Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
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DOI：
10.3390/v13030526
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发表时间：
2021-03-22
期刊：
影响因子：
--
通讯作者：
de Oliveira T
中科院分区：
文献类型：
--
作者：
Engelbrecht S;Delaney K;Kleinhans B;Wilkinson E;Tegally H;Stander T;van Zyl G;Preiser W;de Oliveira T
开普敦是南非第一个经历2019冠状病毒病（COVID-19）大流行全面影响的城市。我们从泰格伯格医院采集了大流行第一个月期间所有疑似病例及其接触者的样本。纳米孔测序产生SARS-CoV-2全基因组。系统发育推断与最大似然和贝叶斯方法被用来确定血统播种当地流行病。已知有三名患者曾在国际旅行，附近一家超市发现了疫情。对50个样本进行测序，产生了46个高质量的基因组。将序列分类为谱系：B、B.1、B.1.1.1、B.1.1.161、B.1.1.29、B.1.8、B.39和B.40。超市疫情中受调查人员（PUI）的所有序列（谱系B.1.8）都属于来自荷兰的一个分支，并得到了良好的支持（p > 0.9）。此外，一个新的突变，5209 A>G，出现在开普敦集群。分子钟分析表明，这发生在2020年3月13日左右（95%置信区间：3月9日至17日）。系统发育重建表明，至少有9个SARS-CoV-2早期引入开普敦，并在购物环境中早期局部传播。基因组监测被成功地用于调查和跟踪早期引入的SARS-CoV-2在开普敦的传播。
Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9–17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.
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DOI：
10.1126/science.aaf5036
发表时间：
2016-04-15
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Faria NR;Azevedo RDSDS;Kraemer MUG;Souza R;Cunha MS;Hill SC;Thézé J;Bonsall MB;Bowden TA;Rissanen I;Rocco IM;Nogueira JS;Maeda AY;Vasami FGDS;Macedo FLL;Suzuki A;Rodrigues SG;Cruz ACR;Nunes BT;Medeiros DBA;Rodrigues DSG;Queiroz ALN;da Silva EVP;Henriques DF;da Rosa EST;de Oliveira CS;Martins LC;Vasconcelos HB;Casseb LMN;Simith DB;Messina JP;Abade L;Lourenço J;Alcantara LCJ;de Lima MM;Giovanetti M;Hay SI;de Oliveira RS;Lemos PDS;de Oliveira LF;de Lima CPS;da Silva SP;de Vasconcelos JM;Franco L;Cardoso JF;Vianez-Júnior JLDSG;Mir D;Bello G;Delatorre E;Khan K;Creatore M;Coelho GE;de Oliveira WK;Tesh R;Pybus OG;Nunes MRT;Vasconcelos PFC
通讯作者：
Vasconcelos PFC
影响因子：
5.3
作者：
Sagulenko P;Puller V;Neher RA
通讯作者：
Neher RA
影响因子：
5.8
作者：
Cleemput, Sara;Dumon, Wim;de Oliveira, Tulio
通讯作者：
de Oliveira, Tulio
影响因子：
5.3
作者：
Duchene, Sebastian;Featherstone, Leo;Baele, Guy
通讯作者：
Baele, Guy
SARS-CoV-2 的全基因组测序：调整 Illumina 协议，在大流行期间快速准确地开展疫情调查
影响因子：
3.5
作者：
Pillay, Sureshnee;Giandhari, Jennifer;de Oliveira, Tulio
通讯作者：
de Oliveira, Tulio