Dataset Information

SARS-CoV-2 tracking in Tunisia through next-generation sequencing: lessons for the future.

ABSTRACT: In this study, data available from GISAID on the whole-genome sequences of SARS-CoV-2 variants circulating in Tunisia were analyzed, and the prevalences of those variants in Tunisia were compared to their prevalences in other North African countries and around the world. Our results show new mutations and different prevalences of some lineages. In particular, new sets of mutations were identified in the spike protein of the virus during the analysis of 85 Tunisian samples, and the lineage B1.160 was found to be the most prevalent (18%) lineage in Tunisia. The prevalence of this lineage in Tunisia was significantly higher than its prevalence worldwide and in samples from neighboring countries (3%). This preliminary study shows the importance of tracking virus variants by next-generation sequencing in order to assess the dynamics of the COVID-19 pandemic and the impact of vaccination on the evolution of the virus.

SUBMITTER: Rebai A

PROVIDER: S-EPMC8017083 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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SARS-CoV-2 tracking in Tunisia through next-generation sequencing: lessons for the future.

Rebai Ahmed A Souissi Amal A Abid Nabil N Masmoudi Saber S

Euro-Mediterranean journal for environmental integration 20210402 2

In this study, data available from GISAID on the whole-genome sequences of SARS-CoV-2 variants circulating in Tunisia were analyzed, and the prevalences of those variants in Tunisia were compared to their prevalences in other North African countries and around the world. Our results show new mutations and different prevalences of some lineages. In particular, new sets of mutations were identified in the spike protein of the virus during the analysis of 85 Tunisian samples, and the lineage B1.160 ...[more]

PMID: 33824883

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Project description:COVID-19 is caused by SARS-CoV-2, several virulent variants of which have emerged since 2019. More than 529 million people have been infected, and at least 6 million have died. Our aim was to develop a fast, accurate, low-cost method for detecting and identifying newly emerging variants of concern (VOCs) that could pose a global threat. The 341-bp DNA sequence of a specific region of the SARS-CoV-2's spike protein was amplified by a one-step PCR on RNA samples from 46 patients. The product was sequenced using next-generation sequencing (NGS). DNA sequences from seven genomes, the original Wuhan isolate and six different representative variants obtained from the GISAID website, were used as references. Complete whole-genome sequences from local isolates were also obtained from the GISAID website, and their RNA was used for comparison. We used an amplicon-based NGS method (termed VOC-NGS) for genotyping and successfully identified all 46 samples. Fifteen (32.6%) were like the original isolate. Twenty-seven were VOCs: nine (19.5%) Alpha, eight (19%) Delta, six (14%) Beta, and four (8.7%) Omicron. Two were variants of interest (VOI): one (2%) Kappa and one (2%) Zeta. Two samples were mixtures of two variants, one of Alpha and Beta and one of Alpha and Delta. The Spearman correlation between whole-genome sequencing (WGS) and VOC-NGS was significant (P < 0.001) with perfect agreement (Kappa = 0.916) for 36/38 (94.7%) samples with VOC-NGS detecting all the known VOCs. Genotyping by VOC-NGS enables rapid screening of high-throughput clinical samples that includes the identification of VOCs and mixtures of variants, at lower cost than WGS. IMPORTANCE The manuscript described SARS-Cov-2 genotyping by VOC-NGS, which presents an ideal balance of accuracy, rapidity, and cost for detecting and globally tracking VOCs and some VOI of SARS-CoV-2. A large number of clinical samples can be tested together. Rapid introduction of new mutations at a specific site of the spike protein necessitates efficient strain detection and identification to enable choice of treatment and the application of vaccination, as well as planning public health policy.

Dataset Information

SARS-CoV-2 tracking in Tunisia through next-generation sequencing: lessons for the future.

Publications

SARS-CoV-2 tracking in Tunisia through next-generation sequencing: lessons for the future.

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