Data_Sheet_1_Updating the Phylodynamics of Yellow Fever Virus 2016–2019 Brazilian Outbreak With New 2018 and 2019 São Paulo Genomes.docx

The recent outbreak of yellow fever (YF) in São Paulo during 2016–2019 has been one of the most severe in the last decades, spreading to areas with low vaccine coverage. The aim of this study was to assess the genetic diversity of the yellow fever virus (YFV) from São Paulo 2016–2019 outbreak, integrating the available genomic data with new genomes from patients from the Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP). Using phylodynamics, we proposed the existence of new IE subclades, described their sequence signatures, and determined their locations and time of origin. Plasma or urine samples from acute severe YF cases (n = 56) with polymerase chain reaction (PCR) positive to YFV were submitted to viral genome amplification using 12 sets of primers. Thirty-nine amplified genomes were subsequently sequenced using next-generation sequencing (NGS). These 39 sequences, together with all the complete genomes publicly available, were aligned and used to determine nucleotide/amino acids substitutions and perform phylogenetic and phylodynamic analysis. All YFV genomes generated in this study belonged to the genotype South American I subgroup E. Twenty-one non-synonymous substitutions were identified among the new generated genomes. We analyzed two major clades of the genotypes IE, IE1, and IE2 and proposed the existence of subclades based on their sequence signatures. Also, we described the location and time of origin of these subclades. Overall, our findings provide an overview of YFV genomic characterization and phylodynamics of the 2016–2019 outbreak contributing to future virological and epidemiological studies.

近期，2016-2019年间圣保罗地区黄热病的爆发，堪称数十年来最为严重的一次，病毒蔓延至疫苗接种率较低的地区。本研究旨在评估2016-2019年圣保罗地区黄热病毒（YFV）的遗传多样性，通过整合现有基因组数据与来自圣保罗大学医学院附属医院（HCFMUSP）患者的全新基因组数据。运用系统发育动力学方法，我们提出了新的IE亚系分支的存在，描述了其序列特征，并确定了其起源地及时间。对56例急性重症黄热病患者的血浆或尿液样本（PCR检测YFV阳性）进行了病毒基因组扩增，使用12套引物。随后，对扩增得到的39个基因组进行下一代测序（NGS）。这39个序列与所有公开可用的完整基因组进行比对，用于确定核苷酸/氨基酸替换，并执行系统发育和系统发育动力学分析。本研究中生成的所有YFV基因组均属于南美I亚群E基因型。在新生成的基因组中，共发现了21个非同义替换。我们对IE、IE1和IE2三个基因型的两个主要分支进行了分析，并根据其序列特征提出了亚系分支的存在。同时，我们也描述了这些亚系分支的地理位置及起源时间。总体而言，我们的研究为2016-2019年黄热病毒基因组特征及系统发育动力学提供了概览，为未来的病毒学和流行病学研究提供了重要参考。