Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya.
Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya.
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DOI：
10.1186/s12864-022-08853-6
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发表时间：
2022-09-01
期刊：
影响因子：
4.4
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中科院分区：
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COVID-19 爆发的基因组监测和识别对于了解 SARS-CoV-2 的遗传多样性、系统发育和谱系非常重要。基因组监测提供了对循环感染、疫苗和其他感染控制方法的稳健性和设计的见解。我们对来自肯尼亚临床人群的 57 个 SARS-CoV-2 分离株进行了测序，其中 55 个通过了现有 tRee (UShER) 工作流程上的超快样本放置的质量检查。肯尼亚两个地区（内罗毕和基安布县）的系统基因组时间分析显示，B.1.1.7（Alpha；n = 32，56.1%）和 B.1（n = 9，15.8%）是主要谱系，表现出低 Ct 值 (5-31)，表明两个地区具有高传染性和变异突变。还在目标种群内的各个采样点检测到谱系 B.1.617.2、B.1.1、A.23.1、A.2.5.1、B.1.596、A 和 B.1.405。谱系和遗传分离株可追溯到中国 (A)、哥斯达黎加 (A.2.5.1)、欧洲 (B.1、B.1.1、A.23.1)、美国 (B.1.405、B.1.596)、南非 (B.1.617.2) 和英国 (B.1.1.7)，表明存在多个引入事件。这项研究代表了内罗毕大都市区的基因组 SARS-CoV-2 流行病学研究之一，并描述了持续监测对大流行控制的重要性。在线版本包含可在 10.1186/s12864-022-08853-6 获取的补充材料。
Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5–31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control. The online version contains supplementary material available at 10.1186/s12864-022-08853-6.
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DOI：
10.1126/science.abj4336
发表时间：
2021-10-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
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通讯作者：
de Oliveira T
影响因子：
4.6
作者：
Acera Mateos P;Balboa RF;Easteal S;Eyras E;Patel HR
通讯作者：
Patel HR
DOI：
10.1126/science.abk0414
发表时间：
2021-11-19
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Brand SPC;Ojal J;Aziza R;Were V;Okiro EA;Kombe IK;Mburu C;Ogero M;Agweyu A;Warimwe GM;Nyagwange J;Karanja H;Gitonga JN;Mugo D;Uyoga S;Adetifa IMO;Scott JAG;Otieno E;Murunga N;Otiende M;Ochola-Oyier LI;Agoti CN;Githinji G;Kasera K;Amoth P;Mwangangi M;Aman R;Ng'ang'a W;Tsofa B;Bejon P;Keeling MJ;Nokes DJ;Barasa E
通讯作者：
Barasa E
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
DOI：
10.1016/s0140-6736(21)00632-2
发表时间：
2021-04-03
期刊：
Lancet (London, England)
影响因子：
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作者：
Salyer SJ;Maeda J;Sembuche S;Kebede Y;Tshangela A;Moussif M;Ihekweazu C;Mayet N;Abate E;Ouma AO;Nkengasong J
通讯作者：
Nkengasong J