What is it about?
Viral mutations are the primary cause of failure to identify the virus. Mismatches may arise between DNA primers and targets, that is, the virus sample, affecting the sensibility of molecular techniques and potentially leading to detection dropouts. However, the mismatch presence may contribute to improve primer-target hybridisation, leading to the pathogen identification. For instance, some SNP identification techniques apply intentional mismatches to identify the polymorphism. We analysed DNA primers designed to identify SARS-CoV-2 coronavirus in reverse transcription loop-mediated isothermal amplification (RT-LAMP). It is a molecular method widely applied to identify different pathogens. It uses 4 to 6 primers to hybridise to the target and is carried out at a constant temperature. The presence of up to three consecutive mismatches in these primers showed an increase in their coverages and also shed light in their effectiveness in identifying wild-type and mutated viral genomes.
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Why is it important?
The mismatch presence analysis in DNA primers presented here may improve a previously analysis of primer design and may contribute to a continuously evaluating the effectiveness of primers for different targets.
Perspectives
This work and the pipeline applied to develop it may contribute to an improvement in different analyses, such as diagnosis techniques. Furthermore, it may broaden the investigation about mismatches behaviour.
Pâmella Miranda
Karolinska Institutet
Read the Original
This page is a summary of: In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection, The Open COVID Journal, February 2024, Bentham Science Publishers,
DOI: 10.2174/0126669587279780240130063422.
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