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 ,