NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, RNA Extraction, and cDNA Synthesis
2.2. Nanopore Sequencing
2.3. Bioinformatics Analysis
3. Results
3.1. Increased Yields of SARS-CoV-2 Reads and Bases with NASCarD Lead to Higher Genome Coverage
3.2. Seven Hours Suffice to Obtain High-Quality Consensus Sequences with NASCarD
3.3. GCS Quality Decreases with Lower Viral Loads
3.4. Effect of the Genetic Divergence of the Reference Sequences on Target Genome Recovery
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Terrazos Miani, M.A.; Borcard, L.; Gempeler, S.; Baumann, C.; Bittel, P.; Leib, S.L.; Neuenschwander, S.; Ramette, A. NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples. Pathogens 2024, 13, 61. https://doi.org/10.3390/pathogens13010061
Terrazos Miani MA, Borcard L, Gempeler S, Baumann C, Bittel P, Leib SL, Neuenschwander S, Ramette A. NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples. Pathogens. 2024; 13(1):61. https://doi.org/10.3390/pathogens13010061
Chicago/Turabian StyleTerrazos Miani, Miguel A., Loïc Borcard, Sonja Gempeler, Christian Baumann, Pascal Bittel, Stephen L. Leib, Stefan Neuenschwander, and Alban Ramette. 2024. "NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples" Pathogens 13, no. 1: 61. https://doi.org/10.3390/pathogens13010061
APA StyleTerrazos Miani, M. A., Borcard, L., Gempeler, S., Baumann, C., Bittel, P., Leib, S. L., Neuenschwander, S., & Ramette, A. (2024). NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples. Pathogens, 13(1), 61. https://doi.org/10.3390/pathogens13010061