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Currently, the 17D and 17DD attenuated substrains are used for vaccine production. The 17D strain is used for vaccine production by several countries, while the 17DD strain is used exclusively in Brazil. The cell passages carried out through the seed-lot system of vaccine production influence the presence of quasispecies causing changes in the stability and immunogenicity of attenuated genotypes by increasing attenuation or virulence. Using next-generation sequencing, we carried out genomic characterization and genetic diversity analysis between vaccine lots of the Brazilian YF vaccine, produced by BioManguinhos\u2013Fiocruz, and used during 11 years of vaccination in Brazil. We present 20 assembled and annotated genomes from the Brazilian 17DD vaccine strain, eight single nucleotide polymorphisms and the quasispecies spectrum reconstruction for the 17DD vaccine, through a pipeline here introduced. The V2IDA pipeline provided a relationship between low genetic diversity, maintained through the seed lot system, and the confirmation of genetic stability of lots of the Brazilian vaccine against YF. Our study sets precedents for use of V2IDA in genetic diversity analysis and in silico stability investigation of attenuated viral vaccines, facilitating genetic surveillance during the vaccine production process.<\/jats:p>","DOI":"10.1098\/rsfs.2020.0063","type":"journal-article","created":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T04:05:22Z","timestamp":1623384322000},"update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data"],"prefix":"10.1098","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3530-7435","authenticated-orcid":false,"given":"Amanda Ara\u00fajo","family":"Serr\u00e3o de Andrade","sequence":"first","affiliation":[{"name":"National Laboratory for Scientific Computing 1 , ,","place":["&gt;Brazil"]},{"name":"Bioinformatics Laboratory (LABINFO), Avenida Get\u00falio Vargas, 333, Quitandinha 25651-075, Petr\u00f3polis, Rio de Janeiro 1 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7768-2199","authenticated-orcid":false,"given":"Andr\u00e9 E. R.","family":"Soares","sequence":"additional","affiliation":[{"name":"National Laboratory for Scientific Computing 1 , ,","place":["&gt;Brazil"]},{"name":"Bioinformatics Laboratory (LABINFO), Avenida Get\u00falio Vargas, 333, Quitandinha 25651-075, Petr\u00f3polis, Rio de Janeiro 1 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7124-2715","authenticated-orcid":false,"given":"Luiz Gonzaga","family":"Paula de Almeida","sequence":"additional","affiliation":[{"name":"National Laboratory for Scientific Computing 1 , ,","place":["&gt;Brazil"]},{"name":"Bioinformatics Laboratory (LABINFO), Avenida Get\u00falio Vargas, 333, Quitandinha 25651-075, Petr\u00f3polis, Rio de Janeiro 1 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1894-3923","authenticated-orcid":false,"given":"Luciane Prioli","family":"Ciapina","sequence":"additional","affiliation":[{"name":"National Laboratory for Scientific Computing 1 , ,","place":["&gt;Brazil"]},{"name":"Bioinformatics Laboratory (LABINFO), Avenida Get\u00falio Vargas, 333, Quitandinha 25651-075, Petr\u00f3polis, Rio de Janeiro 1 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristiane Pinheiro","family":"Pestana","sequence":"additional","affiliation":[{"name":"Fiocruz, Bio-Manguinhos, Recombinant Technology Laboratory (LATER), Brazilian Ministry of Health 2 , ,","place":["&gt;Brazil"]},{"name":"Rio de Janeiro 2 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina Lessa","family":"Aquino","sequence":"additional","affiliation":[{"name":"Fiocruz, Bio-Manguinhos, Recombinant Technology Laboratory (LATER), Brazilian Ministry of Health 2 , ,","place":["&gt;Brazil"]},{"name":"Rio de Janeiro 2 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1584-7234","authenticated-orcid":false,"given":"Marco Alberto","family":"Medeiros","sequence":"additional","affiliation":[{"name":"Fiocruz, Bio-Manguinhos, Recombinant Technology Laboratory (LATER), Brazilian Ministry of Health 2 , ,","place":["&gt;Brazil"]},{"name":"Rio de Janeiro 2 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4632-2086","authenticated-orcid":false,"given":"Ana Tereza","family":"Ribeiro de Vasconcelos","sequence":"additional","affiliation":[{"name":"National Laboratory for Scientific Computing 1 , ,","place":["&gt;Brazil"]},{"name":"Bioinformatics Laboratory (LABINFO), Avenida Get\u00falio Vargas, 333, Quitandinha 25651-075, Petr\u00f3polis, Rio de Janeiro 1 , ,","place":["&gt;Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"175","published-online":{"date-parts":[[2021,6,11]]},"reference":[{"key":"2026010712171796900_RSFS20200063C1","first-page":"870","article-title":"Yellow fever vaccine","volume-title":"Vaccines","author":"Monath","year":"2012"},{"key":"2026010712171796900_RSFS20200063C2","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.jcv.2014.08.030","article-title":"Yellow fever","volume":"64","author":"Monath","year":"2015","journal-title":"J. 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