Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants

TL;DR

This study shows that Sanger sequencing is an effective and accessible method for tracking SARS-CoV-2 variants and recombinants, especially in resource-limited settings.

Contribution

The study validates Sanger sequencing as a cost-effective alternative to NGS for variant surveillance and identifies a recombinant lineage in Brazil.

Findings

Sanger sequencing successfully identified one variant of interest and five variants of concern in Belo Horizonte, Brazil.

The method detected a recombinant SARS-CoV-2 lineage using gene amplification and RT-PCR.

Sanger sequencing proved to be a practical and scalable tool for variant monitoring in low-resource settings.

Abstract

Since the emergence of SARS-CoV-2 in December 2019, more than 12,000 mutations in the virus have been identified. These could cause changes in viral characteristics and directly impact global public health. The emergence of variants is a great concern due to the chance of increased transmissibility and infectivity. Sequencing for surveillance and monitoring circulating strains is extremely necessary as the early identification of new variants allows public health agencies to make faster and more effective decisions to contain the spread of the virus. In the present study, we identified circulating variants in samples collected in Belo Horizonte, Brazil, and detected a recombinant lineage using the Sanger method. The identification of lineages was done through gene amplification of SARS-CoV-2 by Reverse Transcription-Polymerase Chain Reaction (RT-PCR). By using these specific fragments, we were able to differentiate one variant of interest and five circulating variants of concern. We were also able to detect recombinants. Randomly selected samples were sequenced by either Sanger or Next Generation Sequencing (NGS). Our findings validate the effectiveness of Sanger sequencing as a powerful tool for monitoring variants. It is easy to perform and allows the analysis of a larger number of samples in countries that cannot afford NGS.

The online version contains supplementary material available at 10.1007/s42770-024-01387-x.

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