Fast surveillance response reveals the introduction of a new yellow fever virus sub-lineage in 2021, in Minas Gerais, Brazil

BACKGROUND In Brazil, the yellow fever virus (YFV) is maintained in a sylvatic cycle involving wild mosquitoes and non-human primates (NHPs). The virus is endemic to the Amazon region; however, waves of epidemic expansion reaching other Brazilian states sporadically occur, eventually causing spillovers to humans. OBJECTIVES To report a surveillance effort that led to the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021. METHODS A surveillance network was created, encompassing the technology of smartphone applications and coordinated actions of several research institutions and health services to monitor and investigate NHP epizootics. FINDINGS When alerts were spread through the network, samples from NHPs were collected and YFV infection confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and genome sequencing at an interval of only 10 days. Near-complete genomes were generated using the Nanopore MinION sequencer. Phylogenetic analysis indicated that viral genomes were related to the South American genotype I, clustering with a genome detected in the Amazon region (state of Pará) in 2017, named YFVPA/MG sub-lineage. Fast YFV confirmation potentialised vaccination campaigns. MAIN CONCLUSIONS A new YFV introduction was detected in MG 6 years after the beginning of the major outbreak reported in the state (2015-2018). The YFV strain was not related to the sub-lineages previously reported in MG. No human cases have been reported, suggesting the importance of coordinated surveillance of NHPs using available technologies and supporting laboratories to ensure a quick response and implementation of contingency measures to avoid YFV spillover to humans.背景 在巴西，黄热病毒（yellow fever virus, YFV）维持着涉及野生蚊虫与非人类灵长类（non-human primates, NHPs）的丛林循环。该病毒在亚马逊地区呈地方性流行；但疫情扩散浪潮会间歇性波及巴西其他州，最终引发病毒向人类的跨物种传播。 研究目的 报告一项监测工作，该工作首次证实2021年巴西东南部米纳斯吉拉斯州（Minas Gerais, MG）的非人类灵长类感染了黄热病毒。 研究方法 构建了一套监测网络，整合智能手机应用技术，并协调多所研究机构与卫生服务机构的行动，以监测和调查非人类灵长类的兽疫疫情。 研究结果 当监测网络发出警报后，研究人员采集了非人类灵长类样本，并仅用10天时间就通过逆转录定量聚合酶链反应（reverse transcription-quantitative polymerase chain reaction, RT-qPCR）与基因组测序证实了黄热病毒感染。借助纳米孔MinION测序仪（Nanopore MinION sequencer）完成了近乎完整的病毒基因组测序。系统发育分析显示，该病毒基因组与南美I基因型相关，并与2017年在亚马逊地区帕拉州（Pará）检测到的基因组聚类，该支系被命名为YFVPA/MG亚支系。快速的黄热病毒检测能力为疫苗接种行动提供了助力。 主要结论 在该州报告的大规模暴发（2015-2018年）发生6年后，研究人员在米纳斯吉拉斯州检测到了新的黄热病毒输入事件。此次的黄热病毒毒株与此前在该州报告的亚支系均无关联。目前尚无人类感染病例的报告，这表明利用现有技术对非人类灵长类开展协同监测，并为相关实验室提供支持以确保快速响应、落实应急措施，对避免黄热病毒跨物种传播至人类具有重要意义。