Design of specific primer sets for SARS-CoV-2 variants using evolutionary algorithms
2021 Genetic and Evolutionary Computation Conference, GECCO 2021
; : 982-990, 2021.
Article
in English
| Scopus | ID: covidwho-1327724
ABSTRACT
Primer sets are short DNA sequences of 18-22 base pairs, that can be used to verify the presence of a virus, and designed to attach to a specific part of a viral DNA. Designing a primer set requires choosing a region of DNA, avoiding the possibility of hybridization to a similar sequence, as well as considering its GC content and Tm (melting temperature). Coronaviruses, such as SARS-CoV-2, have a considerably large genome (around 30 thousand nucleotides) when compared to other viruses. With the rapid rise and spread of SARS-CoV-2 variants, it has become a priority to breach our lack of specific primers available for diagnosis of this new variants. Here, we propose an evolutionary-based approach to primer design, able to rapidly deliver a high-quality primer set for a target sequence of the virus variant. Starting from viral sequences collected from open repositories, the proposed approach is proven able to uncover a specific primer set for the B.1.1.7 SARS-CoV-2 variant. Only recently identified, B.1.1.7 is already considered potentially dangerous, as it presents a considerably higher transmissibility when compared to other variants. © 2021 ACM.
Full text:
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Collection:
Databases of international organizations
Database:
Scopus
Topics:
Variants
Language:
English
Journal:
2021 Genetic and Evolutionary Computation Conference, GECCO 2021
Year:
2021
Document Type:
Article
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