NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples
Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here,...
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| Format: | Article |
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MDPI AG
2024-01-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/13/1/61 |
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| author | Miguel A. Terrazos Miani Loïc Borcard Sonja Gempeler Christian Baumann Pascal Bittel Stephen L. Leib Stefan Neuenschwander Alban Ramette |
| author_facet | Miguel A. Terrazos Miani Loïc Borcard Sonja Gempeler Christian Baumann Pascal Bittel Stephen L. Leib Stefan Neuenschwander Alban Ramette |
| author_sort | Miguel A. Terrazos Miani |
| collection | DOAJ |
| description | Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called NASCarD (Nanopore Adaptive Sampling with Carrier DNA), which allows a low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using COVID-19 positive samples available during the omicron wave, we demonstrate how the method may lead to >99% genome completeness of the SARS-CoV-2 genome sequences within 7 h of sequencing at a competitive cost. The new approach may have applications beyond SARS-CoV-2 sequencing for other DNA or RNA pathogens in clinical samples. |
| first_indexed | 2024-03-08T10:38:56Z |
| format | Article |
| id | doaj.art-f679f8d420324c5db1a59bce8793aeb6 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-08T10:38:56Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-f679f8d420324c5db1a59bce8793aeb62024-01-26T18:03:45ZengMDPI AGPathogens2076-08172024-01-011316110.3390/pathogens13010061NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical SamplesMiguel A. Terrazos Miani0Loïc Borcard1Sonja Gempeler2Christian Baumann3Pascal Bittel4Stephen L. Leib5Stefan Neuenschwander6Alban Ramette7Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandInstitute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, SwitzerlandWhole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called NASCarD (Nanopore Adaptive Sampling with Carrier DNA), which allows a low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using COVID-19 positive samples available during the omicron wave, we demonstrate how the method may lead to >99% genome completeness of the SARS-CoV-2 genome sequences within 7 h of sequencing at a competitive cost. The new approach may have applications beyond SARS-CoV-2 sequencing for other DNA or RNA pathogens in clinical samples.https://www.mdpi.com/2076-0817/13/1/61beta coronavirusesSARS-CoV-2whole-genome sequencingnext-generation sequencinggenomicsnanopore sequencing |
| spellingShingle | Miguel A. Terrazos Miani Loïc Borcard Sonja Gempeler Christian Baumann Pascal Bittel Stephen L. Leib Stefan Neuenschwander Alban Ramette NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples Pathogens beta coronaviruses SARS-CoV-2 whole-genome sequencing next-generation sequencing genomics nanopore sequencing |
| title | NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples |
| title_full | NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples |
| title_fullStr | NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples |
| title_full_unstemmed | NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples |
| title_short | NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples |
| title_sort | nascard nanopore adaptive sampling with carrier dna a rapid pcr free method for sars cov 2 whole genome sequencing in clinical samples |
| topic | beta coronaviruses SARS-CoV-2 whole-genome sequencing next-generation sequencing genomics nanopore sequencing |
| url | https://www.mdpi.com/2076-0817/13/1/61 |
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