The live attenuated yellow fever (YF) vaccine was developed in the 1930s. 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–Fiocruz, 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.

减毒黄热病 (YF) 活疫苗是在 1930 年代开发的。目前，17D和17DD减毒亚株​​用于疫苗生产。17D 毒株被多个国家用于疫苗生产，而 17DD 毒株仅在巴西使用。通过疫苗生产的种子批系统进行的细胞传代通过增加减毒或毒力影响准种的存在，从而导致减毒基因型的稳定性和免疫原性发生变化。使用下一代测序，我们在巴西 YF 疫苗的疫苗批次之间进行了基因组表征和遗传多样性分析，该疫苗由 BioManguinhos-Fiocruz 生产，并在巴西接种了 11 年。我们展示了来自巴西 17DD 疫苗株的 20 个组装和注释的基因组，8 个单核苷酸多态性和 17DD 疫苗的准种谱重建，通过这里介绍的管道。V2IDA 管道提供了通过种子批次系统维持的低遗传多样性与确认巴西黄热病疫苗批次的遗传稳定性之间的关系。我们的研究开创了使用 V2IDA 进行遗传多样性分析和减毒病毒疫苗的计算机稳定性研究，促进疫苗生产过程中的基因监测。