Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania.
Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania.
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DOI：
10.3389/fmed.2022.1034682
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发表时间：
2022
影响因子：
3.9
通讯作者：
Mpagama, Stellah G.
中科院分区：
文献类型：
--
作者：
Mziray, Shabani Ramadhani;van Zwetselaar, Marco;Kayuki, Charles C.;Mbelele, Peter M.;Makubi, Abel N.;Magesa, Alex S.;Kisonga, Riziki M.;Sonda, Tolbert B.;Kibiki, Gibson S.;Githinji, George;Heysell, Scott K.;Chilongola, Jaffu O.;Mpagama, Stellah G.
关键词：
由严重急性呼吸道综合征冠状病毒2型（SARS-CoV-2）引起的2019冠状病毒病（COVID-19）在全球范围内造成了相当大的发病率和死亡率。坦桑尼亚缺乏SARS-CoV-2基因数据，这对国内追踪这一流行病提出了挑战。我们对在该国分离的SARS-CoV-2进行了测序，以确定流行菌株、突变和致病性，并最终丰富了国际遗传数据库，特别是来自非洲的序列。这项横断面研究使用了2021年1月至5月期间COVID-19聚合酶链反应检测阳性的有症状和无症状成人的鼻咽拭子。使用ARTIC nCoV-2019测序方案第三版制备病毒基因组文库。使用Oxford Nanopore Technologies MinION装置进行全基因组测序（WGS）。使用ARTIC nCoV-2019生物信息学方案版本1.1.0，在ARTIC pipeline版本1.2.1上进行计算机基因组数据分析。根据多重PCR扩增子的凝胶电泳条带强度，69份样本中有29份（42%）符合测序要求。在29株分离株中，26株为相关变异株[β（n = 22）和δ（n = 4）]。其他变体包括Eta（n = 2）和B.1.530（n = 1）。我们在所有β变体中发现了突变的组合（S：D80 A，S：D215 G，S：K417 N，ORF 3a：Q57 H，E：P71 L），而在其他谱系中不存在。B.1.530谱系携带的突变具有非常低的累积全球患病率，这些突变是nsp 13：M233 I、nsp 14：S434 G、ORF 3a：A99 S、S：T22 I和S：N164 H。B.1.530谱系与首次在肯尼亚东南部报道的分离株在遗传学上聚类，表明SARS-CoV-2的区域进化。我们从2021年初在坦桑尼亚收集的样本中提供了Beta，Delta，Eta变体存在的证据以及当地进化的谱系（B.1.530）。这项工作为正在进行的WGS监测提供了一个模型，该模型将被要求为坦桑尼亚和东非新出现和传播的SARS-CoV-2多样性提供信息。
Coronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally. Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic. We sequenced SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa. This cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021. Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three. Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device. In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0. Twenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons. Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)]. Other variants included Eta (n = 2) and B.1.530 (n = 1). We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages. The B.1.530 lineage carried mutations with very low cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H. The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2. We provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.530) from samples collected in early 2021 in Tanzania. This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.
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通讯作者：
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