Journal
NATURE COMMUNICATIONS
Volume 12, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-021-24078-9
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Funding
- National Genomics Infrastructure in Stockholm - Science for Life Laboratory
- Knut and Alice Wallenberg Foundation
- Swedish Research Council
- National Natural Science Foundation of China [81972475]
- Chinese Postdoctoral Science Foundation [2019T120593, 2018M630787]
- Dipartimenti di Eccellenza 2018-2022 [D15D18000410001]
- Fondazione Piemontese per la Ricerca sul Cancro (INTEGRAZIONI DIAGNOSTICA IN ONCOLOGIA-INTERONC FPRC 5x1000 MIUR 2017)
- SciLifeLab/KAW National COVID-19 Research Program project grant, Research Area Viral Sequence Evolution
- Swedish Foundation for Strategic Research [SSF BD15-0095]
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Genomic surveillance of SARS-CoV-2 variants is crucial, and a new sequencing method, COVseq, allows cost-effective and scalable surveillance that can be easily adapted to other viruses.
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses. Genomic surveillance of SARS-CoV-2 is crucial to monitor the spread of variants of concern. A new sequencing method enables cost-effective SARS-CoV-2 genomic surveillance at scale and is easily adaptable to other viruses.
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