Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern

Miranda, Pâmella; Barbosa, Vivianne Basílio; Weber, Gerald

doi:10.1007/978-3-030-91814-9_15

Advances in Bioinformatics and Computational Biology

2021

DOI: 10.1007/978-3-030-91814-9_15

|View full text |Cite

Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern

Pâmella Miranda

Vivianne Basílio Barbosa

Gerald Weber

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...

Citation Types

Supporting

Mentioning

Contrasting

Year Published

2024

Publication Types

Select...

Article1

Relationship

Self Cite1

Independent0

Authors

Journals

Cited by 1 publication

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection

Miranda,

Alves,

do Monte-Neto

et al. 2024

TOCOVIDJ

Self Cite

View full text Add to dashboard Cite

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.

show abstract

In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection

Miranda,

Alves,

do Monte-Neto

et al. 2024

TOCOVIDJ

Self Cite

View full text Add to dashboard Cite

show abstract

scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.

Contact Info

hi@scite.ai

10624 S. Eastern Ave., Ste. A-614

Henderson, NV 89052, USA

Blog Terms and Conditions API Terms Privacy Policy Contact Cookie Preferences Do Not Sell or Share My Personal Information

Made with 💙 for researchers

Part of the Research Solutions Family.

Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern

Cited by 1 publication

References 7 publications

In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection

In silico Thermodynamic Evaluation of the Effectiveness of RT-LAMP Primers for SARS-CoV-2 Variants Detection

Contact Info

Product

Resources

About