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Here, we present a streamlined workflow\u2014COVseq\u2014which 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.<\/jats:p>","DOI":"10.1038\/s41467-021-24078-9","type":"journal-article","created":{"date-parts":[[2021,6,23]],"date-time":"2021-06-23T06:06:11Z","timestamp":1624428371000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3322-1697","authenticated-orcid":false,"given":"Michele","family":"Simonetti","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6430-4236","authenticated-orcid":false,"given":"Ning","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3910-6497","authenticated-orcid":false,"given":"Luuk","family":"Harbers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Grazia","family":"Milia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Brossa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9089-7370","authenticated-orcid":false,"given":"Thi Thu","family":"Huong Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0480-8296","authenticated-orcid":false,"given":"Francesco","family":"Cerutti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrico","family":"Berrino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Sapino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6499-9082","authenticated-orcid":false,"given":"Magda","family":"Bienko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonino","family":"Sottile","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4698-598X","authenticated-orcid":false,"given":"Valeria","family":"Ghisetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3019-6978","authenticated-orcid":false,"given":"Nicola","family":"Crosetto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,6,23]]},"reference":[{"key":"24078_CR1","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1056\/NEJMoa2001017","volume":"382","author":"N Zhu","year":"2020","unstructured":"Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727\u2013733 (2020).","journal-title":"N. Engl. J. Med."},{"key":"24078_CR2","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1002\/gch2.1018","volume":"1","author":"S Elbe","year":"2017","unstructured":"Elbe, S. & Buckland\u2010Merrett, G. Data, disease and diplomacy: GISAID\u2019s innovative contribution to global health. Glob. Chall. 1, 33\u201346 (2017).","journal-title":"Glob. Chall."},{"key":"24078_CR3","doi-asserted-by":"publisher","first-page":"1800","DOI":"10.3389\/fmicb.2020.01800","volume":"11","author":"D Mercatelli","year":"2020","unstructured":"Mercatelli, D. & Giorgi, F. M. Geographic and genomic distribution of SARS-CoV-2 mutations. Front. Microbiol. 11, 1800 (2020).","journal-title":"Front. Microbiol."},{"key":"24078_CR4","unstructured":"Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. 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