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Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks.<\/ns4:p>\n                  <ns4:p>SMART (Switching Mechanism at the 5\u2032 end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach \u2018SMART-9N\u2019 and a version compatible rapid adapters \u00a0available from Oxford Nanopore Technologies \u2018Rapid SMART-9N\u2019. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)\/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.21114.r56455, Edward Cunningham-Oakes, University of Liverpool, Liverpool, 16 May 2023, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-241\/v2#referee-response-56455","order":0,"name":"referee-response-56455","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.21114.r56454, Mirela D'arc Ferreira da Costa, Instituto de Biologia, Departamento de Gen\u00e9tica, Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Federal University of Rio de Janeiro, Rio de Janeiro, 04 May 2023, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/6-241\/v2#referee-response-56454","order":1,"name":"referee-response-56454","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by a Medical Research Council-S\u00e3o Paulo Research Foundation (FAPESP) CADDE partnership award (MR\/S0195\/1 and FAPESP 18\/14389-0) (https:\/\/caddecentre.org);  FAPESP\/Newton Funds (FAPESP 2017\/08012-9), Bill & Melinda Gates Foundation (INV-034540 and INV-034652), and I.M.C (FAPESP 2018\/17176-8).\nM.S.R. is supported by the Faculdade de Medicina da Universidade de S\u00e3o Paulo (FMUSP). T.M.C. (2019\/07544-2), C.A.M.S. (2019\/21301-5), F.C.S.S. (2018\/25468-9), J.G.J. (2018\/17176-8, 2019\/12000-1, 18\/14389-0) and E.C.S (2018\/14389-0) are supported by FAPESP. P.S.A. is supported by Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES) (88887.596940\/2021-00). W.M.S is supported by FAPESP (2017\/13981-0, 2019\/24251-9), Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico (CNPq) (408338\/2018-0), and the National Institutes of Health (AI120942). D.S.C is supported by the Clarendon Fund and by the Department of Zoology, University of Oxford. M.R.A is supported by CAPES (88887.356527\/2019-00). N.R.F. is supported by a Wellcome Trust Royal Society Sir Henry Dale Fellowship (204311). N.J.L. and J.Q. are supported by the Wellcome ARTIC network (206298). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}