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
Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania.
Kibong'oto Infectious Diseases Hospital, Sanya Juu, Tanzania.
Front Med (Lausanne). 2023 Jan 4;9:1034682. doi: 10.3389/fmed.2022.1034682. eCollection 2022.
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. 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 ( = 22); and Delta ( = 4)]. Other variants included Eta ( = 2) and B.1.530 ( = 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.
2019冠状病毒病（COVID-19）由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起，在全球范围内导致了相当高的发病率和死亡率。来自坦桑尼亚的SARS-CoV-2基因数据匮乏，给该国追踪疫情带来了挑战。我们对该国分离出的SARS-CoV-2进行了测序，以确定流行毒株、突变情况和系统发育关系，最终丰富国际基因数据库，特别是增加来自非洲的序列。
这项横断面研究利用了2021年1月至5月期间COVID-19聚合酶链反应检测呈阳性的有症状和无症状成年人的鼻咽拭子。使用ARTIC nCoV-2019测序方案第三版制备病毒基因组文库。使用牛津纳米孔技术公司的MinION设备进行全基因组测序（WGS）。使用ARTIC nCoV-2019生物信息学方案1.1.0在ARTIC管道1.2.1版本上进行基因组数据分析。
69个样本中有29个（42%）根据多重PCR扩增子的凝胶电泳条带强度符合测序要求。在29个分离株中，26个是值得关注的变异株[贝塔（=22）；和德尔塔（=4）]。其他变异株包括埃塔（=2）和B.1.530（=1）。我们在所有贝塔变异株中发现了突变组合（S：D80A、S：D215G、S：K417N、ORF3a：Q57H、E：P71L），而在其他谱系中不存在。B.1.530谱系携带的突变在全球累计流行率非常低，这些突变是nsp13：M233I、nsp14：S434G、ORF3a：A99S、S：T22I和S：N164H。B.1.530谱系在系统发育上与首次在肯尼亚东南部报告的分离株聚类，表明SARS-CoV-2的区域进化。
我们提供了证据，证明2021年初在坦桑尼亚采集的样本中存在贝塔、德尔塔、埃塔变异株以及一个本地进化的谱系（B.1.530）。这项工作为正在进行的WGS监测提供了一个模型，这将有助于了解坦桑尼亚和东非新出现和正在传播的SARS-CoV-2多样性。
