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

被引：118

作者：

Wilkinson, Eduan ^{[1
,2
]}

Giovanetti, Marta ^{[3
,4
]}

Tegally, Houriiyah ^{[1
]}

San, James E. ^{[1
]}

Lessells, Richard ^{[1
]}

Cuadros, Diego ^{[5
]}

Martin, Darren P. ^{[6
,7
]}

Rasmussen, David A. ^{[8
,9
]}

Zekri, Abdel-Rahman N. ^{[10
]}

Sangare, Abdoul K. ^{[11
]}

Ouedraogo, Abdoul-Salam ^{[12
]}

Sesay, Abdul K. ^{[13
]}

Priscilla, Abechi ^{[14
]}

Kemi, Adedotun-Sulaiman ^{[14
]}

Olubusuyi, Adewunmi M. ^{[15
]}

Oluwapelumi, Adeyemi O. O. ^{[16
]}

Hammami, Adnene ^{[17
]}

Amuri, Adrienne A. ^{[18
,19
]}

Sayed, Ahmad ^{[20
]}

Ouma, Ahmed E. O. ^{[21
]}

Elargoubi, Aida ^{[22
,23
]}

Ajayi, Nnennaya A. ^{[24
]}

Victoria, Ajogbasile F. ^{[14
]}

Kazeem, Akano ^{[14
]}

George, Akpede ^{[25
]}

Trotter, Alexander J. ^{[26
]}

Yahaya, Ali A. ^{[27
]}

Keita, Alpha K. ^{[28
,29
]}

Diallo, Amadou ^{[30
]}

Kone, Amadou ^{[31
]}

Souissi, Amal ^{[32
]}

Chtourou, Amel ^{[17
]}

Gutierrez, Ana, V ^{[26
]}

Page, Andrew J. ^{[26
]}

Vinze, Anika ^{[33
]}

Iranzadeh, Arash ^{[6
,7
]}

Lambisia, Arnold ^{[34
]}

Ismail, Arshad ^{[35
]}

Rosemary, Audu ^{[36
]}

Sylverken, Augustina ^{[37
]}

Femi, Ayoade ^{[14
]}

Ibrahimi, Azeddine ^{[38
]}

Marycelin, Baba ^{[39
]}

Oderinde, Bamidele S. ^{[39
]}

Bolajoko, Bankole ^{[14
]}

Dhaala, Beatrice ^{[40
]}

Herring, Belinda L. ^{[27
]}

Njanpop-Lafourcade, Berthe-Marie ^{[27
]}

Kleinhans, Bronwyn ^{[41
]}

McInnis, Bronwyn ^{[10
]}

机构：

[1] Univ KwaZulu Natal, Nelson R Mandela Sch Med, KwaZulu Natal Res Innovat & Sequencing Platform K, Durban, South Africa

[2] Stellenbosch Univ, Ctr Epidem Response & Innovat CERI, Sch Data Sci & Computat Thinking, Stellenbosch, South Africa

[3] Fundacao Oswaldo Cruz, Lab Flavivirus, Rio De Janeiro, Brazil

[4] Univ Fed Minas Gerais, Lab Genet Celular & Mol, Belo Horizonte, MG, Brazil

[5] Univ Cincinnati, Dept Geog & GIS, Cincinnati, OH USA

[6] Univ Cape Town, Inst Infect Dis & Mol Med, Dept Integrat Biomed Sci, Computat Biol Div, Cape Town, South Africa

[7] Univ Cape Town, Wellcome Ctr Infect Dis Africa, Inst Infect Dis & Mol Med, Div Med Virol, Cape Town, South Africa

[8] North Carolina State Univ, Dept Entomol & Plant Pathol, Raleigh, NC USA

[9] North Carolina State Univ, Bioinformat Res Ctr, Raleigh, NC USA

[10] Cairo Univ, Natl Canc Inst, Canc Biol Dept, Virol & Immunol Unit, Cairo 11796, Egypt

[11] Ctr Infect Charles Merieux Mali CICM Mali, Bamako, Mali

[12] Souro Sanou Univ Hosp, Bacteriol & Virol Dept, Bobo Dioulasso, Burkina Faso

[13] MRCG LSHTM Genom Lab, Fajara, Gambia

[14] Redeemers Univ, African Ctr Excellence Genom Infect Dis ACEGID, Ede, Osun State, Nigeria

[15] Univ Ibadan, Coll Med, Dept Virol, Ibadan, Nigeria

[16] Univ Ilorin, Coll Hlth Sci, Fac Basic Clin Sci, Dept Med Microbiol & Parasitol, Ilorin, Nigeria

[17] Univ sFax, Fac Med sFax, Lab Microbiol, CHU Habib Bourguiba, Sfax, Tunisia

[18] Inst Natl Rech Biomed INRB, Pathogen Sequencing Lab, Kinshasa, DEM REP CONGO

[19] Univ Kinshasa UNIKIN, Kinshasa, DEM REP CONGO

[20] Childrens Canc Hosp, Genom Res Program, Cairo, Egypt

[21] Africa Ctr Dis Control & Prevent Africa CDC, Inst Pathogen Genom, Addis Ababa, Ethiopia

[22] Fac Pharm Monastir, Lab Transmissible Dis & Biol Act Subst LR99ES27, Monastir, Tunisia

[23] Univ Hosp Monastir, Lab Microbiol, Monastir, Tunisia

[24] Alex Ekwueme Fed Univ, Internal Med Dept, Teaching Hosp, Abakaliki, Nigeria

[25] Irrua Specialist Teaching Hosp, Irrua, Nigeria

[26] Quadram Inst Biosci, Norwich, Norfolk, England

[27] World Hlth Org, Africa Reg, Brazzaville, Rep Congo

[28] Univ Conakry, Ctr Rech & Format Infectiol Guin CERFIG, Conakry, Guinea

[29] Montpellier Univ, TransVIHMI, IRD, INSERM, Montpellier, France

[30] Inst Pasteur, Virol Dept, Dakar, Senegal

[31] Mali Univ Clin Res Ctr UCRC, Bamako, Mali

[32] Univ Sfax, Ctr Biotechnol Sfax, Lab Mol & Cellular Screening Proc, Sfax, Tunisia

[33] Broad Inst Harvard & MIT, Cambridge, MA USA

[34] KEMRI Wellcome Trust Res Programme KEMRI CGMR C, Kilifi, Kenya

[35] Natl Hlth Lab Serv NHLS, Natl Inst Communicable Dis NICD, Johannesburg, South Africa

[36] Nigerian Inst Med Res, Lagos, Nigeria

[37] Charite, Inst Virol, Berlin, Germany

[38] Mohammed V Univ, Rabat Med & Pharm Sch, Med Biotechnol Lab, Rabat, Morocco

[39] Univ Maiduguri Teaching Hosp, Dept Immunol, PMB 1414, Maiduguri, Nigeria

[40] MRC UVRI & LSHTM Uganda Res Unit, Entebbe, Uganda

[41] Stellenbosch Univ, Fac Med & Hlth Sci, Div Med Virol, Cape Town, South Africa

[42] Univ Yaounde I, Biotechnol Ctr, Yaounde, Cameroon

[43] CDC Fdn, Yaounde, Cameroon

[44] Univ Chicago, Dept Ecol & Evolut, 940 E 57Th St, Chicago, IL 60637 USA

[45] Inst Pasteur Madagascar, Virol Unit, Antananarivo, Madagascar

[46] Univ Nebraska Med Ctr, Omaha, NE USA

[47] Univ Witwatersrand, Sch Pathol, Antibody Immun Res Unit, Johannesburg, South Africa

[48] CHU Bouake, Lab Unite Diagnost Virus Fievres Hemorrag & Virus, Bouake, Cote Ivoire

[49] Pwani Univ, Sch Publ Hlth, Kilifi, Kenya

[50] Swiss Trop & Publ Hlth Inst, Basel, Switzerland

来源：

SCIENCE | 2021年 / 374卷 / 6566期

基金：

英国生物技术与生命科学研究理事会;

关键词：

EARLY TRANSMISSION;

D O I：

10.1126/science.abj4336

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

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页码：423 / +

页数：32

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