Moreira Salles Ana Paula, de Seixas Santos Nastri Ana Catharina, Ho Yeh-Li, Vilas Boas Casadio Luciana, Emanuel Amgarten Deyvid, Justo Arévalo Santiago, Soares Gomes-Gouvea Michele, Jose Carrilho Flair, de Mello Malta Fernanda, Rebello Pinho João Renato
Department of Gastroenterology (LIM07), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
Clinical Laboratory of Hospital Israelita Albert Einstein, São Paulo, Brazil.
Front Microbiol. 2022 Apr 14;13:811318. doi: 10.3389/fmicb.2022.811318. eCollection 2022.
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 ( = 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.
2016 - 2019年期间，圣保罗最近爆发的黄热病（YF）是过去几十年中最严重的疫情之一，疫情蔓延到了疫苗接种覆盖率较低的地区。本研究的目的是评估2016 - 2019年圣保罗黄热病疫情期间黄热病毒（YFV）的遗传多样性，将现有的基因组数据与圣保罗大学医学院临床医院（HCFMUSP）患者的新基因组整合在一起。通过系统发育动力学分析，我们提出了新的IE亚分支的存在，描述了它们的序列特征，并确定了它们的位置和起源时间。对聚合酶链反应（PCR）检测YFV呈阳性的急性重症黄热病病例（n = 56）的血浆或尿液样本，使用12组引物进行病毒基因组扩增。随后，使用下一代测序（NGS）对39个扩增的基因组进行测序。将这39个序列与所有公开可用的完整基因组进行比对，以确定核苷酸/氨基酸替换情况，并进行系统发育和系统发育动力学分析。本研究中产生的所有YFV基因组均属于南美I基因型E亚组。在新产生的基因组中鉴定出21个非同义替换。我们分析了基因型IE的两个主要分支IE1和IE2，并根据它们的序列特征提出了亚分支的存在。此外，我们描述了这些亚分支的位置和起源时间。总体而言，我们的研究结果概述了2016 - 2019年疫情期间YFV的基因组特征和系统发育动力学，为未来的病毒学和流行病学研究提供了帮助。
