Data_Sheet_2_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.

近年来，2016至2019年间圣保罗市黄热病（YF）的爆发成为近几十年来最为严重的疫情之一，疫情蔓延至疫苗接种覆盖率较低的地区。本研究旨在评估2016至2019年圣保罗市黄热病爆发中黄热病毒（YFV）的遗传多样性，通过整合可用的基因组数据与来自圣保罗大学医学院附属医院（HCFMUSP）的患者新基因组数据进行综合分析。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，描述了它们的序列特征，并确定了它们的起源地和出现时间。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组引物。随后，对扩增的39个基因组进行了下一代测序（NGS）。这39个序列与所有公开可用的完整基因组一起进行比对，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亚组E。在新生成的基因组中，识别出21个非同义替换。我们对IE、IE1和IE2基因型的两个主要分支进行了分析，并根据它们的序列特征提出了亚系分支的存在。此外，我们还描述了这些亚系的起源地和出现时间。总体而言，我们的研究为2016至2019年黄热病毒基因组特征和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做出了贡献。