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

Houriiyah Tegally , James San , Matthew Cotten , Monika Moir , Bryan Tegomoh , Gerald Mboowa , Darren Martin , Cheryl Baxter , Arnold Lambisia , Amadou Diallo (1) , Daniel Amoako , Moussa Diagne (1) , Abay Sisay , Abdel-Rahman Zekri , Abdou Salam Gueye , Abdoul Sangare , Abdoul-Salam Ouedraogo , Abdourahmane Sow , Abdualmoniem Musa , Abdul Sesay , Abe Abias , Adam Elzagheid , Adamou Lagare (2) , Adedotun-Sulaiman Kemi , Aden Elmi Abar , Adeniji Johnson , Adeola Fowotade , Adeyemi Oluwapelumi , Adrienne Amuri , Agnes Juru , Ahmed Kandeil , Ahmed Mostafa , Ahmed Rebai , Ahmed Sayed , Akano Kazeem , Aladje Balde , Alan Christoffels , Alexander Trotter , Allan Campbell , Alpha Keita (3, 4) , Amadou Kone , Amal Bouzid , Amal Souissi , Ambrose Agweyu , Amel Naguib , Ana Gutierrez , Anatole Nkeshimana , Andrew Page , Anges Yadouleton , Anika Vinze , Anise Happi , Anissa Chouikha (5, 6) , Arash Iranzadeh , Arisha Maharaj , Armel Batchi-Bouyou , Arshad Ismail , Augustina Sylverken , Augustine Goba , Ayoade Femi , Ayotunde Sijuwola , Baba Marycelin , Babatunde Salako , Bamidele Oderinde , Bankole Bolajoko , Bassirou Diarra , Belinda Herring , Benjamin Tsofa , Bernard Lekana-Douki , Bernard Mvula , Berthe-Marie Njanpop-Lafourcade , Blessing Marondera , Bouh Abdi Khaireh , Bourema Kouriba , Bright Adu , Brigitte Pool , Bronwyn Mcinnis , Cara Brook (7, 8) , Carolyn Williamson , Cassien Nduwimana , Catherine Anscombe , Catherine Pratt , Cathrine Scheepers , Chantal Akoua-Koffi , Charles Agoti , Chastel Mapanguy , Cheikh Loucoubar (1) , Chika Onwuamah , Chikwe Ihekweazu , Christian Malaka (9) , Christophe Peyrefitte (1) , Chukwa Grace , Chukwuma Omoruyi , Clotaire Rafaï , Collins Morang’a , Cyril Erameh , Daniel Lule , Daniel Bridges , Daniel Mukadi-Bamuleka , Danny Park , David Rasmussen , David Baker , David Nokes , Deogratius Ssemwanga , Derek Tshiabuila , Dominic Amuzu , Dominique Goedhals , Donald Grant , Donwilliams Omuoyo , Dorcas Maruapula , Dorcas Wanjohi , Ebenezer Foster-Nyarko , Eddy Lusamaki (10, 11, 4) , Edgar Simulundu , Edidah Ong’era , Edith Ngabana , Edward Abworo , Edward Otieno , Edwin Shumba , Edwine Barasa , El Bara Ahmed , Elhadi Ahmed , Emmanuel Lokilo , Enatha Mukantwari , Eromon Philomena , Essia Belarbi , Etienne Simon-Loriere (12) , Etilé Anoh , Eusebio Manuel , Fabian Leendertz , Fahn Taweh , Fares Wasfi (5, 6) , Fatma Abdelmoula , Faustinos Takawira , Fawzi Derrar (13) , Fehintola Ajogbasile , Florette Treurnicht , Folarin Onikepe , Francine Ntoumi , Francisca Muyembe , Frank Ragomzingba , Fred Dratibi , Fred-Akintunwa Iyanu , Gabriel Mbunsu , Gaetan Thilliez , Gemma Kay , George Akpede , Gert van Zyl , Gordon Awandare , Grace Kpeli , Grit Schubert , Gugu Maphalala , Hafaliana Ranaivoson (8) , Hannah Omunakwe , Harris Onywera , Haruka Abe , Hela Karray , Hellen Nansumba , Henda Triki (5, 6) , Herve Albéric Adje Kadjo (14) , Hesham Elgahzaly , Hlanai Gumbo , Hota Mathieu , Hugo Kavunga-Membo , Ibtihel Smeti , Idowu Olawoye , Ifedayo Adetifa , Ikponmwosa Odia , Ilhem Boutiba Ben Boubaker , Iluoreh Ahmed Muhammad , Isaac Ssewanyana , Isatta Wurie , Iyaloo Konstantinus , Jacqueline Wemboo Afiwa Halatoko , James Ayei , Janaki Sonoo , Jean-Claude Makangara , Jean-Jacques Tamfum , Jean-Michel Heraud (1, 8) , Jeffrey Shaffer , Jennifer Giandhari , Jennifer Musyoki , Jerome Nkurunziza , Jessica Uwanibe , Jinal Bhiman , Jiro Yasuda , Joana Morais , Jocelyn Kiconco , John Sandi , John Huddleston , John Odoom , John Morobe , John Gyapong , John Kayiwa , Johnson Okolie , Joicymara Xavier , Jones Gyamfi , Joseph Wamala , Joseph Bonney , Joseph Nyandwi , Josie Everatt , Joweria Nakaseegu , Joyce Ngoi , Joyce Namulondo , Judith Oguzie , Julia Andeko , Julius Lutwama , Juma Mogga , Justin O’grady , Katherine Siddle , Kathleen Victoir (15) , Kayode Adeyemi , Kefentse Tumedi , Kevin Carvalho , Khadija Said Mohammed , Koussay Dellagi (15) , Kunda Musonda , Kwabena Duedu , Lamia Fki-Berrajah , Lavanya Singh , Lenora Kepler , Leon Biscornet , Leonardo de Oliveira Martins , Lucious Chabuka , Luicer Olubayo , Lul Deng Ojok , Lul Lojok Deng , Lynette Ochola-Oyier , Lynn Tyers , Madisa Mine , Magalutcheemee Ramuth , Maha Mastouri , Mahmoud Elhefnawi , Maimouna Mbanne (1) , Maitshwarelo Matsheka , Malebogo Kebabonye , Mamadou Diop (1) , Mambu Momoh , Maria da Luz Lima Mendonça , Marietjie Venter , Marietou Paye , Martin Faye (1) , Martin Nyaga , Mathabo Mareka , Matoke-Muhia Damaris , Maureen Mburu , Maximillian Mpina , Michael Owusu , Michael Wiley , Mirabeau Tatfeng , Mitoha Ondo’o Ayekaba , Mohamed Abouelhoda , Mohamed Amine Beloufa (13) , Mohamed Seadawy , Mohamed Khalifa , Mooko Marethabile Matobo , Mouhamed Kane (1) , Mounerou Salou , Mphaphi Mbulawa , Mulenga Mwenda , Mushal Allam , My Phan , Nabil Abid , Nadine Rujeni , Nadir Abuzaid , Nalia Ismael , Nancy Elguindy , Ndeye Marieme Top (1) , Ndongo Dia (1) , Nédio Mabunda , Nei-Yuan Hsiao , Nelson Boricó Silochi , Ngiambudulu Francisco , Ngonda Saasa , Nicholas Bbosa , Nickson Murunga , Nicksy Gumede , Nicole Wolter , Nikita Sitharam , Nnaemeka Ndodo , Nnennaya Ajayi , Noël Tordo (16) , Nokuzola Mbhele , Norosoa Razanajatovo (8) , Nosamiefan Iguosadolo , Nwando Mba , Ojide Kingsley , Okogbenin Sylvanus , Oladiji Femi , Olubusuyi Adewumi , Olumade Testimony , Olusola Ogunsanya , Oluwatosin Fakayode , Onwe Ogah , Ope-Ewe Oludayo , Ousmane Faye (1) , Pamela Smith-Lawrence , Pascale Ondoa , Patrice Combe (17) , Patricia Nabisubi , Patrick Semanda , Paul Oluniyi , Paulo Arnaldo , Peter Kojo Quashie , Peter Okokhere , Philip Bejon , Philippe Dussart (8) , Phillip Bester , Placide Mbala , Pontiano Kaleebu , Priscilla Abechi , Rabeh El-Shesheny , Rageema Joseph , Ramy Karam Aziz , René Essomba , Reuben Ayivor-Djanie , Richard Njouom (18) , Richard Phillips , Richmond Gorman , Robert Kingsley , Rosa Maria D. E. S. A. Neto Rodrigues , Rosemary Audu , Rosina Carr , Saba Gargouri , Saber Masmoudi , Sacha Bootsma , Safietou Sankhe (1) , 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 Ahmed , Side Mohamed Ahmed , Siham Elhamoumi , Sikhulile Moyo , Silvia Lutucuta , Simani Gaseitsiwe , Simbirie Jalloh , Soa Fy Andriamandimby (8) , Sobajo Oguntope , Solène Grayo (16) , Sonia Lekana-Douki , Sophie Prosolek , Soumeya Ouangraoua , Stephanie van Wyk , Stephen Schaffner , Stephen Kanyerezi , Steve Ahuka-Mundeke , Steven Rudder , Sureshnee Pillay , Susan Nabadda , Sylvie Behillil (19) , Sylvie Budiaki , Sylvie van der Werf (19) , Tapfumanei Mashe , Thabo Mohale , Thanh Le-Viet , Thirumalaisamy Velavan , Tobias Schindler , Tongai Maponga , Trevor Bedford , Ugochukwu Anyaneji , Ugwu Chinedu , Upasana Ramphal , Uwem George , Vincent Enouf (19) , Vishvanath Nene , Vivianne Gorova , Wael Roshdy , Wasim Abdul Karim , William Ampofo , Wolfgang Preiser , Wonderful Choga , Yahaya Ali Ahmed , Yajna Ramphal , Yaw Bediako , Yeshnee Naidoo , Yvan Butera , Zaydah de Laurent , Ahmed Ouma , Anne von Gottberg , George Githinji , Matshidiso Moeti , Oyewale Tomori , Pardis Sabeti , Amadou Sall (1) , Samuel Oyola , Yenew Tebeje , Sofonias Tessema , Tulio de Oliveira , Christian Happi , Richard Lessells , John Nkengasong , Eduan Wilkinson , Aaron 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 Konou , Abo Shama , O. Abosede , S. Abouelnaga , Abraham Ali , Abraham Kwabena Anang , Abraham Tesfaye , Adam Khan , Adamu Tayachew , Adane Mihret , Adba Alfatih Alemam , Adede Hawi , A. Adesegun , Adey Feleke Desta , Adib Ghassan , Adjaratou Traoré , B. 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 Kayed , Ahmed El-Taweel , Ahmed Elsayed , Ahmed Gad , Ahmed Fakhfakh , Ahmed Kandeil , M. Ahmed , Ahmed Mostafa , O. Ahmed , Ahmed Reggad , Ahmed Taha , Ahyong Vida , Aicha Bensalem , Aida Sivro , Aissam Hachid , F. Ajili , F.V. Ajogbasile , Akim Adegnika , Akoele Siliadin , Akwii Patience Natasha , Aladje Balde , Alan Lemtudo , Alaoui Sanaa-Amine , A. 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 Maiga , Amadou Alpha Sall , Amadou Daou , Amal Naguib , Amal Souiri , Amal Zouaki , Amalou Ghita , Amandine Mveang-Nzoghe , Amariane Koné , Amariane Koné , Ambroise Ahouidi , Amel Benyahia , Amel Nagiub , K. 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 Luquette , Andreas Shiningavamwe , Andres Moreira-Soto , Andrew Azman , Andrew Bennett , Andrew Tarupiwa , Anga Latifa , Ange Badjo , Angel Angelov , Angela Brisebarre , Angela 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 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 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 Taiwo , S. Baboo , B. 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 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 Lindsey , Benjamin 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 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 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 Arnold , Catherine Okoi , Cecilia Waruhiu , Celestin Godwe , Celestina Obiekea , Celine Nkenfou , L. Chabuka , Chakib Nejjari , H. Chambaro , D. Chanda , K. Changula , Charifa Drissi Touzani , Charles Kayuki , Charles Nyagupe , Charles Ssuuna , Charoute Hicham , Chaselynn Watters , H. Chawech , Cheikh Sokhna , Chenaoui Mohamed , Chiamaka Nwuba , C. Chilufya , Chimaobi Chukwu , Chinyere Anyika , P.J. Chipimo , S. Chitanga , M. Chitenje , M. Chiwaula , Chouati Taha , Chris Mansell , Christelle Butel , Christian Devaux , Christian Drosten , Christian Ranaivoson , Christian Utpatel , Christophe Malabat , A. Chtourou , G. Chukwu , Claudia Daubenberger , Clement Kakai , Clement Masakwe , Clotaire Donatien Rafai , Collins Chenwi , Collins Misita , Collins Muli , Corine Geurtsvankessel , Corinne Maufrais , Coulibaly Mbegnan , M. Crawford , Cristina 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 Mettle , Demba Koita , Dennis Kenyi Lodiongo , Dennis Laryea , Dennis Wandera , Dereje Leta , Dersi Noureddine , Desire Takou , Dessalegn Abeje Tefera , Dhwani Batra , Dia Ndongo , A. Diab , Diabou Diagne , Diane 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 de Oliveira Filho , Edmira Maria da Costa , Edward Kiritu , Efrem Lim , Egon 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 Latif , Emame Edu , Emanuele Orsini , Emilio Skarwan , Emily Stefanov , Emmanuel Nasinghe , Emmanuel Nepolo , Emmanuel Ogunbayo , Emmanuelle Munger , Emmanuelle Permal , Emna Gaies , H. Ennibi , Ennibi Khalid , Erasmus Kotey , Erasmus Smit , Eric 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 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 , R. 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 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. Gosnell , A. Gottberg , Grace Angong Belournou , Grace Oni , Grace Vincent , Gregory Wani , Guedi Ali Barreh , Guillermo Garcia , Guohong Deng , N. 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 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 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 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 Mutungi , Joe Mutungi , Joel Fleury Djoba Siawaya , Joel Koivogui , Joep de Ligt , John Njuguna , John Rumunu , John Tembo , John Waitumbi , Johnson Adeniji , Jonathan Rigby , Jorn Hellemans , Joseph Fokam , Joseph 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 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 Jerome , Keke René , Kena Swanson , Kenneth Maeka , Keren Okyerebea Attiku , Kevin Sanders , Kevine Zang Ella , Keyru Tuki , Khabab Elhag , Khadim Gueye , Khaled Amer , Khalid Ennibi Mostafa , N. Kharat , Z. Khumalo , Kilian Stoecker , L. Kim , Kimberly 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 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 Long , Kyra Grantz , Lacy Simons , Laetitia Serrano , Laila Elsawy , Laila Sbabou , Lallepak Lamboni , Larinda 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 Ian , F. Lista , M.M. Liwewe , Lloyd Mulenga , Logan Voegtly , Loide Shipingana , Loris Micelli , Lorreta Kwasah , Loubna Allam , Louise Lefrançois , Loukman Salma , Lucas Amenga-Etego , Ludivine Brechar , Ludovic Mewono , Luis 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 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. Manraj , T. Mansour , Maowia 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 Antwerpen , Marouane Melloul , Martin Maidadi Foudi , Martine Peeters , Marvin Hsiao , Mary Dealmeida , Mary Lalemi , Mary-Ann Davies , K. Masahiro , Masse Sambou , M. Mathabo , Mathew Parker , Mathias 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 Aïssi , Méline Bizard , Merabet Mouad , Meriem Laamarti , Messanh Douffan , S. Mhalla , Michael Addidle , Michael Marks , Michael Nagel , Michael 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. Mzumara , N. N'Dilimabaka , Nabila Soara , A. Nabli , Nadia El Mrimar , Nadia Rodrigues , Nadia Sitoe , Nafisatou Leye , A. Naguib , K. Nalubamba , Nancy 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. Niatou-Singa , Nicaise 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 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 , 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 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 Essone , Paulina Joãozinho da Costa Jarra Manneh , Pauline Yacine Sene , Paulo Paixão , Pavitra Roychoudhury , Peace Uche , Pei Zhou , Penda Malhado Diallo , A. Pereira , Petas Akogbeto , Peter Bauer , Peter Skidmore , Petra Raimond , Phasha-Muchemenye Mmatshepho , Philip Ashton , C. Philip , Philip El-Duah , Philip Soglo , Philip Wonder Phiri , Philipp Wagner , Philippe Colson , Philippe Dussart (8) , Philippe Lavrard Meyer , Phillip Ashton , Phionah Tushabe , Pierre-Edouard Fournier , Piet Maes , Popova 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 Mentag , Rahma Ahmed , Raiva Algheriani , Rajiha Simbi , Ramalia Chabi Abubeker , Ramon Nari , Ramy Lorenzo-Redondo , A. Raouf , Raoul Saizonou , Raphael Lumembe , Ravena Mubichi , Regina 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 Daniels , Rodrigue Bikangui , Rodrigue Kohoun , Rodrigue Kamga , Rodrigue Mintsa Nguema , Roger Shapiro , J. Rogers , Rogers Kamulegeya , Rokaia Laamrti , Roméo Aimé Laclong Lontchi , Ronald Kiiza , Ronald 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 Fageer , Samia Abdou Girgis , M. Samir , O. Samir , Samira Benkeroum , Samira Ibrahim , Samira 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 Charlene , Sondes Henson , Sonia Haddad , 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 Eggan , Stephen Ochola , Stephen Wanok , Steven 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 Thomas , Thongbotho Mphoyakgosi , Thushan de Silva , Tim Roloff , Timothy Blackmore , Tiziana Rollo , Tom Lutalo , Tomade A.M. Ibrahim , T. Tombolomako , Tomiwa Adepetun , C. Tomkins-Tinch , Tony Wawina-Bokalanga , Tope Sobajo , Touil Nadia , Touria Essayagh , Toy Nwako , 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 M'Cormack , Virginia Hope , Vivi Hue-Trang Lieu , Vololoniaina Raharinosy , Wadegu Meshack , N. Wadonda , J. Wadula , Wael Ali , Waidi Sule , Wallace 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 Moatasim , 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 Imam , Zekiba Tarnagda , Zemmouri Faouzia , J. Zhang , Zhenghui Li , Zimmerman Maiga , Zohour Kasmy , Minko Zong , A. Zorgani , Zouheir Yassine , Zoukaneirii Issa , P. Zulu , Zuzheng Xiang

1 Institut Pasteur de Dakar
2 CERMES - Centre de Recherche Médicale et Sanitaire (Niamey, Niger)
3 Université Gamal Abdel Nasser de Conakry
4 TransVIHMI - Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes
5 Institut Pasteur de Tunis
6 UTM - Université de Tunis El Manar
7 University of Chicago
8 Institut Pasteur de Madagascar
9 Institut Pasteur de Bangui
10 INRB - Institut National de Recherche Biomédicale [Kinshasa]
11 UNIKIN - University of Kinshasa
12 Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses
13 Institut Pasteur d'Algérie
14 Institut Pasteur de Côte d'Ivoire
15 Direction Internationale de l'Institut Pasteur
16 Institut Pasteur de Guinée
17 Centre Hospitalier de Mayotte
18 Centre Pasteur du Cameroun
19 GMV-ARN (UMR_3569 / U-Pasteur_2) - Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Domains: Life Sciences [q-bio]

Houriiyah Tegally, James San, Matthew Cotten, Monika Moir, Bryan Tegomoh, et al.. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science, 2022, 378 (6615), ⟨10.1126/science.abq5358⟩. ⟨pasteur-04096669⟩