Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic

IF 1.6 Q4 INFECTIOUS DISEASES

Journal of clinical virology plus Pub Date : 2025-04-15 DOI:10.1016/j.jcvp.2025.100212

Nicholaus P. Mnyambwa , Jinxin Gao , Alex Magesa , Edina Mgimba , Swaminathan Mahesh , Pawan Angra , Juma Kisuse , Clara Lubinza , Lawrence Mapunda , Aman Wilfred , Godfather Kimaro , George P. Judicate , Ambele Eliah , Augustino Msanga , Senkoro Mbazi , Esther Ngadaya , Mukurasi Kokuhabwa , Jackson P. Mushumbusi , Medard Beyanga , Wangeci Gatei , Sayoki Mfinanga

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Abstract

Background

Genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Tanzania remain scarce in GISAID, thus hindering our understanding of how the pandemic evolved in the country.

Methods

We performed whole genome sequencing on SARS-CoV-2 samples collected between March 2021 and December 2022 to characterize the virus in Tanzania. Nasal and oropharyngeal swabs were collected from patients seeking health care, incoming travelers as well as from outgoing travelers undergoing pre-travel COVID-19 testing (required for flight boarding). Sample collection, and testing were coordinated by the National Public Health Laboratory.

Results

Among 515 samples, 260 (50.49 %) were from outgoing travelers, 227 (44.08 %) Covid-19 suspects seeking care, and 28 (5.44 %) incoming travelers identified at the airport. The majority of the samples came from Dar es Salaam (n = 380, 73.7 %), the country's largest city and the main port of entry. We identified 74 Pango lineages from all the samples, with Omicron 430 (83.50 %) and Delta 79 (15 %) variants being predominant. From the 380 Dar es Salaam samples, 67 Pango lineages were identified, showing both overlapping and unique lineages in each sample type.

Conclusion

Our findings reveal a dynamic circulation of SARS-CoV-2 variants over time, with Delta predominantly observed in 2021 and Omicron in 2022 in Tanzania. The temporal prevalence of the identified lineages was consistent with the global epidemiology of the virus. Sustained and expanded genomic surveillance is recommended to track and respond effectively to emerging variants.

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大流行期间在坦桑尼亚获得的SARS-CoV-2序列的基因组分析

来自坦桑尼亚的严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）的基因组序列在GISAID中仍然很少，因此阻碍了我们对该国大流行如何演变的理解。方法对2021年3月至2022年12月在坦桑尼亚采集的SARS-CoV-2样本进行全基因组测序，以表征该病毒。从寻求医疗保健的患者、入境旅客以及接受旅行前COVID-19检测（登机所需）的出境旅客中收集鼻和口咽拭子。样本收集和检测由国家公共卫生实验室协调。结果515份样本中，260份（50.49%）来自出境旅客，227份（44.08%）来自寻求治疗的Covid-19疑似病例，28份（5.44%）来自机场发现的入境旅客。大多数样本来自该国最大城市和主要入境口岸达累斯萨拉姆（n = 380, 73.7%）。我们从所有样本中鉴定出74个Pango谱系，其中Omicron 430（83.50%）和Delta 79（15%）变体占主导地位。从达累斯萨拉姆的380个样本中，鉴定出67个Pango血统，每种样本类型都显示出重叠和独特的血统。我们的研究结果揭示了SARS-CoV-2变异随时间的动态循环，在坦桑尼亚主要观察到Delta变异在2021年，Omicron变异在2022年。所确定谱系的时间流行率与病毒的全球流行病学一致。建议持续和扩大基因组监测，以跟踪和有效应对新出现的变异。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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