A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.
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DOI：
10.1126/science.abj4336
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发表时间：
2021-10-22
期刊：
影响因子：
--
通讯作者：
de Oliveira T
中科院分区：
文献类型：
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作者：
Wilkinson E;Giovanetti M;Tegally H;San JE;Lessells R;Cuadros D;Martin DP;Rasmussen DA;Zekri AN;Sangare AK;Ouedraogo AS;Sesay AK;Priscilla A;Kemi AS;Olubusuyi AM;Oluwapelumi AOO;Hammami A;Amuri AA;Sayed A;Ouma AEO;Elargoubi A;Ajayi NA;Victoria AF;Kazeem A;George A;Trotter AJ;Yahaya AA;Keita AK;Diallo A;Kone A;Souissi A;Chtourou A;Gutierrez AV;Page AJ;Vinze A;Iranzadeh A;Lambisia A;Ismail A;Rosemary A;Sylverken A;Femi A;Ibrahimi A;Marycelin B;Oderinde BS;Bolajoko B;Dhaala B;Herring BL;Njanpop-Lafourcade BM;Kleinhans B;McInnis B;Tegomoh B;Brook C;Pratt CB;Scheepers C;Akoua-Koffi CG;Agoti CN;Peyrefitte C;Daubenberger C;Morang'a CM;Nokes DJ;Amoako DG;Bugembe DL;Park D;Baker D;Doolabh D;Ssemwanga D;Tshiabuila D;Bassirou D;Amuzu DSY;Goedhals D;Omuoyo DO;Maruapula D;Foster-Nyarko E;Lusamaki EK;Simulundu E;Ong'era EM;Ngabana EN;Shumba E;El Fahime E;Lokilo E;Mukantwari E;Philomena E;Belarbi E;Simon-Loriere E;Anoh EA;Leendertz F;Ajili F;Enoch FO;Wasfi F;Abdelmoula F;Mosha FS;Takawira FT;Derrar F;Bouzid F;Onikepe F;Adeola F;Muyembe FM;Tanser F;Dratibi FA;Mbunsu GK;Thilliez G;Kay GL;Githinji G;van Zyl G;Awandare GA;Schubert G;Maphalala GP;Ranaivoson HC;Lemriss H;Anise H;Abe H;Karray HH;Nansumba H;Elgahzaly HA;Gumbo H;Smeti I;Ayed IB;Odia I;Ben Boubaker IB;Gaaloul I;Gazy I;Mudau I;Ssewanyana I;Konstantinus I;Lekana-Douk JB;Makangara JC;Tamfum JM;Heraud JM;Shaffer JG;Giandhari J;Li J;Yasuda J;Mends JQ;Kiconco J;Morobe JM;Gyapong JO;Okolie JC;Kayiwa JT;Edwards JA;Gyamfi J;Farah J;Nakaseegu J;Ngoi JM;Namulondo J;Andeko JC;Lutwama JJ;O'Grady J;Siddle K;Adeyemi KT;Tumedi KA;Said KM;Hae-Young K;Duedu KO;Belyamani L;Fki-Berrajah L;Singh L;Martins LO;Tyers L;Ramuth M;Mastouri M;Aouni M;El Hefnawi M;Matsheka MI;Kebabonye M;Diop M;Turki M;Paye M;Nyaga MM;Mareka M;Damaris MM;Mburu MW;Mpina M;Nwando M;Owusu M;Wiley MR;Youtchou MT;Ayekaba MO;Abouelhoda M;Seadawy MG;Khalifa MK;Sekhele M;Ouadghiri M;Diagne MM;Mwenda M;Allam M;Phan MVT;Abid N;Touil N;Rujeni N;Kharrat N;Ismael N;Dia N;Mabunda N;Hsiao NY;Silochi NB;Nsenga N;Gumede N;Mulder N;Ndodo N;Razanajatovo NH;Iguosadolo N;Judith O;Kingsley OC;Sylvanus O;Peter O;Femi O;Idowu O;Testimony O;Chukwuma OE;Ogah OE;Onwuamah CK;Cyril O;Faye O;Tomori O;Ondoa P;Combe P;Semanda P;Oluniyi PE;Arnaldo P;Quashie PK;Dussart P;Bester PA;Mbala PK;Ayivor-Djanie R;Njouom R;Phillips RO;Gorman R;Kingsley RA;Carr RAA;El Kabbaj S;Gargouri S;Masmoudi S;Sankhe S;Lawal SB;Kassim S;Trabelsi S;Metha S;Kammoun S;Lemriss S;Agwa SHA;Calvignac-Spencer S;Schaffner SF;Doumbia S;Mandanda SM;Aryeetey S;Ahmed SS;Elhamoumi S;Andriamandimby S;Tope S;Lekana-Douki S;Prosolek S;Ouangraoua S;Mundeke SA;Rudder S;Panji S;Pillay S;Engelbrecht S;Nabadda S;Behillil S;Budiaki SL;van der Werf S;Mashe T;Aanniz T;Mohale T;Le-Viet T;Schindler T;Anyaneji UJ;Chinedu U;Ramphal U;Jessica U;George U;Fonseca V;Enouf V;Gorova V;Roshdy WH;Ampofo WK;Preiser W;Choga WT;Bediako Y;Naidoo Y;Butera Y;de Laurent ZR;Sall AA;Rebai A;von Gottberg A;Kouriba B;Williamson C;Bridges DJ;Chikwe I;Bhiman JN;Mine M;Cotten M;Moyo S;Gaseitsiwe S;Saasa N;Sabeti PC;Kaleebu P;Tebeje YK;Tessema SK;Happi C;Nkengasong J;de Oliveira T
在非洲国家，很难追踪严重急性呼吸综合征冠状病毒2(SARS-CoV-2)大流行的影响，这主要是因为数据不完整。Wilkinson等人。精选的病毒基因组于2021年从非洲大陆的几个国家收集。2020年期间，每个非洲国家的疫情都是由输入性病例引发的，这些病例大多来自欧洲。随着疫情的发展，非洲国家的病例数量可能比报告的高出许多倍，随后的大流行浪潮似乎更加严重。因此，出现了在非洲大陆蔓延的高传播型变种，必须将非洲国家纳入全球控制努力。CA-新冠肺炎在非洲大流行的早期阶段以欧洲进口产品为主，其次是当地一代变种。到目前为止，严重急性呼吸综合征冠状病毒2(SARS-CoV-2)大流行在非洲的发展是异质性的，其全面影响尚不清楚。在这项研究中，我们使用来自33个非洲国家和两个海外地区的8746个基因组的数据集描述了基因组流行病学。我们表明，大多数国家的疫情是由主要来自欧洲的输入引发的，在早期引入国际旅行限制后，这种输入减少了。随着大流行的进展，在许多国家的持续传播和日益增加的流动性导致了许多令人担忧和感兴趣的变种的出现和在该大陆内的传播，例如B.1.351、B.1.525、A.23.1和C.1.1。尽管低抽样率和盲点扭曲了调查结果，但研究结果强调，非洲在全球大流行应对中绝不能掉队，否则它可能成为新变种的来源。
The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al. curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA The early phases of the COVID-19 pandemic in Africa were dominated by European imports, followed by the local generation of variants. 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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DOI：
10.1056/nejmoa2102214
发表时间：
2021-05-20
期刊：
The New England journal of medicine
影响因子：
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作者：
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DOI：
10.1016/j.ijid.2020.11.128
发表时间：
2021-03
期刊：
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
影响因子：
--
作者：
Giandhari J;Pillay S;Wilkinson E;Tegally H;Sinayskiy I;Schuld M;Lourenço J;Chimukangara B;Lessells R;Moosa Y;Gazy I;Fish M;Singh L;Sedwell Khanyile K;Fonseca V;Giovanetti M;Carlos Junior Alcantara L;Petruccione F;de Oliveira T
通讯作者：
de Oliveira T