Author | Miranda, Pâmella | |
Author | Alves, Pedro Augusto | |
Author | Monte Neto, Rubens Lima do | |
Author | Weber, Gerald | |
Access date | 2024-04-05T19:20:56Z | |
Available date | 2024-04-05T19:20:56Z | |
Document date | 2024 | |
Citation | MIRANDA, Pâmella et al. In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection. The Open COVID Journal, v. 4, n. 1, 2024. DOI: 10.2174/0126669587279780240130063422 | en_US |
ISSN | 2666-9587 | en_US |
URI | https://www.arca.fiocruz.br/handle/icict/63427 | |
Language | eng | en_US |
Publisher | Bentham Open | en_US |
Related document | https://www.arca.fiocruz.br/handle/icict/62543 | en_US |
Rights | open access | en_US |
Title | In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection. | en_US |
Type | Article | en_US |
Abstract | Background: Viral mutations are the primary cause of mismatches in primer-target hybridisation, affecting the sensibility of molecular techniques, and potentially leading to detection dropouts. Despite its importance, little is known about the quantitative effect of mismatches in primer-target hybridisation. We have used up-to-date and highly detailed thermodynamic model parameters of DNA mismatches to evaluate the sensibility to variants of SARS-CoV-2 RT-LAMP primers.
Methods: We aligned 18 RT-LAMP primer sets, which underwent clinical validation, to the genomes of the wild-type strain (ws), 7 variants and 4 subvariants, and calculated hybridisation temperatures allowing up to three consecutive mismatches. We calculated the coverage when the mismatched melting temperature fell by more than 5°C in comparison to the matched alignments. If no mismatches were considered, the average coverage found was 94% for ws, falling to the lowest value for Omicron, i.e., 84%.
Results: However, considering mismatches, the coverage was much higher, i.e., 97% (ws) to 88% (Omicron). Stabilizing mismatches (higher melting temperatures) accounted for roughly 1/3 of this increase. The number of primer dropouts increased for each new variant; however, the effect was much less severe if mismatches were considered.
Conclusion: We suggest using melting temperature calculations to continuously assess the trend of primer dropouts. | en_US |
Affilliation | Universidade Federal de Minas Gerais. Departamento de Fı́sica. Belo Horizonte, MG, Brazil/Universidade Federal de Minas Gerais. Programa Interunidades de Pós-Graduação em Bioinformática. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil/Fundação Oswaldo Cruz. Centro de Tecnologia em Vacinas, Belo Horizonte, MG, Brazil | en_US |
Affilliation | Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Universidade Federal de Minas Gerais. Departamento de Fı́sica. Belo Horizonte, MG, Brazil | en_US |
Subject | DNA mismatches | en_US |
Subject | Diagnosis | en_US |
Subject | LAMP primer design | en_US |
Subject | SARS-CoV-2 | en_US |
Subject | DNA thermodynamic models | en_US |
Subject | Melting temperature calculations | en_US |