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. 2021 Oct 22;374(6566):423-431.
doi: 10.1126/science.abj4336. Epub 2021 Sep 9.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Eduan Wilkinson #  1   2 , Marta Giovanetti #  3   4 , Houriiyah Tegally #  1 , James E San #  1 , Richard Lessells  1 , Diego Cuadros  5 , Darren P Martin  6   7 , David A Rasmussen  8   9 , Abdel-Rahman N Zekri  10 , Abdoul K Sangare  11 , Abdoul-Salam Ouedraogo  12 , Abdul K Sesay  13 , Abechi Priscilla  14 , Adedotun-Sulaiman Kemi  14 , Adewunmi M Olubusuyi  15 , Adeyemi O O Oluwapelumi  16 , Adnène Hammami  17 , Adrienne A Amuri  18   19 , Ahmad Sayed  20 , Ahmed E O Ouma  21 , Aida Elargoubi  22   23 , Nnennaya A Ajayi  24 , Ajogbasile F Victoria  14 , Akano Kazeem  14 , Akpede George  25 , Alexander J Trotter  26 , Ali A Yahaya  27 , Alpha K Keita  28   29 , Amadou Diallo  30 , Amadou Kone  31 , Amal Souissi  32 , Amel Chtourou  17 , Ana V Gutierrez  26 , Andrew J Page  26 , Anika Vinze  33 , Arash Iranzadeh  6   7 , Arnold Lambisia  34 , Arshad Ismail  35 , Audu Rosemary  36 , Augustina Sylverken  37 , Ayoade Femi  14 , Azeddine Ibrahimi  38 , Baba Marycelin  39 , Bamidele S Oderinde  39 , Bankole Bolajoko  14 , Beatrice Dhaala  40 , Belinda L Herring  27 , Berthe-Marie Njanpop-Lafourcade  27 , Bronwyn Kleinhans  41 , Bronwyn McInnis  10 , Bryan Tegomoh  42 , Cara Brook  43   44 , Catherine B Pratt  45 , Cathrine Scheepers  35   46 , Chantal G Akoua-Koffi  47 , Charles N Agoti  34   48 , Christophe Peyrefitte  30 , Claudia Daubenberger  49 , Collins M Morang'a  50 , D James Nokes  34   51 , Daniel G Amoako  35 , Daniel L Bugembe  40 , Danny Park  33 , David Baker  26 , Deelan Doolabh  7 , Deogratius Ssemwanga  40   52 , Derek Tshiabuila  1 , Diarra Bassirou  30 , Dominic S Y Amuzu  50 , Dominique Goedhals  53 , Donwilliams O Omuoyo  34 , Dorcas Maruapula  54 , Ebenezer Foster-Nyarko  26 , Eddy K Lusamaki  18   19 , Edgar Simulundu  55 , Edidah M Ong'era  34 , Edith N Ngabana  18   19 , Edwin Shumba  56 , Elmostafa El Fahime  57 , Emmanuel Lokilo  18 , Enatha Mukantwari  58 , Eromon Philomena  14 , Essia Belarbi  59 , Etienne Simon-Loriere  60 , Etilé A Anoh  47 , Fabian Leendertz  59 , Faida Ajili  61 , Fakayode O Enoch  62 , Fares Wasfi  63 , Fatma Abdelmoula  32   64 , Fausta S Mosha  27 , Faustinos T Takawira  65 , Fawzi Derrar  66 , Feriel Bouzid  32 , Folarin Onikepe  14 , Fowotade Adeola  67 , Francisca M Muyembe  18   19 , Frank Tanser  68   69   70 , Fred A Dratibi  27 , Gabriel K Mbunsu  19 , Gaetan Thilliez  26 , Gemma L Kay  26 , George Githinji  34   71 , Gert van Zyl  41   72 , Gordon A Awandare  50 , Grit Schubert  59 , Gugu P Maphalala  73 , Hafaliana C Ranaivoson  44 , Hajar Lemriss  74 , Happi Anise  14 , Haruka Abe  75 , Hela H Karray  17 , Hellen Nansumba  76 , Hesham A Elgahzaly  77 , Hlanai Gumbo  65 , Ibtihel Smeti  32 , Ikhlas B Ayed  32 , Ikponmwosa Odia  25 , Ilhem Boutiba Ben Boubaker  78   79 , Imed Gaaloul  22 , Inbal Gazy  80 , Innocent Mudau  7 , Isaac Ssewanyana  76 , Iyaloo Konstantinus  81 , Jean B Lekana-Douk  82 , Jean-Claude C Makangara  18   19 , Jean-Jacques M Tamfum  18   19 , Jean-Michel Heraud  30   44 , Jeffrey G Shaffer  83 , Jennifer Giandhari  1 , Jingjing Li  84 , Jiro Yasuda  75 , Joana Q Mends  85 , Jocelyn Kiconco  52 , John M Morobe  34 , John O Gyapong  85 , Johnson C Okolie  14 , John T Kayiwa  40 , Johnathan A Edwards  68   86 , Jones Gyamfi  85 , Jouali Farah  87 , Joweria Nakaseegu  52 , Joyce M Ngoi  50 , Joyce Namulondo  52 , Julia C Andeko  82 , Julius J Lutwama  40 , Justin O'Grady  26 , Katherine Siddle  33 , Kayode T Adeyemi  14 , Kefentse A Tumedi  88 , Khadija M Said  34 , Kim Hae-Young  89 , Kwabena O Duedu  85 , Lahcen Belyamani  38 , Lamia Fki-Berrajah  17 , Lavanya Singh  1 , Leonardo de O Martins  26 , Lynn Tyers  7 , Magalutcheemee Ramuth  90 , Maha Mastouri  22   23 , Mahjoub Aouni  22 , Mahmoud El Hefnawi  91 , Maitshwarelo I Matsheka  88 , Malebogo Kebabonye  92 , Mamadou Diop  30 , Manel Turki  32 , Marietou Paye  33 , Martin M Nyaga  93 , Mathabo Mareka  94 , Matoke-Muhia Damaris  95 , Maureen W Mburu  34 , Maximillian Mpina  49   96   97 , Mba Nwando  98 , Michael Owusu  99 , Michael R Wiley  45 , Mirabeau T Youtchou  100 , Mitoha O Ayekaba  96 , Mohamed Abouelhoda  101   102 , Mohamed G Seadawy  103 , Mohamed K Khalifa  20 , Mooko Sekhele  94 , Mouna Ouadghiri  38 , Moussa M Diagne  30 , Mulenga Mwenda  104 , Mushal Allam  35 , My V T Phan  40 , Nabil Abid  79   105 , Nadia Touil  106 , Nadine Rujeni  107   108 , Najla Kharrat  32 , Nalia Ismael  109 , Ndongo Dia  30 , Nedio Mabunda  109 , Nei-Yuan Hsiao  7   110 , Nelson B Silochi  96 , Ngoy Nsenga  27 , Nicksy Gumede  27 , Nicola Mulder  111 , Nnaemeka Ndodo  98 , Norosoa H Razanajatovo  44 , Nosamiefan Iguosadolo  14 , Oguzie Judith  14 , Ojide C Kingsley  112 , Okogbenin Sylvanus  25 , Okokhere Peter  25 , Oladiji Femi  113 , Olawoye Idowu  14 , Olumade Testimony  14 , Omoruyi E Chukwuma  67 , Onwe E Ogah  114 , Chika K Onwuamah  36   115 , Oshomah Cyril  25 , Ousmane Faye  30 , Oyewale Tomori  14 , Pascale Ondoa  56 , Patrice Combe  116 , Patrick Semanda  76 , Paul E Oluniyi  14 , Paulo Arnaldo  109 , Peter K Quashie  50 , Philippe Dussart  44 , Phillip A Bester  53 , Placide K Mbala  18   19 , Reuben Ayivor-Djanie  85 , Richard Njouom  117 , Richard O Phillips  118 , Richmond Gorman  118 , Robert A Kingsley  26 , Rosina A A Carr  85 , Saâd El Kabbaj  119 , Saba Gargouri  17 , Saber Masmoudi  32 , Safietou Sankhe  30 , Salako B Lawal  36 , Samar Kassim  77 , Sameh Trabelsi  120 , Samar Metha  33 , Sami Kammoun  121 , Sanaâ Lemriss  119 , Sara H A Agwa  77 , Sébastien Calvignac-Spencer  59 , Stephen F Schaffner  33 , Seydou Doumbia  31 , Sheila M Mandanda  18   19 , Sherihane Aryeetey  122 , Shymaa S Ahmed  122 , Siham Elhamoumi  33 , Soafy Andriamandimby  44 , Sobajo Tope  14 , Sonia Lekana-Douki  82 , Sophie Prosolek  26 , Soumeya Ouangraoua  123   124 , Steve A Mundeke  18   19 , Steven Rudder  26 , Sumir Panji  111 , Sureshnee Pillay  1 , Susan Engelbrecht  41   72 , Susan Nabadda  76 , Sylvie Behillil  125 , Sylvie L Budiaki  94 , Sylvie van der Werf  125 , Tapfumanei Mashe  65 , Tarik Aanniz  38 , Thabo Mohale  35 , Thanh Le-Viet  26 , Tobias Schindler  49   96 , Ugochukwu J Anyaneji  1 , Ugwu Chinedu  14 , Upasana Ramphal  1   69   126 , Uwanibe Jessica  14 , Uwem George  14 , Vagner Fonseca  1   4   127 , Vincent Enouf  125 , Vivianne Gorova  128   129 , Wael H Roshdy  122 , William K Ampofo  50 , Wolfgang Preiser  41   72 , Wonderful T Choga  54   130 , Yaw Bediako  50 , Yeshnee Naidoo  1 , Yvan Butera  107   131   132 , Zaydah R de Laurent  34 , Amadou A Sall  30 , Ahmed Rebai  32 , Anne von Gottberg  35   133 , Bourema Kouriba  12 , Carolyn Williamson  7   69   110 , Daniel J Bridges  104 , Ihekweazu Chikwe  98 , Jinal N Bhiman  35   133 , Madisa Mine  134 , Matthew Cotten  40   135 , Sikhulile Moyo  54   136 , Simani Gaseitsiwe  54   136 , Ngonda Saasa  55 , Pardis C Sabeti  33 , Pontiano Kaleebu  40 , Yenew K Tebeje  21 , Sofonias K Tessema  21 , Christian Happi  14 , John Nkengasong  21 , Tulio de Oliveira  1   2   69   137
Affiliations

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Eduan Wilkinson et al. Science. .

Abstract

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

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Figures

Fig. 1.
Fig. 1.. SARS-CoV-2 sequences in Africa.
(A) Map of the African continent with the number of SARS-CoV-2 sequences reflected in GISAID as of 5 May 2021. (B) Regression plot of the number of viral sequences versus the number of reported COVID-19 cases in various African countries as of 5 May 2021. Countries with >500 sequences are labeled. The shaded region indicates the 95% confidence interval. (C) Progressive distribution of the top 20 PANGO lineages on the African continent. (D) Temporal sampling of SARS-CoV-2 sequences in African countries (ordered by total number of sequences) through time, with VOCs of note highlighted and annotated according to their PANGO lineage assignment.
Fig. 2.
Fig. 2.. Phylogenetic reconstruction of the SARS-CoV-2 pandemic on the continent of Africa.
(A) Time-resolved maximum likelihood tree containing 8746 high-quality African SARS-CoV-2 near-full-genome sequences analyzed against a backdrop of global reference sequences. VOIs and VOCs are highlighted on the phylogeny. (B) Sources of viral introductions into African countries characterized as external introductions from the rest of the world versus internal introductions from other African countries. (C) Total external viral introductions over time into Africa. (D) The number of viral imports and exports into and out of various African countries depicted as internal (between African countries, in pink) or external (between African and non-African countries, in blue and gray).
Fig. 3.
Fig. 3.. Genetic profile of VOCs and VOIs under investigation.
(A) Root-to-tip regression plots for four lineages of interest. C.1 and A.23 show continued evolution into VOIs C.1.1 and A.23.1, respectively. r, coefficient of correlation; r2, coefficient of determination. (B) Genome maps of four VOCs and VOIs, where the spike region is shown in detail and in color and the rest of the genome is shown in gray. ORF, open reading frame; NTD, N-terminal domain; RBD, receptor binding domain; RBM, receptor binding motif; SD1, subdomain 1; SD2, subdomain 2.
Fig. 4.
Fig. 4.. Phylogeographic reconstruction of the spread of four VOCs and VOIs across the African continent.
(A to D) Phylogeographic reconstruction of the spread of four VOCs and VOIs across the African continent using sequences showing strict continuous transmission across geographical regions: B.1.351 (A), B.1.525 (B), A.23/A.23.1 (C), and C.1/C.1.1 (D). Curved lines denote the direction of transmission in the counterclockwise direction. Solid lines show transmission paths as inferred by phylogeographic reconstruction and colored by date, whereas dashed lines show the known travel history of the particular case considered.
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