Comparative Bioinformatic Analysis Reveals Conserved Regions in SARS-CoV-2 Genome for RAPID Pandemic Response
Abstract
:1. Introduction
2. Results
2.1. Comparative Analysis of Whole-Genome Data Using Bioinformatic Tools Revealed Conserved Regions of SARS-CoV-2
2.2. Data Availability
2.3. Code Availability
2.4. Evaluation of SET1 Primer Selectivity and Optimization of One-Step RT-qPCR Assay Using Synthetic DNA and RNA
2.5. Evaluation of SET1 Primers Using the Shorter RAPID One-Step RT-qPCR Protocol on Nucleic Acid Isolated from Saliva
2.6. Validation of the Shortened RAPID One-Step qPCR Assay Using Various Positive and Negative Samples
2.7. Optimization and Significant Reduction in Time of the One-Step qPCR Method, Enhancing Sensitivity for Future SARS-CoV-2 Variants
2.8. Validation of the Optimized Assay Using Positive Samples, including a Critical Case Study
3. Discussion
4. Materials and Methods
- -
- Nucleic acid was extracted using the Seegene STARlet equipment following the manufacturer’s protocol.
- -
- Allplex™ 2019-nCoV Assay was ordered from Seegene (Cat. No. RP10243X).
- Ordered reagents:
- -
- GoTaq® 1-Step RT-qPCR System (Promega, Cat. No. A6020) was used for the one-step qPCR.
- -
- Primer sets (Prime time® Std qPCR Assay (500rXn), as well as synthetic RNA and DNA were custom ordered from Integrated DNA Technologies (IDT).
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Karpuj, M.V.; Shaytov, D.R.; Shemer-Avni, Y.; Gideon, M.; Frenkel, Z.M.; Sivan, S. Comparative Bioinformatic Analysis Reveals Conserved Regions in SARS-CoV-2 Genome for RAPID Pandemic Response. Int. J. Mol. Sci. 2024, 25, 5764. https://doi.org/10.3390/ijms25115764
Karpuj MV, Shaytov DR, Shemer-Avni Y, Gideon M, Frenkel ZM, Sivan S. Comparative Bioinformatic Analysis Reveals Conserved Regions in SARS-CoV-2 Genome for RAPID Pandemic Response. International Journal of Molecular Sciences. 2024; 25(11):5764. https://doi.org/10.3390/ijms25115764
Chicago/Turabian StyleKarpuj, Marcela Viviana, D. R. Shaytov, Yonat Shemer-Avni, Michael Gideon, Zakharia M. Frenkel, and Sarit Sivan. 2024. "Comparative Bioinformatic Analysis Reveals Conserved Regions in SARS-CoV-2 Genome for RAPID Pandemic Response" International Journal of Molecular Sciences 25, no. 11: 5764. https://doi.org/10.3390/ijms25115764