NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples

Author:

Terrazos Miani Miguel A.1,Borcard Loïc1,Gempeler Sonja1,Baumann Christian1,Bittel Pascal1,Leib Stephen L.1,Neuenschwander Stefan1,Ramette Alban1ORCID

Affiliation:

1. Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, Switzerland

Abstract

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.

Funder

Swiss National Science Foundation—Bridge Discovery

Multidisciplinary Center for Infectious Diseases, Bern, Switzerland

Publisher

MDPI AG

Subject

Infectious Diseases,Microbiology (medical),General Immunology and Microbiology,Molecular Biology,Immunology and Allergy

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