jennifer Musyoki Jerome Nkurunziza Jessica N. Uwanibe Jinal N. Bhiman Jiro Yasuda Joana Morais Jocelyn Kiconco John D. Sandi John Huddleston John K. Odoom John M. Morobe John O. Gyapong John T. Kayiwa Johnson C. Okolie Joicymara S. Xavier Jones Gyamfi Joseph F. Wamala Joseph H. K. Bonney Joseph Nyandwi Josie Everatt Joweria Nakaseegu Joyce M. Ngoi Joyce Namulondo Judith U. Oguzie Julia C. Andeko Julius J. Lutwama Juma J. H. Mogga Justin O’Grady Katherine J. Siddle Kathleen Victoir Kayode T. Adeyemi Kefentse A. Tumedi Kevin S. Carvalho Khadija Said Mohammed Koussay Dellagi Kunda G. Musonda Kwabena O. Duedu Lamia Fki-Berrajah Lavanya Singh Lenora M. Kepler Leon Biscornet Leonardo de Oliveira Martins Lucious Chabuka Luicer Olubayo Lul Deng Ojok Lul Lojok Deng Lynette I. Ochola-Oyier Lynn Tyers Madisa Mine Magalutcheemee Ramuth Maha Mastouri Mahmoud ElHefnawi Maimouna Mbanne Maitshwarelo I. Matsheka Malebogo Kebabonye Mamadou Diop Mambu Momoh Maria da Luz Lima Mendonça Marietjie Venter Marietou F. Paye Martin Faye Martin M. Nyaga Mathabo Mareka Matoke-Muhia Damaris Maureen W. Mburu Maximillian G. Mpina Michael Owusu Michael R. Wiley Mirabeau Y. Tatfeng Mitoha Ondo’o Ayekaba Mohamed Abouelhoda Mohamed Amine Beloufa Mohamed G. Seadawy Mohamed K. Khalifa Mooko Marethabile Matobo Mouhamed Kane Mounerou Salou Mphaphi B. Mbulawa Mulenga Mwenda Mushal Allam My V. T. Phan Nabil Abid Nadine Rujeni Nadir Abuzaid Nalia Ismael Nancy Elguindy Ndeye Marieme Top Ndongo Dia Nédio Mabunda Nei-yuan Hsiao Nelson Boricó Silochi Ngiambudulu M. Francisco Ngonda Saasa Nicholas Bbosa Nickson Murunga Nicksy Gumede Nicole Wolter Nikita Sitharam Nnaemeka Ndodo Nnennaya A. Ajayi Noël Tordo Nokuzola Mbhele Norosoa H. Razanajatovo Nosamiefan Iguosadolo Nwando Mba Ojide C. Kingsley Okogbenin Sylvanus Oladiji Femi Olubusuyi M. Adewumi Olumade Testimony Olusola A. Ogunsanya Oluwatosin Fakayode Onwe E. Ogah Ope-Ewe Oludayo Ousmane Faye Pamela Smith-Lawrence Pascale Ondoa Patrice Combe Patricia Nabisubi Patrick Semanda Paul E. Oluniyi Paulo Arnaldo Peter Kojo Quashie Peter O. Okokhere Philip Bejon Philippe Dussart Phillip A. Bester Placide K. Mbala Pontiano Kaleebu Priscilla Abechi Rabeh El-Shesheny Rageema Joseph Ramy Karam Aziz René G. Essomba Reuben Ayivor-Djanie Richard Njouom Richard O. Phillips Richmond Gorman Robert A. Kingsley Rosa Maria D. E. S. A. Neto Rodrigues Rosemary A. Audu Rosina A. A. Carr Saba Gargouri Saber Masmoudi Sacha Bootsma Safietou Sankhe Sahra Isse Mohamed Saibu Femi Salma Mhalla Salome Hosch Samar Kamal Kassim Samar Metha Sameh Trabelsi Sara Hassan Agwa Sarah Wambui Mwangi Seydou Doumbia Sheila Makiala-Mandanda Sherihane Aryeetey Shymaa S. Ahmed Side Mohamed Ahmed Siham Elhamoumi Sikhulile Moyo Silvia Lutucuta Simani Gaseitsiwe Simbirie Jalloh Soa Fy Andriamandimby Sobajo Oguntope Solène Grayo Sonia Lekana-Douki Sophie Prosolek Soumeya Ouangraoua Stephanie van Wyk Stephen F. Schaffner Stephen Kanyerezi Steve Ahuka-Mundeke Steven Rudder Sureshnee Pillay Susan Nabadda Sylvie Behillil Sylvie L. Budiaki Sylvie van der Werf Tapfumanei Mashe Thabo Mohale Thanh Le-Viet Thirumalaisamy P. Velavan Tobias Schindler Tongai G. Maponga Trevor Bedford Ugochukwu J. Anyaneji Ugwu Chinedu Upasana Ramphal Uwem E. George Vincent Enouf Vishvanath Nene Vivianne Gorova Wael H. Roshdy Wasim Abdul Karim William K. Ampofo Wolfgang Preiser Wonderful T. Choga Yahaya Ali Ahmed Yajna Ramphal Yaw Bediako Yeshnee Naidoo Yvan Butera Zaydah R. de Laurent Ahmed E. O. Ouma Anne von Gottberg George Githinji Matshidiso Moeti Oyewale Tomori Pardis C. Sabeti Amadou A. Sall Samuel O. Oyola Yenew K. Tebeje Sofonias K. Tessema Tulio de Oliveira Christian Happi Richard Lessells John Nkengasong Eduan Wilkinson Aaron L. Shibemba Abasi Ene Obong Abayomi Fadeyi Abbad Anas Abd Elazeez Shabaan Abd Monaem Adel Abd Moniem Ain Shoka W. Abdelhamid Abdelilah Laraqui Abdelkader Laatiris Abdelkrim Meziane Bellefquih Abdellah Faouzi F. Abdelmoulah Abdelomunim Essabbar Abderrahmane Bimouhen Abderraouf Hilali I. Abdo Abdou Padane Abdoul Karim Sangaré Abdoul Karim Soumah Abdoulaye Djimde Abdoulaye Toure Abdoulie Kanteh Abdulla Bashein Abdullah Salama Abe Lojuan Abebe Genetu Bayih Abel Abera Negash Abel Lissom N. Abid Abla A. Konou Abo Shama O. Abosede S. Abouelnaga Abraham Ali Abraham Kwabena Anang Abraham Tesfaye Adam K. Khan Adamu Tayachew Adane Mihret Adba Alfatih AlEmam Adede Hawi A. Adesegun Adey Feleke Desta Adib Ghassan Adjaratou Traoré B. A. Adjiratou Aissatou Adodo Sadji Adrian Egli Adriano Mendes Adugna Abera Adul Candé Afaf Alaoui Afonso Pedro B. Agbodzi A.M. Ageez Ahidjo Ayouba Ahlam Alarif Ahmed E Kayed Ahmed El-Taweel Ahmed Elsayed Ahmed F. Gad Ahmed Fakhfakh Ahmed Kandeil M. Ahmed Ahmed Mostafa O. S. Ahmed Ahmed Reggad Ahmed Taha Ahyong Vida Aicha Bensalem Aida Sivro Aissam Hachid F. Ajili F.V. Ajogbasile Akim A. Adegnika Akoele Siliadin Akwii Patience Natasha Aladje Balde Alan Lemtudo Alaoui Sanaa-amine A. M. Alaruusi Alassane Ouro-Medeli Albert Nyunja Alberto Rizzo Alemseged Abdissa Alemu Tike Debela Alessandro Mancon Alessandro Marcello Alexander Goredema Alexander Greninger Alexis Ndjolo Alexis Niyomwungere Alfredo Mari Alfredo Mayor M.A. Ali Ali Zumla Alia Ben Kahla Alia Grad Alice Kabanda Alie Tia Alimou Camara Alimuddin Zumla Alle Baba Dieng Almoustapha I. Maiga Amadou Alpha Sall Amadou Daou Amal Naguib Amal Souiri Amal Zouaki Amalou Ghita Amandine Mveang-Nzoghe Amariane Koné Amariane M. M. Koné Ambroise Ahouidi Amel Benyahia Amel Nagiub K. E. Amer Ameyo Dorkenoo Amina Barkat Aminata Dia Aminata Mbaye Aminata Mboup Aminata Sileymane Thiam Amine Idriss Lahlou Amira Suliaman Wadi Amivi Ehlan Amujal Marion Amuri Aziza Amy Strydom Anass Abbad Anatole Nkeshimana Andargachew Mulu Anderrahmane Maaroufi Andrea E. Luquette Andreas Shiningavamwe Andres Moreira-Soto Andrew Azman Andrew J. Bennett Andrew Tarupiwa Anga Latifa Ange Badjo Angel Angelov Angela Brisebarre Angela M. Detweiler Angoune Ndong Anja Werno Anna Julienne Selbe NDiaye Anna-Lena Sander B. Annajr Annamaria D'Aprile Anne van der Linden Annemiek van der Eijk Annette Erhart Anou M. Somboro Anoumou Dagnran Anthony Ahumibe Anthony Levasseur Antje van der Linden Antoine Dara Anu Jegede-Williams M. Aouni A. Arjarquah Arlene Uwituze Arlo Upton Armel Poda Arsène Somé Arsène Zongo Arsenia Massinga K.M. Asare Ashaba Fred Katabazi Asma Ferjani Assane Dieng Astou Gaye-Gaye N. Atiga Atsbeha G. Weldemariam Augustina Arjaquah A. Auld Awa Ba-Diallo Awatef ElMoussi Awunyo Sena Aya Mohamed Ayman Farghaly B. Ayo-Ale F. Ayoade Ayola Akim Adegnika Ayong More Ayorinde Babatunde James Azami Nawfel Azaria Diergaardt Azuka Patrick Okwuraiwe Babafemi O. Taiwo S. B. Baboo B. S. Bahadoor A.A. Bahnassy Bakary Sanyang U. Bakry Bamba Fatoumata Touré Bamidele Iwalokun R. Banda S. Bane Bankole Johnson Barada Cisse Barbra Murwira Bas Oude Munnink Armel L. Batchi-Bouyou R. Batra Beatrice Dhaala Belayachi Lamiae A.B. Belkhir I. Ben Ayed Ben Morton Ben Moussa Ben Wulf Bénédicte Ndeboko Benhida Rachid Benjamiin B. Lindsey Benjamin H. Foulkes Benjamin Hounkpatin Benjamin Selekon M. Bensaid Bernard Mpairwe Bernard Ssentalo Bagaya Bert Vanmechelen Bertrand Lell Beth Mutai Bethlehem Adnew Beuty Makamure B. Bighignoli Birahim Piere Ndiaye Bishwo N. Adhikari S.M. Bitrou Blaise MBoringong Akenji Bode Shobayo Boitumelo Zuze Bonifacio Manguire Nlavo Bouchra Belfquih Bouchra Boujemla Bouna Yatassaye Bouzidi Aymane Brian Andika Bright K. Yemi Bronwyn Kleinhans Bruna Galvao Bubacar Delgado Pinto Embaló Bulelani Manene Butoyi Pascal Camille Capel Campbell Anu Carine Tchibozo Carla Madeira Carlos Cortes Carniel Elisabeth Carol Kifude Carolle Yanique Tayimetha Catherine E. Arnold Catherine Okoi Cecilia Waruhiu Celestin Godwe Celestina Obiekea Celine Nkenfou L. B. Chabuka Chakib Nejjari H. Chambaro D. Chanda K. Changula Charifa Drissi Touzani Charles Kayuki Charles Nyagupe Charles Ssuuna Charoute Hicham Chaselynn M. Watters H. Chawech Cheikh Sokhna Chenaoui Mohamed Chiamaka Nwuba C. Chilufya Chimaobi Chukwu Chinyere Anyika P.J. Chipimo S. Chitanga M. Chitenje M. J. Chiwaula Chouati Taha Chris Mansell Christelle Butel Christian A. Devaux Christian Drosten Christian Ranaivoson Christian Utpatel Christophe Malabat A. Chtourou G. Chukwu Claudia Daubenberger Clement G. Kakai Clement Masakwe Clotaire Donatien Rafai Collins Chenwi Collins M. Misita Collins Muli Corine H. GeurtsvanKessel Corinne Maufrais Coulibaly Mbegnan M. Crawford Cristina M. Tato Cyrus Yiaba N. D'Amore Dabiri Damilari Dalia Ramadan D. Damena Daniel Ouso Daniela Pisanelli Danilo Licastro David Hammer David Nieuwenhuijse David Patrick Kateete David Wilkinson Davy Leger Mouangala Dawit Hailu Alemayehu R.M. Dawood R. De Sanctis Deborah N. A. Mettle Demba Koita Dennis Kenyi Lodiongo Dennis Laryea Dennis N. Wandera Dereje Leta Dersi Noureddine Desire Takou Dessalegn Abeje Tefera Dhwani Batra Dia Ndongo A. Diab Diabou Diagne Diane A. Mabika Diané Bamourou Dianke Samaté B. Diarra Didier Raoult Dieudonne Mutangana Dineo Emang Tshiamo. Gape Nyepetsi Diosdado Odjama Nseng Ada Djimabi Salah Donatella Cedola Doris Harding Dorothy Yeboah-Manu Dossou Ange Dowbiss Meta Djomsi Dragana Drinkovic C. Draper Dumbuya Foday Sahr Ebenezer Odewale Eclou Sedjro Edang-Minko Armand Edgar Kigozi Edith Koskei Edith Nkwembe Edmilson F. de Oliveira Filho Edmira Maria da Costa Edward Kiritu Efrem S. Lim Egon A. Ozer B. Egyir Ehab Abdelkader Abuelenein Eitel Mpoudi Ngole El Aliani Aissam El Ansari Fatima Zahra El Hamouchi Adil El Oualid Abdelmjid H. El-Shaqnqery M. El-Zayat Elamin Abualas Elannaz Hicham A. Elargoubi Eleni Kidane Elham Rizgalla M.M. Elhoseny F.W. Elhosieny Elisabeth Carniel Elizabeth Nyakarungu S.M. Elkhateeb Elmostafa Benaissa Elmostafa El Fahime M. Elouanass M.H. Elsissy Elvyre Mbongo-Nkama Elwaleed M. Elamin Sara A.I Latif Emame Edu Emanuele Orsini Emilio Skarwan Emily K. Stefanov Emmanuel Nasinghe Emmanuel Nepolo Emmanuel Ogunbayo Emmanuelle Munger Emmanuelle Permal Emna Gaies H. Ennibi Ennibi Khalid Erasmus Kotey Erasmus Smit Eric A. Lelo Eric Adu Eric Delaporte Eric Katagirya Eric Kezakarayagwa Eric Muthanje Erica Luis Maria Magalhães Ernest Asiedu Esemu Livo Esperance Umumararungu Esther Chitechi Esther Omuseni Etoundi Mballa Alain Evelyn Bonney Quansah Evelyn Y. Bonney M.H. Ezzelarab Faatu Cassama Fabien Roch Niama Fabio Arena G. Faggioni E. Fahsbender Faith Sigei Faouzi Abdellah Farah Jouali H. Farawyla Farida Hilali Fatima Chgouri Fatima El Falaki Fatima Zahra El ansari Fatma Ebied Fatna Bssaibis Fattah Al Onifade Faye Ousmane Fayez Ahmed Khardine Fayez Khardine A.V. Fedorov Fekadu Alemu Fekkak Jamal Fengming Sun Fetouma Doudou A.E. Fikry S. Fillo Fiorenza Bracchitta Firmin Kaboré L. Fki-berrajah Flora Donati Florence Fenollar Foday Sahr Samuel Sorie O. Folarino Francine Folorunsho Francisca Kabatesi Francisco Muyembe-Mawete François Malagon Franklin Kiemdé Franklyn Egbe Asiedu-Bekoe Frédéric Nkongho Frederick Lemoine Tei-Maya R. H. Freitas T. Fuh-Neba I. Gaaloul Gabriel Kabamba Gadissa Gutema Gaies Emna Galadima Gadzama Galal Mahmoud Garba Ouangole S. Gargouri R. Garry Gary McAuliffe Gathii Kimita Gédéon Prince Manouana Gelanew Tesfaye George Awinda George B. Kyei George Michuki Georgelin Nguema Ondo Gerhard van Rooyen Gert Marais Getachew Abichu Getachew Tesfaye Beyene Getachew Tollera Getnet Hailu Ghamaz Hamza Ghazi Kayali Ghizlane El Amin Gibson Mhlanga Gilbert Kibet Gildas Hounkanrin F. Giordani Gizaw Teka Godfrey Masete R. Goldstone C. Gomaa Gomaa Mokhtar Gora Lo B. I. Gosnell A. Gottberg Grace Angong Belournou Grace Oni Grace Vincent Gregory Wani Guedi Ali Barreh Guillermo Garcia Guohong Deng N. P. Guseva Guy Paterne Malonga Mbembo Guy Stéphane Padzys S. Gwayi Habiba Ben Romdhane Habiba Naija Haby Diallo A. Hadad M.M. Hafez Hafsia Ladhari Hagar Elshora Hailu Dadi Hajjaji Mohammed Hakima Kabbaj Hala Hafez A. Halafawy Halidou Tinto Halimatou Diop Ndiaye Hamadi Assane T.N. Hamdani M.S. Hamdy Hamidah Namagembe M. Hammad A. Hammami Hamza Gharmaz Hana Sofia Andersson Hanae Dakka Hanen El Jebari Hany K. Soliman Harmak Houda R. Harvey Hasnae Benkirane Hassan Aguenaou Hassan Ihazmad R. Hassan W. Hassan Hatem Ahmed Heitzer Sogodogo Helena Seth-Smith Helisoa Razafimanjato Hellen Koka Hemlali Mouhssine Henry Mwebesa Hermes Perez Herve Christian Paho Tchoudjin Hicham Elannaz Hicham Oumzil Hilda Opoku Frempong Hinson Fidelia Hoda Ezz Elarab Hong Xie Houda Benrahma Housna Arrouchi Houssem Guedouar Hu Luo Hubert Bassène Huiqing Si Ian Goodfellow Ibrahima Guindo Ibrahima Halilou Idil Salah Abdillahi Idriss-Amine Lahlou Idrissa Diawara Ifunanya Egoh F.A. Ige A.A. Iknane Ikram Bnouyahia Ikram Omar Osman Ilhem Boutiba Ben Boubaker Iman Abdillahi Hassan Iman Foda Imane Smyej Imen Kacem Imen Mdini Imen Mkada Inacio Mandomando Iñaki Comas Ines Mdini L. Inglês Innocent Mudau Ireoluwa Yinka JOEL Irina Chestakova Irving Cancino Isaac Phiri Ismael Pierrick Mikelet Boussoukou A. Ismail Israel Osei-Wusu Issaka Maman Ivan Barilar Ivy A. Asante Izuwayo Gerard Jaafar Heikel Jacob Souopgui Jacques Marx D. Jalal Jalal Nourlil Jalil El Atar Jalila Ben Khelil Jalila Rahoui Jamal Fekkak James Mutisya James Ussher Jan Felix Exler Jane MaCauley Janet Majanja N. Jannoo Jarra Manneh Jasmin Scharnberg Jasmin Schlotterbeck Jasper Chimedza Jawad Bouzid Jean B. Niyibigira Jean Claude Djontu Jean Maritz Jean-Claude Makangara Cigolo Jean-louis Monemou Jeanne d’Arc Umuringa Jeremy Delerce Jerome Ndaruhutse Jerome Nkurunziza Jesse Addo Asamoah Jill Sherwood Jing Wang Joan Marti-Carerras Joe K. Mutungi Joe Mutungi Joel Fleury Djoba Siawaya Joel Koivogui Joep de Ligt John Njuguna John Rumunu John Tembo John Waitumbi Johnson A. Adeniji Jonathan Rigby Jorn Hellemans Joseph Fokam Joseph L. DeRisi Joseph Makhema Joseph Mugisha Joseph Ojonugwa Shaibu Joseph Oliver-Commey Josephine Bwogi Josh Freeman Josiah Ayoola Isong Josphat Nyataya Joy Ayoola Joyce Appiah-Kubi Judd F. Hultquist Jude Gedeon Judith Sokei Julia Howard Julia Schneider Julian Campbell Juliet Elvy A.B. Jumaa Justin Lee Justin Lessler Justin O'Grady Kaba Kourouma Kais Ghedira K. Kalantar Kamela Mahlakwane S. Kamoun Kangwa Mulonga P.C. Kapata F. Kapaya M. Kapin'a H. Karray Hakim W. Kasambara Kasmi Yassine Kassahun Tesfaye Kathleen Subramoney A.D. Katyshev N. Kayeyi Kayla Barnes Kayla Delaney E.V. Kazorina Kedumetse Seru S. Keita Keith Durkin Keith R Jerome Keke K. René Kena Swanson Kenneth K. Maeka Keren Okyerebea Attiku Kevin Sanders Kevine Zang Ella Keyru Tuki Khabab A. Elhag Khadim Gueye Khaled Amer Khalid Ennibi Mostafa N. Kharat Z. Khumalo Kilian Stoecker L. Kim Kimberly A. Bishop-Lilly J. Kimotho Kitane Driss Lahlou Kofi Bonney Kokou Tegueni Kolawole Wasiu Wahab E.V. Kolomoets Komal Jain Kominist Asmamaw Komlan Kossi Kondwani Jambo Kouadio T. Yao Kouriba Dürr Kra Ouffoué Y.M. Krasnov Krishna Kumar Kandaswamy Kristian Andersen A.A. Kritsky Kumbelembe David Kutlo Macheke V.V. Kutyrev S. Kwenda Kwitaka Maluzi Kwok Lee Kyle A. Long Kyra Grantz Lacy M. Simons Laetitia Serrano Laila Elsawy Laila Sbabou Lallepak Lamboni LaRinda A. Holland Lasata Shrestha Lassana Sangaré Latifa Anga Lauren Jelly Laurien Hoornaert Le Thi Kieu Linh Legodile Kooepile Leigh-Anne MC Intyre Léon Mutesa Leona Okoli Léopold Ouedraogo Kuate-lere Lesego D. Leta A. Letaief G. Liboro Lilian Kanjau L. Lin Linda Boatemaa Linda Houhamdi Lipkin W. Ian F. Lista M.M. Liwewe Lloyd Mulenga Logan J. Voegtly Loide Shipingana Loris Micelli Lorreta Kwasah Loubna Allam Louise Lefrançois Loukman Salma Lucas N. Amenga-Etego Ludivine Brechar Ludovic Mewono Luis A. Estrella Lusia Mhuulu Lwanga Newton M. Ulrich M.T. Mogotsi Maaroufi Abderrahmane W. Mad W.Y. Madi Madlen Stange S. Magdeldin Maher Kharrat B. Mahlangu Mahmoud Shehata N. Mahrous A. Maida Makhtar Camara T. Makori K. Malama Malena S. Bestehorn-Willmann I. Malolo Mamadou Beye Cheikh Ibrahima Lo Mamadou Bhoye Keita Mamadou Saliou Bah Mamadou Saliou Sow Mamoudou Harouna Djingarey Mamoudou Maiga Manal Hamdy Elsaid Manal Hamdy Zahran Mandiou Diakite Manel Ben Sassi Mangombi Pambou N. Manickchund Manoli Torres Puente S. S. Manraj T. Mansour Maowia M. Mukhtar Marcel Tongo Marchoudi Nabila Margaret Mills Maria Artesi Maria Pia Patrizio Maria Rita Gismondo Maria Rosaria Lipsi Mariam Kehinde SULAIMAN Mariama Kujabi Marie Amougou Marie Claire Okomo Marie Madeleine Chabert-Consen Marie-Astrid Vernet Marie-Pierre Hayette Mariem Gdoura Marijke Reynders Marion Barbet Marion Koopmans Marjan Boter Mark Siedner Markos Abebe Markus H. Antwerpen Marouane Melloul Martin Maidadi Foudi Martine Peeters Marvin Hsiao Mary DeAlmeida Mary Lalemi Mary-Ann Davies K. Masahiro Masse Sambou M. Mathabo Mathew D. Parker Mathias C. Walter H. Mathur Matt Blakiston Matt Storey Matthew Bates Matthew Rogers Matthias Pauthner Maud Vanpeene Maurizio Margaglione Max Bloomfield May Abdelfattah May Sherif Soliman Mbengué Fall K. Mdlalose Meei-Li Huang S. Mehta Mélanie Albert Melchior A. Joël Aïssi Méline Bizard Merabet Mouad Meriem Laamarti Messanh Douffan S. Mhalla Michael Addidle Michael Marks Michael Nagel Michael V. Deschenes Micheala Davids Michelle Balm Michelle Lin Michelle Tan A. Mihrete Mikhail Olayinka BUHARI Milanca Agostinho Cá Mildred Adusei-Poku Milkah Mwangi Mina Kamel J. Miranda Mireille Prince-David Miriam Eshun Misaki Wayengera Mitali Mishra Mjid Eloualid Mly Abdelaziz Elalaoui A. Mnguni F. Mnyameni Mogomotsi Matshaba T. Mohale Mohamed Abdel-Salam Elgohary Mohamed Ahmed Ali Mohamed Ben Moussa Mohamed Chenaoui Mohamed El Sayes Mohamed Elhadidi Mohamed Gomaa Seadawy Mohamed Hassan Abdoelraheem Mohamed Hassany Mohamed Houmed Aboubaker K.S. Mohamed Mohamed Kamal Mohamed Rhajaoui Mohamed Seadawy Mohamed Shamel Mohamed Shemis K.S. Mohammed Mohammed Walid Chemao Elfihri Mohcine Bennani Mechita Mokhtar Gomaa Molalegne Bitew M. Momoh Mona O.A. Alkarim Monemo Pacome Monilade Akinola A. Monte G. Monuir M. Monze M. Mooko A.N. Morales Moreira-Soto Andres Moriba Povogui Mosepele Mosepele Moses Chilufya Moses Joloba Moses Luutu Mostafa Elouennass Mostfa Elhoseiny Mostfa Elnakib Mostfa Yakout Mouhcine Gardoul Mouhssine Hemlali A. Mouity Matoumba Mouna Ben Sassi Mouna Safer Mouneem Essabbar Moustapha Mbow Moustapha Nzamba Maloum Moustapha Sakho Moyinoluwa Odugbemi P. Mtshali B. Mubemba Muchaneta Mugabe M. Mufinda Muhammad Faisal Muinah Adenike Fowora Mukantwari Enatha W. Muleya Muntaser elTayeb Ibrahim F. Mupeta Murebwayire Clarisse Mushal Ali Mushal Allam Mustapha Mouallif S.N. Muuo W. Mwangomba Myriam Seffar T. E. Mzumara N. N'dilimabaka Nabila Soara A. Nabli Nadia El Mrimar Nadia Rodrigues Nadia Sitoe Nafisatou Leye A. Naguib K. S. Nalubamba Nancy M. El Guindy Nandi Siegfried Nardjes Hihi Narjis Amar E.A. Naryshkina Nathalia Endjala Nathalia Garus-Oas Nathan Kapata Ndack Ndiaye Ndahafa Frans N.T. Ndam Ndéye Coumba Touré Kane Ndiaye Ndack Ndine Fainguem Ndodo Nnaemeka Ndumbu Pentikainen L. Ndwiga Nedio Mabunda N. Neff A.A. Negash Nejla Stambouli Z. Neto A.M. Ngonga Dikongo W. Ngosa Ngozi Mirabel Otuonye F. S. Niatou-Singa Nicaise T. Ndam Nicholas Feasey Nicholas Mwikwabe J. Nicod Nicole Vidal Nikki Freed Nischay Mishra Nissaf Ben Alaya Nitin Savaliya Noah Baker Noé Patrick Mbondoukwe Nokukhanya Mdlalose Nonso Nduka Noura M Abo Shama Nourlil Jalal Nsubuga Gideon N. Ntuli Nuro Abilio Nyam Itse Yusuf Oby Wayoro M. Ochwoto Ofonime Ebong L. Ofori-Boadu Okomo Assoumou Marie Claire Ola Elroby Olabisi Olabisi Olajumoke Ojo Popoola L. Olfert Olin Silander Olufemi Obafemi Olufemi Samuel Amoo Olukunke Oluwasemowo Olusola Anuoluwapo Akanbi Oluwakemi Laguda-Akingba Oluwatimilehin Adewumi Omar Askander Omar Elahmer S. Omar S. Omilabu Omnia Kutkat Omoare Adesuyi Omondi Francis Carey Onalethata Lesetedi E. Ongera Ontlametse T. Bareng C.K. Onwuamah O. Ope-Ewe Osama Mansour Oscar Kanjerwa F. Oteng Otmane Touzani Oumaima Ait Si Mohammed Oumy Diop Ouna Ouadghiri Ousseynou Gueye C. Owusu-Nyantakyi A. Oyefolu Oyeronke Ayansola P Nthiga S. Palomba L. Panja Papa Alassane Diaw D. Park Pasacaline Manga H. Patel Patience Motshosi M. Patoo Patrick Amoth Patrick Descheemaeker Patrick Mavingui Patrick Tuyisenge M. Pattoo Paul Dobi Paul Liberator Paulin N. Essone Paulina Joãozinho da Costa Jarra Manneh Pauline Yacine Sene Paulo A. Carralero R.R. Paixão Pavitra Roychoudhury Peace O. Uche Pei Zhou Penda Malhado Diallo A. Pereira Petas Akogbeto Peter Bauer Peter T. Skidmore Petra Raimond Phasha-Muchemenye Mmatshepho Philip Ashton C. Philip Philip El-Duah Philip M. Soglo Philip Wonder Phiri Philipp Wagner Philippe Colson Philippe Dussart Philippe Lavrard Meyer Phillip Ashton Phionah Tushabe Pierre-Edouard Fournier Piet Maes Popova A. Yu Portia Manangazira Praise Adewumi Qi Yang Quaneeta Mohktar E.B. Quansah P. Quashie Rabia Quedraogo Rachel Maqsood Rachid Githii Rachid Abi Rachid Benhida Rachid El Jaoudi Rahaman A. Mentag Rahma Ahmed Raiva Algheriani Rajiha Simbi Ramalia Chabi Abubeker Ramon Nari Ramy Lorenzo-Redondo Galal A. Raouf Raoul Saizonou Raphael Lumembe Ravena Mubichi Regina Z. Cer Reham Dawood Reham Kassab Rehema Liyai A. Rehn Rei José Pereira Reina Sikkema Rfaki Abderrazak Riad Mounir Armanious Riadh Daghfous Riadh Gouider Richard Adegbola Richard Lino Loro Lako Richard Molenkamp Richard Webby Richmond Yeboah S. Rick Rida Tagajdid Rine Zeh Nfor Rivalyn Nakoune Yandoko Robert Newton Robert Rutayisire Rodney S. Daniels Rodrigue Bikangui Rodrigue K. Kohoun Rodrigue Kamga Rodrigue Mintsa Nguema Roger Shapiro J. Rogers Rogers Kamulegeya Rokaia Laamrti Roméo Aimé Laclong Lontchi Ronald Kiiza Ronald M. Galiwango Rosella De Nittis W.H. Roshdy Rotimi Myrabelle Avome Houechenou Roua Ben Othman Rui Inndi M.A. Saad Saaïd Amzazi Sabin Nsanzimana Sada Diallo Y.A. Sadji Safae El Mazouri Safae Elkochri Safae Ghoulame Safiatou Karidioula Safietou Sankhe Sahr Gevao P.F. Sahr J.O. Saibu Saïdou Ouedraogo S. Saiid Sainabou Laye Ndure Sakoba Keita D. Salah Salah Eldin Hussein H. Salah A.A. Saleh M. Saleh Salifou Sourakatou Sally Roberts Salma Abid Salma Sayed M. Salou O.B. Salu Sam Lissauer Sam O'neilla Oye Bingono Samba Ndiour Sameira M. Fageer Samia Abdou Girgis M. Samir O. Samir Samira Benkeroum Samira F. Ibrahim Samira M. Fageer Samira Zoa Assoumou Samirah Saiid Samoel Ashimosi Khamadi Samson Konongoi Limbaso Samuel Armoo Samuel Kirimunda Samuel Sorie Samwel Lifumo Symekher Samwel Owaka Sana Ferjani Sanaa Alaoui-Amine Sander Anna-Lena Sankhe Safietou Santiago Jiménez-Serrano Santigie Kamara Sara Chammam Sara Mahmoud Sarah Jefferies Sarah Rubin Sarah Stanley Saraswathi Sathees Saro Abdella Sarra Chamman Savannah Mwesigwa H. Sawa M.G. Seadawy Sean Ellis Sébastien Bontems Sefetogi Ramaologa Sekesai Zinyowera Selassie Kumordjie Sen Claudine Henriette Ngomtcho Sena Awunyo Serge Alain Sadeuh-Mba Serigne Saliou Niane Seth Okeyo Settimia Altamura Seyram Bless Agbenyo Shah Mohamed Bakhash Shahin Lockman Shahinaz.A. Bedri Shaimaa Soliman L. Shalaby Shannon Wilson Sharmini Muttaiyah Sharon Abimbola Sharon Hsu S.A. Shcherbakova Shebbar Osiany Shereen Shawky Sherine Helmy A.P. Shevtsova Shimaa Moustafa Shirlee Wohl Shirley Johane Sidonie A.M. Kagnissode Silvanos Mukunzi Opanda Sim Mayaphi Simão Tchuda Bióté Simeone Dal Monego Simon Peter Ruhweza Simone Eckstein Sindayiheba Reuben N. Sinyange Sivaramakrishna Rachakonda Soa Fy Andriam Sofia Viegas Sokhna Sogodogo Sola Ndongo Solomon Ajibaye Sombo Langat Somda Soro Georgina Fwoloshi Sonal P. Charlene Sondes Henson Sonia V. Haddad Bedié E.A. Sosedova Souad Kartti Souissi Amira Souleymane Mboup Soundélé Maïté Sounkalo Dao Sourakatou Salifou Srinivas Reddy Pallerla Stefan Niemann Steffen Borrmann Stephen Asiimwe Stephen M. Eggan Stephen Ochola Stephen Wanok Steven J. Reynolds Subomi Olorunnimbe Sudhir Bunga C. Sujeewon Sunday Babatunde Susan Engelbrecht Susan Morpeth Susan Taylor Susann Handrick Swaibu Gatare Sylvie Melingui S.L. Symeker Syntyche Devatchagni A.G. Taha Taha Chouati Taha Maatoug Tahar Bajjou A. Takada K.A. Taloa Tamrayehu Seyoum M. Tan Tania Stander Tanja Niemann Tarek Aanniz Tarek Refaat Elnagdy Raafat Zaher Tatenda Takawira C. Tato D.A. Tefera Tei-Maya Fred Tesfaye Gelanew Tesfaye Rufael Thanh Le Viet Thela Tefelo Thérèse Kagoné Thibaut Armel Cherif Gnimadi K. Thiongo Thomas Briese Van L. Thomas Thongbotho Mphoyakgosi Thushan I de Silva Tim Roloff Timothy Blackmore Tiziana Rollo Tom Lutalo Tomade A.M. Ibrahim T. B. Tombolomako Tomiwa Adepetun C. Tomkins-Tinch Tony Wawina-Bokalanga Tope Sobajo Touil Nadia Touria Essayagh Toy Nwako Traoré H. Triki R. Tsiry Tsiry Randriambolamanantsoa Tumisang Madisa M. Turki C.A. Ugwu Uyi Emokpae Valeria Delli Carri Valeria Micheli G. Van Rooyen M. Vanaerschot Vanessa Magnussen Vanessa Mohr Vani Sathyendran Veronica Playle R. Viana U. Vickos Victor Max Corman Victor Mukonka Victor Ofula Vida Ahyong Vincent Appiah Vincent Bours Violette V. M'cormack Virginia Hope Vivi Hue-Trang Lieu Vololoniaina Raharinosy Wadegu Meshack N. Wadonda J. Wadula Wael Ali Waidi Sule Wallace D Bulimo Warren Cyrus Yiaba C.N. Waruhiu Wasfi Fares R. Webby A.G. Weldemariam Wendy Karen Jo R. Woelfel S. Wolh I. Wurie Xavier Crespin Xiaoyun Ren Xiuhua Wang Ya.M. Krasnov Yacine Amet Dia Yacine DIA Seni Ndiaye Yacob Mohamed Yusuf Yacouba Sawadogo Yahya Yadouleton Yakob Gebregziabher Maidane Yao Tsegay Yasser Layibo Yassine El Hady Yassmin Sekhsokh Yawo A. Moatasim Sadji C. Yeboah Youbi Mohammed Yousif Rabih Makki Youssef Akhoud Yuri Ushijima Yusuf Jimoh Yvette Badou J. Matoke D. Zablon J.O. Zablon Zaineb Hamzaoui Zakia Regragui Zara Wuduri Zein Souma Zeinab Ali Waberi Zeinab S. Imam Zekiba Tarnagda Zemmouri Faouzia J. Zhang Zhenghui Li Zimmerman Maiga Zohour Kasmy Minko O. Zong A. Zorgani Zouheir Yassine Zoukaneirii Issa P. Zulu Zuzheng Xiang
Title: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Description:
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.

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