The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance-Reference-Cited by-同舟云学术

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

Published:2022-10-07 Issue:6615 Volume:378 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Tegally Houriiyah¹²^ORCID,San James E.¹²^ORCID,Cotten Matthew³⁴^ORCID,Moir Monika¹^ORCID,Tegomoh Bryan⁵⁶,Mboowa Gerald⁷^ORCID,Martin Darren P.⁸⁹,Baxter Cheryl¹¹⁰^ORCID,Lambisia Arnold W.¹¹^ORCID,Diallo Amadou¹²^ORCID,Amoako Daniel G.¹³¹⁴^ORCID,Diagne Moussa M.¹²,Sisay Abay¹⁵¹⁶^ORCID,Zekri Abdel-Rahman N.¹⁷^ORCID,Gueye Abdou Salam¹⁸,Sangare Abdoul K.¹⁹,Ouedraogo Abdoul-Salam²⁰,Sow Abdourahmane²¹,Musa Abdualmoniem O.²²²³²⁴^ORCID,Sesay Abdul K.²⁵,Abias Abe G.²⁶,Elzagheid Adam I.²⁷^ORCID,Lagare Adamou²⁸,Kemi Adedotun-Sulaiman²⁹,Abar Aden Elmi³⁰,Johnson Adeniji A.³¹³²,Fowotade Adeola³³³⁴,Oluwapelumi Adeyemi O.³⁵³⁶^ORCID,Amuri Adrienne A.³⁷³⁸^ORCID,Juru Agnes³⁹,Kandeil Ahmed⁴⁰^ORCID,Mostafa Ahmed⁴⁰^ORCID,Rebai Ahmed⁴¹^ORCID,Sayed Ahmed⁴²,Kazeem Akano⁴³⁴⁴,Balde Aladje⁴⁵⁴⁶,Christoffels Alan⁷⁴⁷^ORCID,Trotter Alexander J.⁴⁸^ORCID,Campbell Allan⁴⁹^ORCID,Keita Alpha K.⁵⁰⁵¹,Kone Amadou⁵²,Bouzid Amal⁴¹⁵³,Souissi Amal⁴¹^ORCID,Agweyu Ambrose¹¹^ORCID,Naguib Amel⁵⁴,Gutierrez Ana V.⁴⁸^ORCID,Nkeshimana Anatole⁵⁵,Page Andrew J.⁴⁸^ORCID,Yadouleton Anges⁵⁶^ORCID,Vinze Anika⁵⁷,Happi Anise N.⁴³,Chouikha Anissa⁵⁸⁵⁹^ORCID,Iranzadeh Arash⁸⁹,Maharaj Arisha¹,Batchi-Bouyou Armel L.⁶⁰⁶¹,Ismail Arshad¹³^ORCID,Sylverken Augustina A.⁶²⁶³^ORCID,Goba Augustine⁶⁴⁶⁵,Femi Ayoade⁴³⁴⁴^ORCID,Sijuwola Ayotunde E.⁴³,Marycelin Baba⁶⁶⁶⁷^ORCID,Salako Babatunde L.²⁹³²^ORCID,Oderinde Bamidele S.⁶⁶,Bolajoko Bankole⁴³,Diarra Bassirou⁵²^ORCID,Herring Belinda L.¹⁸,Tsofa Benjamin¹¹^ORCID,Lekana-Douki Bernard⁶⁸⁶⁹^ORCID,Mvula Bernard⁷⁰,Njanpop-Lafourcade Berthe-Marie¹⁸,Marondera Blessing T.⁷¹,Khaireh Bouh Abdi⁷²⁷³,Kouriba Bourema¹⁹^ORCID,Adu Bright⁷⁴^ORCID,Pool Brigitte⁷⁵,McInnis Bronwyn¹⁷^ORCID,Brook Cara⁷⁶⁷⁷^ORCID,Williamson Carolyn⁹¹⁰⁷⁸^ORCID,Nduwimana Cassien⁵⁵,Anscombe Catherine⁷⁹⁸⁰,Pratt Catherine B.⁸¹^ORCID,Scheepers Cathrine¹³⁸²^ORCID,Akoua-Koffi Chantal G.⁸³⁸⁴,Agoti Charles N.¹¹⁸⁵,Mapanguy Chastel M.⁶⁰⁸⁶,Loucoubar Cheikh¹²,Onwuamah Chika K.⁸⁷^ORCID,Ihekweazu Chikwe⁸⁸,Malaka Christian N.⁸⁹^ORCID,Peyrefitte Christophe¹²,Grace Chukwa⁴³⁴⁴^ORCID,Omoruyi Chukwuma E.³³³⁴,Rafaï Clotaire D.⁹⁰,Morang’a Collins M.⁹¹^ORCID,Erameh Cyril⁹²^ORCID,Lule Daniel B.³^ORCID,Bridges Daniel J.⁹³^ORCID,Mukadi-Bamuleka Daniel³⁷,Park Danny⁵⁷^ORCID,Rasmussen David A.⁹⁴⁹⁵^ORCID,Baker David⁴⁸,Nokes David J.¹¹⁹⁶^ORCID,Ssemwanga Deogratius³⁹⁷^ORCID,Tshiabuila Derek²^ORCID,Amuzu Dominic S. Y.⁹¹^ORCID,Goedhals Dominique⁹⁸,Grant Donald S.⁶⁴⁶⁵⁹⁹^ORCID,Omuoyo Donwilliams O.¹¹,Maruapula Dorcas¹⁰⁰,Wanjohi Dorcas W.⁷,Foster-Nyarko Ebenezer⁴⁸,Lusamaki Eddy K.³⁷³⁸⁵¹^ORCID,Simulundu Edgar¹⁰¹^ORCID,Ong’era Edidah M.¹¹,Ngabana Edith N.³⁷³⁸,Abworo Edward O.¹⁰²,Otieno Edward¹¹^ORCID,Shumba Edwin⁷¹,Barasa Edwine¹¹^ORCID,Ahmed El Bara¹⁰³¹⁰⁴,Ahmed Elhadi A.²³,Lokilo Emmanuel³⁷^ORCID,Mukantwari Enatha¹⁰⁵^ORCID,Philomena Eromon⁴³,Belarbi Essia¹⁰⁶^ORCID,Simon-Loriere Etienne¹⁰⁷^ORCID,Anoh Etilé A.⁸³^ORCID,Manuel Eusebio¹⁰⁸,Leendertz Fabian¹⁰⁶,Taweh Fahn M.¹⁰⁹,Wasfi Fares⁵⁸^ORCID,Abdelmoula Fatma⁴¹¹¹⁰,Takawira Faustinos T.³⁹,Derrar Fawzi¹¹¹^ORCID,Ajogbasile Fehintola V.⁴³,Treurnicht Florette¹¹²¹¹³,Onikepe Folarin⁴³⁴⁴^ORCID,Ntoumi Francine⁶⁰¹¹⁴,Muyembe Francisca M.³⁷³⁸,Ragomzingba Frank E. Z.¹¹⁵,Dratibi Fred A.¹¹⁶¹⁸,Iyanu Fred-Akintunwa⁴³^ORCID,Mbunsu Gabriel K.³⁸,Thilliez Gaetan⁴⁸^ORCID,Kay Gemma L.⁴⁸^ORCID,Akpede George O.⁹²,van Zyl Gert U.¹¹⁷¹¹⁸^ORCID,Awandare Gordon A.⁹¹,Kpeli Grace S.¹¹⁹¹²⁰,Schubert Grit¹⁰⁶,Maphalala Gugu P.¹²¹,Ranaivoson Hafaliana C.⁷⁷^ORCID,Omunakwe Hannah E.¹²²^ORCID,Onywera Harris⁷^ORCID,Abe Haruka¹²³^ORCID,Karray Hela¹²⁴^ORCID,Nansumba Hellen¹²⁵,Triki Henda⁵⁸,Kadjo Herve Albéric Adje¹²⁶,Elgahzaly Hesham¹²⁷^ORCID,Gumbo Hlanai³⁹,Mathieu Hota¹²⁸,Kavunga-Membo Hugo³⁷,Smeti Ibtihel⁴¹,Olawoye Idowu B.⁴³,Adetifa Ifedayo M. O.⁸⁸¹²⁹^ORCID,Odia Ikponmwosa⁹²,Ben Boubaker Ilhem Boutiba¹³⁰¹³¹,Muhammad Iluoreh Ahmed⁴³,Ssewanyana Isaac¹²⁵,Wurie Isatta¹³²,Konstantinus Iyaloo S.¹³³,Halatoko Jacqueline Wemboo Afiwa¹³⁴,Ayei James²⁶,Sonoo Janaki¹³⁵,Makangara Jean-Claude C.³⁷³⁸^ORCID,Tamfum Jean-Jacques M.³⁷³⁸,Heraud Jean-Michel¹²⁷⁷^ORCID,Shaffer Jeffrey G.¹³⁶^ORCID,Giandhari Jennifer²^ORCID,Musyoki Jennifer¹¹,Nkurunziza Jerome¹³⁷,Uwanibe Jessica N.⁴³,Bhiman Jinal N.¹³¹¹³^ORCID,Yasuda Jiro¹²³^ORCID,Morais Joana¹³⁸¹³⁹^ORCID,Kiconco Jocelyn⁹⁷,Sandi John D.⁶⁴⁶⁵,Huddleston John¹⁴⁰^ORCID,Odoom John K.⁷⁴,Morobe John M.¹¹^ORCID,Gyapong John O.¹¹⁹^ORCID,Kayiwa John T.³,Okolie Johnson C.⁴³,Xavier Joicymara S.¹¹⁴¹¹⁴²^ORCID,Gyamfi Jones¹¹⁹^ORCID,Wamala Joseph F.¹⁴³,Bonney Joseph H. K.⁷⁴,Nyandwi Joseph⁵⁵¹⁴⁴,Everatt Josie¹³,Nakaseegu Joweria⁹⁷,Ngoi Joyce M.⁹¹,Namulondo Joyce⁹⁷,Oguzie Judith U.⁴³⁴⁴^ORCID,Andeko Julia C.⁶⁸,Lutwama Julius J.³^ORCID,Mogga Juma J. H.¹⁴³,O’Grady Justin⁴⁸,Siddle Katherine J.⁵⁷^ORCID,Victoir Kathleen¹⁴⁵,Adeyemi Kayode T.⁴³⁴⁴,Tumedi Kefentse A.¹⁴⁶^ORCID,Carvalho Kevin S.¹⁴⁷^ORCID,Mohammed Khadija Said¹¹^ORCID,Dellagi Koussay¹⁴⁵,Musonda Kunda G.¹⁴⁸,Duedu Kwabena O.¹¹⁹¹²⁰^ORCID,Fki-Berrajah Lamia¹²⁴,Singh Lavanya²^ORCID,Kepler Lenora M.⁹⁴⁹⁵^ORCID,Biscornet Leon⁷⁵^ORCID,de Oliveira Martins Leonardo⁴⁸,Chabuka Lucious¹⁴⁹,Olubayo Luicer⁸^ORCID,Ojok Lul Deng²⁶,Deng Lul Lojok²⁶,Ochola-Oyier Lynette I.¹¹^ORCID,Tyers Lynn⁹^ORCID,Mine Madisa¹⁵⁰,Ramuth Magalutcheemee¹³⁵^ORCID,Mastouri Maha¹⁵¹¹⁵²^ORCID,ElHefnawi Mahmoud¹⁵³^ORCID,Mbanne Maimouna¹²,Matsheka Maitshwarelo I.¹⁴⁶^ORCID,Kebabonye Malebogo¹⁵⁴,Diop Mamadou¹²,Momoh Mambu⁶⁴⁶⁵¹⁵⁵,Lima Mendonça Maria da Luz¹⁴⁷^ORCID,Venter Marietjie¹⁵⁶^ORCID,Paye Marietou F.⁵⁷,Faye Martin¹²,Nyaga Martin M.¹⁵⁷,Mareka Mathabo¹⁵⁸,Damaris Matoke-Muhia¹⁵⁹^ORCID,Mburu Maureen W.¹¹,Mpina Maximillian G.¹⁶⁰¹⁶¹¹⁶²^ORCID,Owusu Michael¹⁶³^ORCID,Wiley Michael R.⁸¹¹⁶⁴^ORCID,Tatfeng Mirabeau Y.¹⁶⁵,Ayekaba Mitoha Ondo’o¹⁶¹,Abouelhoda Mohamed¹⁶⁶¹⁶⁷,Beloufa Mohamed Amine¹¹¹,Seadawy Mohamed G.¹⁶⁸¹⁶⁹,Khalifa Mohamed K.¹⁷⁰^ORCID,Matobo Mooko Marethabile¹⁵⁸,Kane Mouhamed¹²,Salou Mounerou¹⁷¹,Mbulawa Mphaphi B.¹⁵⁴,Mwenda Mulenga⁹³^ORCID,Allam Mushal¹⁷²^ORCID,Phan My V. T.³^ORCID,Abid Nabil¹⁵¹¹⁷³^ORCID,Rujeni Nadine¹⁷⁴¹⁷⁵,Abuzaid Nadir¹⁷⁶,Ismael Nalia¹⁷⁷,Elguindy Nancy⁵⁴,Top Ndeye Marieme¹²^ORCID,Dia Ndongo¹²,Mabunda Nédio¹⁷⁷,Hsiao Nei-yuan⁹⁷⁸^ORCID,Silochi Nelson Boricó¹⁶¹^ORCID,Francisco Ngiambudulu M.¹³⁸^ORCID,Saasa Ngonda¹⁷⁸^ORCID,Bbosa Nicholas³,Murunga Nickson¹¹,Gumede Nicksy¹⁸,Wolter Nicole¹³¹¹³^ORCID,Sitharam Nikita¹,Ndodo Nnaemeka⁸⁸^ORCID,Ajayi Nnennaya A.¹⁷⁹^ORCID,Tordo Noël¹⁸⁰,Mbhele Nokuzola⁹,Razanajatovo Norosoa H.⁷⁷,Iguosadolo Nosamiefan⁴³,Mba Nwando⁸⁸,Kingsley Ojide C.¹⁸¹,Sylvanus Okogbenin⁹²,Femi Oladiji¹⁸²^ORCID,Adewumi Olubusuyi M.³¹³²^ORCID,Testimony Olumade⁴³⁴⁴,Ogunsanya Olusola A.⁴³,Fakayode Oluwatosin¹⁸³,Ogah Onwe E.¹⁸⁴,Oludayo Ope-Ewe⁴³,Faye Ousmane¹²^ORCID,Smith-Lawrence Pamela¹⁵⁴,Ondoa Pascale⁷¹,Combe Patrice¹⁸⁵,Nabisubi Patricia¹⁸⁶¹⁸⁷^ORCID,Semanda Patrick¹²⁵^ORCID,Oluniyi Paul E.⁴³^ORCID,Arnaldo Paulo¹⁷⁷^ORCID,Quashie Peter Kojo⁹¹^ORCID,Okokhere Peter O.⁹²¹⁸⁸,Bejon Philip¹¹^ORCID,Dussart Philippe⁷⁷^ORCID,Bester Phillip A.¹⁸⁹,Mbala Placide K.³⁷³⁸,Kaleebu Pontiano³⁹⁷,Abechi Priscilla⁴³⁴⁴,El-Shesheny Rabeh⁴⁰¹⁹⁰^ORCID,Joseph Rageema⁹,Aziz Ramy Karam¹⁹¹¹⁹²,Essomba René G.¹⁹³¹⁹⁴,Ayivor-Djanie Reuben⁹¹¹¹⁹¹²⁰^ORCID,Njouom Richard¹⁹⁵,Phillips Richard O.⁶³^ORCID,Gorman Richmond⁶³,Kingsley Robert A.⁴⁸,Neto Rodrigues Rosa Maria D. E. S. A.¹⁹⁶¹⁹⁷,Audu Rosemary A.²⁹^ORCID,Carr Rosina A. A.¹¹⁹¹²⁰^ORCID,Gargouri Saba¹²⁴,Masmoudi Saber⁴¹,Bootsma Sacha¹⁴³,Sankhe Safietou¹²^ORCID,Mohamed Sahra Isse¹⁹⁸,Femi Saibu⁴³,Mhalla Salma¹³¹¹⁹⁹,Hosch Salome¹⁶⁰²⁰⁰^ORCID,Kassim Samar Kamal¹²⁷^ORCID,Metha Samar⁵⁷,Trabelsi Sameh²⁰¹,Agwa Sara Hassan¹²⁷^ORCID,Mwangi Sarah Wambui⁷,Doumbia Seydou⁵²^ORCID,Makiala-Mandanda Sheila³⁷³⁸,Aryeetey Sherihane⁶³,Ahmed Shymaa S.⁵⁴^ORCID,Ahmed Side Mohamed¹⁰³,Elhamoumi Siham⁵⁷,Moyo Sikhulile¹⁰⁰²⁰²^ORCID,Lutucuta Silvia¹³⁸,Gaseitsiwe Simani¹⁰⁰²⁰²,Jalloh Simbirie⁶⁴⁶⁵,Andriamandimby Soa Fy⁷⁷^ORCID,Oguntope Sobajo⁴³,Grayo Solène¹⁸⁰,Lekana-Douki Sonia⁶⁸^ORCID,Prosolek Sophie⁴⁸,Ouangraoua Soumeya²⁰³²⁰⁴^ORCID,van Wyk Stephanie¹,Schaffner Stephen F.⁵⁷^ORCID,Kanyerezi Stephen¹⁸⁶¹⁸⁷^ORCID,Ahuka-Mundeke Steve³⁷³⁸,Rudder Steven⁴⁸,Pillay Sureshnee²^ORCID,Nabadda Susan¹²⁵,Behillil Sylvie²⁰⁵^ORCID,Budiaki Sylvie L.¹⁵⁸^ORCID,van der Werf Sylvie²⁰⁵^ORCID,Mashe Tapfumanei³⁹²⁰⁶,Mohale Thabo¹³^ORCID,Le-Viet Thanh⁴⁸^ORCID,Velavan Thirumalaisamy P.¹¹⁴²⁰⁷^ORCID,Schindler Tobias¹⁶⁰¹⁶¹²⁰⁰^ORCID,Maponga Tongai G.¹¹⁷^ORCID,Bedford Trevor¹⁴⁰²⁰⁸^ORCID,Anyaneji Ugochukwu J.²^ORCID,Chinedu Ugwu⁴³⁴⁴^ORCID,Ramphal Upasana²¹⁰²⁰⁹^ORCID,George Uwem E.⁴³^ORCID,Enouf Vincent²⁰⁵^ORCID,Nene Vishvanath¹⁰²,Gorova Vivianne²¹⁰²¹¹,Roshdy Wael H.⁵⁴^ORCID,Karim Wasim Abdul¹,Ampofo William K.²¹²,Preiser Wolfgang¹¹⁷¹¹⁸^ORCID,Choga Wonderful T.¹⁰⁰²¹³,Ahmed Yahaya Ali¹⁸^ORCID,Ramphal Yajna¹,Bediako Yaw⁹¹²¹⁴^ORCID,Naidoo Yeshnee²,Butera Yvan¹⁷⁴²¹⁵²¹⁶^ORCID,de Laurent Zaydah R.¹¹^ORCID,Ouma Ahmed E. O.⁷,von Gottberg Anne¹³¹¹³^ORCID,Githinji George¹¹²¹⁷^ORCID,Moeti Matshidiso¹⁸,Tomori Oyewale⁴³^ORCID,Sabeti Pardis C.⁵⁷^ORCID,Sall Amadou A.¹²,Oyola Samuel O.¹⁰²,Tebeje Yenew K.⁷,Tessema Sofonias K.⁷,de Oliveira Tulio¹²¹⁰²¹⁸^ORCID,Happi Christian⁴³⁴⁴^ORCID,Lessells Richard²^ORCID,Nkengasong John⁷,Wilkinson Eduan¹²^ORCID,Shibemba Aaron L.,Obong Abasi Ene,Fadeyi Abayomi,Anas Abbad,Shabaan Abd Elazeez,Adel Abd Monaem,Shoka Abd Moniem Ain,Abdelhamid W.,Laraqui Abdelilah,Laatiris Abdelkader,Bellefquih Abdelkrim Meziane,Faouzi Abdellah,Abdelmoulah F.,Essabbar Abdelomunim,Bimouhen Abderrahmane,Hilali Abderraouf,Abdo I.,Padane Abdou,Sangaré Abdoul Karim,Soumah Abdoul Karim,Djimde Abdoulaye,Toure Abdoulaye,Kanteh Abdoulie,Bashein Abdulla,Salama Abdullah,Lojuan Abe,Bayih Abebe Genetu,Negash Abel Abera,Lissom Abel,Abid N.,Konou Abla A.,Shama Abo,Abosede O.,Abouelnaga S.,Ali Abraham,Anang Abraham Kwabena,Tesfaye Abraham,Khan Adam K.,Tayachew Adamu,Mihret Adane,AlEmam Adba Alfatih,Hawi Adede,Adesegun A.,Desta Adey Feleke,Ghassan Adib,Traoré Adjaratou,Adjiratou Aissatou B. A.,Sadji Adodo,Egli Adrian,Mendes Adriano,Abera Adugna,Candé Adul,Alaoui Afaf,Pedro Afonso,Agbodzi B.,Ageez A.M.,Ayouba Ahidjo,Alarif Ahlam,Kayed Ahmed E,El-Taweel Ahmed,Elsayed Ahmed,Gad Ahmed F.,Fakhfakh Ahmed,Kandeil Ahmed,Ahmed M.,Mostafa Ahmed,Ahmed O. S.,Reggad Ahmed,Taha Ahmed,Vida Ahyong,Bensalem Aicha,Sivro Aida,Hachid Aissam,Ajili F.,Ajogbasile F.V.,Adegnika Akim A.,Siliadin Akoele,Natasha Akwii Patience,Balde Aladje,Lemtudo Alan,Sanaa-amine Alaoui,Alaruusi A. M.,Ouro-Medeli Alassane,Nyunja Albert,Rizzo Alberto,Abdissa Alemseged,Debela Alemu Tike,Mancon Alessandro,Marcello Alessandro,Goredema Alexander,Greninger Alexander,Ndjolo Alexis,Niyomwungere Alexis,Mari Alfredo,Mayor Alfredo,Ali M.A.,Zumla Ali,Ben Kahla Alia,Grad Alia,Kabanda Alice,Tia Alie,Camara Alimou,Zumla Alimuddin,Dieng Alle Baba,Maiga Almoustapha I.,Sall Amadou Alpha,Daou Amadou,Naguib Amal,Souiri Amal,Zouaki Amal,Ghita Amalou,Mveang-Nzoghe Amandine,Koné Amariane,Koné Amariane M. M.,Ahouidi Ambroise,Benyahia Amel,Nagiub Amel,Amer K. E.,Dorkenoo Ameyo,Barkat Amina,Dia Aminata,Mbaye Aminata,Mboup Aminata,Thiam Aminata Sileymane,Lahlou Amine Idriss,Wadi Amira Suliaman,Ehlan Amivi,Marion Amujal,Aziza Amuri,Strydom Amy,Abbad Anass,Nkeshimana Anatole,Mulu Andargachew,Maaroufi Anderrahmane,Luquette Andrea E.,Shiningavamwe Andreas,Moreira-Soto Andres,Azman Andrew,Bennett Andrew J.,Tarupiwa Andrew,Latifa Anga,Badjo Ange,Angelov Angel,Brisebarre Angela,Detweiler Angela M.,Ndong Angoune,Werno Anja,NDiaye Anna Julienne Selbe,Sander Anna-Lena,Annajr B.,D'Aprile Annamaria,van der Linden Anne,van der Eijk Annemiek,Erhart Annette,Somboro Anou M.,Dagnran Anoumou,Ahumibe Anthony,Levasseur Anthony,van der Linden Antje,Dara Antoine,Jegede-Williams Anu,Aouni M.,Arjarquah A.,Uwituze Arlene,Upton Arlo,Poda Armel,Somé Arsène,Zongo Arsène,Massinga Arsenia,Asare K.M.,Katabazi Ashaba Fred,Ferjani Asma,Dieng Assane,Gaye-Gaye Astou,Atiga N.,Weldemariam Atsbeha G.,Arjaquah Augustina,Auld A.,Ba-Diallo Awa,ElMoussi Awatef,Sena Awunyo,Mohamed Aya,Farghaly Ayman,Ayo-Ale B.,Ayoade F.,Adegnika Ayola Akim,More Ayong,James Ayorinde Babatunde,Nawfel Azami,Diergaardt Azaria,Okwuraiwe Azuka Patrick,Taiwo Babafemi O.,Baboo S. B.,Bahadoor B. S.,Bahnassy A.A.,Sanyang Bakary,Bakry U.,Touré Bamba Fatoumata,Iwalokun Bamidele,Banda R.,Bane S.,Johnson Bankole,Cisse Barada,Murwira Barbra,Munnink Bas Oude,Batchi-Bouyou Armel L.,Batra R.,Dhaala Beatrice,Lamiae Belayachi,Belkhir A.B.,Ben Ayed I.,Morton Ben,Moussa Ben,Wulf Ben,Ndeboko Bénédicte,Rachid Benhida,Lindsey Benjamiin B.,Foulkes Benjamin H.,Hounkpatin Benjamin,Selekon Benjamin,Bensaid M.,Mpairwe Bernard,Bagaya Bernard Ssentalo,Vanmechelen Bert,Lell Bertrand,Mutai Beth,Adnew Bethlehem,Makamure Beuty,Bighignoli B.,Ndiaye Birahim Piere,Adhikari Bishwo N.,Bitrou S.M.,Akenji Blaise MBoringong,Shobayo Bode,Zuze Boitumelo,Nlavo Bonifacio Manguire,Belfquih Bouchra,Boujemla Bouchra,Yatassaye Bouna,Aymane Bouzidi,Andika Brian,Yemi Bright K.,Kleinhans Bronwyn,Galvao Bruna,Embaló Bubacar Delgado Pinto,Manene Bulelani,Pascal Butoyi,Capel Camille,Anu Campbell,Tchibozo Carine,Madeira Carla,Cortes Carlos,Elisabeth Carniel,Kifude Carol,Tayimetha Carolle Yanique,Arnold Catherine E.,Okoi Catherine,Waruhiu Cecilia,Godwe Celestin,Obiekea Celestina,Nkenfou Celine,Chabuka L. B.,Nejjari Chakib,Chambaro H.,Chanda D.,Changula K.,Touzani Charifa Drissi,Kayuki Charles,Nyagupe Charles,Ssuuna Charles,Hicham Charoute,Watters Chaselynn M.,Chawech H.,Sokhna Cheikh,Mohamed Chenaoui,Nwuba Chiamaka,Chilufya C.,Chukwu Chimaobi,Anyika Chinyere,Chipimo P.J.,Chitanga S.,Chitenje M.,Chiwaula M. J.,Taha Chouati,Mansell Chris,Butel Christelle,Devaux Christian A.,Drosten Christian,Ranaivoson Christian,Utpatel Christian,Malabat Christophe,Chtourou A.,Chukwu G.,Daubenberger Claudia,Kakai Clement G.,Masakwe Clement,Rafai Clotaire Donatien,Chenwi Collins,Misita Collins M.,Muli Collins,GeurtsvanKessel Corine H.,Maufrais Corinne,Mbegnan Coulibaly,Crawford M.,Tato Cristina M.,Yiaba Cyrus,D'Amore N.,Damilari Dabiri,Ramadan Dalia,Damena D.,Ouso Daniel,Pisanelli Daniela,Licastro Danilo,Hammer David,Nieuwenhuijse David,Kateete David Patrick,Wilkinson David,Mouangala Davy Leger,Alemayehu Dawit Hailu,Dawood R.M.,De Sanctis R.,Mettle Deborah N. A.,Koita Demba,Lodiongo Dennis Kenyi,Laryea Dennis,Wandera Dennis N.,Leta Dereje,Noureddine Dersi,Takou Desire,Tefera Dessalegn Abeje,Batra Dhwani,Ndongo Dia,Diab A.,Diagne Diabou,Mabika Diane A.,Bamourou Diané,Samaté Dianke,Diarra B.,Raoult Didier,Mutangana Dieudonne,Nyepetsi Dineo Emang Tshiamo. Gape,Ada Diosdado Odjama Nseng,Salah Djimabi,Cedola Donatella,Harding Doris,Yeboah-Manu Dorothy,Ange Dossou,Djomsi Dowbiss Meta,Drinkovic Dragana,Draper C.,Sahr Dumbuya Foday,Odewale Ebenezer,Sedjro Eclou,Armand Edang-Minko,Kigozi Edgar,Koskei Edith,Nkwembe Edith,de Oliveira Filho Edmilson F.,Maria da Costa Edmira,Kiritu Edward,Lim Efrem S.,Ozer Egon A.,Egyir B.,Abuelenein Ehab Abdelkader,Ngole Eitel Mpoudi,Aissam El Aliani,Zahra El Ansari Fatima,Adil El Hamouchi,Abdelmjid El Oualid,El-Shaqnqery H.,El-Zayat M.,Abualas Elamin,Hicham Elannaz,Elargoubi A.,Kidane Eleni,Rizgalla Elham,Elhoseny M.M.,Elhosieny F.W.,Carniel Elisabeth,Nyakarungu Elizabeth,Elkhateeb S.M.,Benaissa Elmostafa,El Fahime Elmostafa,Elouanass M.,Elsissy M.H.,Mbongo-Nkama Elvyre,Latif Elwaleed M. 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B.,Adepetun Tomiwa,Tomkins-Tinch C.,Wawina-Bokalanga Tony,Sobajo Tope,Nadia Touil,Essayagh Touria,Nwako Toy,Traoré ,Triki H.,Tsiry R.,Randriambolamanantsoa Tsiry,Madisa Tumisang,Turki M.,Ugwu C.A.,Emokpae Uyi,Carri Valeria Delli,Micheli Valeria,Van Rooyen G.,Vanaerschot M.,Magnussen Vanessa,Mohr Vanessa,Sathyendran Vani,Playle Veronica,Viana R.,Vickos U.,Corman Victor Max,Mukonka Victor,Ofula Victor,Ahyong Vida,Appiah Vincent,Bours Vincent,M'cormack Violette V.,Hope Virginia,Lieu Vivi Hue-Trang,Raharinosy Vololoniaina,Meshack Wadegu,Wadonda N.,Wadula J.,Ali Wael,Sule Waidi,Bulimo Wallace D,Yiaba Warren Cyrus,Waruhiu C.N.,Fares Wasfi,Webby R.,Weldemariam A.G.,Jo Wendy Karen,Woelfel R.,Wolh S.,Wurie I.,Crespin Xavier,Ren Xiaoyun,Wang Xiuhua,Krasnov Ya.M.,Dia Yacine Amet,Ndiaye Yacine DIA Seni,Yusuf Yacob Mohamed,Sawadogo Yacouba,Yadouleton Yahya,Maidane Yakob Gebregziabher,Tsegay Yao,Layibo Yasser,El Hady Yassine,Sekhsokh Yassmin,Moatasim Yawo A.,Sadji ,Yeboah C.,Mohammed Youbi,Makki Yousif Rabih,Akhoud Youssef,Ushijima Yuri,Jimoh Yusuf,Badou Yvette,Zablon J. Matoke D.,Zablon J.O.,Hamzaoui Zaineb,Regragui Zakia,Wuduri Zara,Souma Zein,Waberi Zeinab Ali,Imam Zeinab S.,Tarnagda Zekiba,Faouzia Zemmouri,Zhang J.,Li Zhenghui,Maiga Zimmerman,Kasmy Zohour,Zong Minko O.,Zorgani A.,Yassine Zouheir,Issa Zoukaneirii,Zulu P.,Xiang Zuzheng, ,

Affiliation:

1. Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.

2. KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

3. MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.

4. MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

5. The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon.

6. CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA.

7. Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia.

8. Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa.

9. Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

10. Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.

11. KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.

12. Institut Pasteur de Dakar, Dakar, Senegal.

13. National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.

14. School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa.

15. Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.

16. Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.

17. Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt.

18. World Health Organization, Africa Region, Brazzaville, Republic of the Congo.

19. Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali.

20. Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso.

21. West African Health Organisation, Bobo-Dioulasso, Burkina Faso.

22. Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan.

23. Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan.

24. General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan.

25. MRC Unit The Gambia at LSHTM, Fajara, Gambia.

26. National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan.

27. Libyan Biotechnology Research Center, Tripoli, Libya.

28. Center for Medical and Sanitary Research (CERMES), Niamey, Niger.

29. The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria.

30. Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti.

31. Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria.

32. Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria.

33. Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria.

34. Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria.

35. Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria.

36. The Pirbright Institute, Woking, UK.

37. Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo.

38. Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo.

39. National Microbiology Reference Laboratory, Harare, Zimbabwe.

40. Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt.

41. Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.

42. Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt.

43. African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria.

44. Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria.

45. Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau.

46. University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau.

47. SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.

48. Quadram Institute Bioscience, Norwich, UK.

49. Central Public Health Reference Laboratories, Freetown, Sierra Leone.

50. Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea.

51. TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France.

52. University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali.

53. Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.

54. Central Public Health Laboratories (CPHL), Cairo, Egypt.

55. National Institute of Public Health, Bujumbura, Burundi.

56. Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin.

57. Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.

58. Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia.

59. Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia.

60. Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo.

61. Marien Ngouabi, Brazzaville, Republic of the Congo.

62. Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana.

63. Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.

64. Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone.

65. Ministry of Health and Sanitation, Freetown, Sierra Leone.

66. Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria.

67. Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria.

68. Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon.

69. Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon.

70. National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi.

71. African Society for Laboratory Medicine, Addis Ababa, Ethiopia.

72. National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti.

73. Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti.

74. Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.

75. Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles.

76. Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.

77. Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.

78. National Health Laboratory Service (NHLS), Cape Town, South Africa.

79. Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.

80. Liverpool School of Tropical Medicine, Liverpool, UK.

81. University of Nebraska Medical Center (UNMC), Omaha, NE, USA.

82. SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.

83. CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire.

84. UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire.

85. School of Public Health, Pwani University, Kilifi, Kenya.

86. Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo.

87. Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria.

88. Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria.

89. Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic.

90. Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic.

91. West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana.

92. Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.

93. PATH, Lusaka, Zambia.

94. Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.

95. Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.

96. School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK.

97. Uganda Virus Research Institute, Entebbe, Uganda.

98. PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa.

99. College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone.

100. Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.

101. Macha Research Trust, Choma, Zambia.

102. International Livestock Research Institute (ILRI), Nairobi, Kenya.

103. INRSP, Nouakchott, Mauritania.

104. Faculté de Médecine de Nouakchott, Nouakchott, Mauritani.

105. Rwanda National Reference Laboratory, Kigali, Rwanda.

106. Robert Koch-Institute, Berlin, Germany.

107. G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France.

108. Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola.

109. National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia.

110. Faculty of Pharmacy of Monastir, Monastir, Tunisia.

111. National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria.

112. Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.

113. School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.

114. Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany.

115. Ministère de Santé Publique et de la Solidarité Nationale, Ndjamena, Chad.

116. WHO Int Comoros, Moroni, Union of Comoros.

117. Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.

118. National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa.

119. UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana.

120. Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana.

121. Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini.

122. Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria.

123. Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.

124. CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia.

125. Central Public Health Laboratories (CPHL), Kampala, Uganda.

126. Institut Pasteur de Côte d’Ivoire, Departement des Virus Epidemiques, Abidjan, Côte d’Ivoire.

127. Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt.

128. Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad.

129. Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.

130. Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia.

131. University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia.

132. College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone.

133. Namibia Institute of Pathology, Windhoek, Namibia.

134. National Institute of Hygiene, Lomé, Togo.

135. Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius.

136. Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.

137. WHO Burundi, Gitega, Burundi.

138. Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola.

139. Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola.

140. Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

141. Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.

142. Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil.

143. WHO South Sudan, Juba, South Sudan.

144. Faculty of Medicine, University of Burundi, Bujumbura, Burundi.

145. Pasteur Network, Institut Pasteur, Paris, France.

146. Botswana Institute for Technology Research and Innovation, Gaborone, Botswana.

147. Instituto Nacional de Saúde Pública, Praia, Cape Verde.

148. Zambia National Public Health Institute, Lusaka, Zambia.

149. Public Health Institute of Malawi, Lilongwe, Malawi.

150. National Health Laboratory, Gaborone, Botswana.

151. Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.

152. Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia.

153. Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt.

154. Ministry of Health and Wellness, Gaborone, Botswana.

155. Eastern Technical University of Sierra Leone, Kenema, Sierra Leone.

156. Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.

157. Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.

158. National Reference Laboratory Lesotho, Maseru, Lesotho.

159. Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya.

160. Swiss Tropical and Public Health Institute, Basel, Switzerland.

161. Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea.

162. Ifakara Health Insitute, Ifakara, Tanzania.

163. Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.

164. PraesensBio, Lincoln, NE, USA.

165. Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria.

166. Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt.

167. King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia.

168. Biological Prevention Department, Ministry of Defence, Cairo, Egypt.

169. Faculty of Science, Fayoum University, Fayoum, Egypt.

170. Molecular Pathology Lab, Children’s Cancer Hospital, Cairo, Egypt.

171. LaboratoireBiolim FSS/Université de Lomé, Lomé, Togo.

172. Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates.

173. High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia.

174. Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.

175. School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.

176. Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan.

177. Instituto Nacional de Saúde (INS), Marracuene, Mozambique.

178. Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.

179. Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.

180. Institut Pasteur de Guinée, Conarky, Guinea.

181. Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.

182. Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria.

183. Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria.

184. Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.

185. Mayotte Hospital Center, Mayotte, France.

186. The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda.

187. Immunology and Molecular Biology, Makerere University, Kampala, Uganda.

188. Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria.

189. Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa.

190. Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt.

191. Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.

192. Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt.

193. National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon.

194. Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon.

195. Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon.

196. Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe.

197. Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe.

198. National Public Health Reference Laboratory (NPHRL), Mogadishu, Somalia.

199. Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia.

200. University of Basel, Basel, Switzerland.

201. Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia.

202. Harvard T.H. Chan School of Public Health, Boston, MA, USA.

203. Centre MURAZ, Ouagadougou, Burkina Faso.

204. National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso.

205. National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France.

206. World Health Organization, Harare, Zimbabwe.

207. Vietnamese-German Center for Medical Research, Hanoi, Vietnam.

208. Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA.

209. Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa.

210. World Health Organization, WHO Lesotho, Maseru, Lesotho.

211. Med24 Medical Centre, Ruwa, Zimbabwe.

212. Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.

213. Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa.

214. Yemaachi Biotech, Accra, Ghana.

215. Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.

216. Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium.

217. Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.

218. Department of Global Health, University of Washington, Seattle, WA, USA.

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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