Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec.
Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec.
复制标题
魁北克省一家综合成人医院爆发 SARS-CoV-2 的基因组流行病学和相关临床结果。
DOI：
10.1101/2021.05.29.21257760
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Smith,MartinA
中科院分区：
文献类型：
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作者：
Paré,Bastien;Rozendaal,Marieke;Morin,Sacha;Poujol,Raphaël;Mostefai,Fatima;Grenier,Jean-Christophe;Kaufmann,Léa;Xing,Henry;Sanchez,Miguelle;Yechouron,Ariane;Racette,Ronald;Hussin,Julie;Wolf,Guy;Pavlov,Ivan;Smith,MartinA
加拿大魁北克省首例确诊的 COVID-19 病例于 2020 年 2 月 25 日在凡尔登医院出现。一个月后，该医院出现局部疫情暴发。我们对 2020 年 3 月 31 日至 4 月 17 日期间在两家当地医院的所有 SARS-CoV-2 阳性样本的鼻咽拭子进行了平铺扩增子全基因组纳米孔测序，以评估此次疫情的病毒多样性。我们报告了来自 242 名个体（包括工作人员和患者）的 264 个病毒基因组，以及相关的临床特征和结果，以及纵向样本、技术复制和魁北克省首次公开传播的 SARS-CoV-2 基因组。病毒谱系评估确定了两家医院的多个分支，其中凡尔登疫情中的一个主要分支，表明存在医院获得性传播。降维确定了两个逃避监督谱系分配方法的分支，包括穿山甲，并确定了与良好的患者预后显着相关的某些症状（头痛、肌痛和喉咙痛）。我们还解决了标准 SARS-CoV-2 生物信息学程序的某些局限性，特别是在呈现多种病毒单倍型时。
The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess the viral diversity of the outbreak. We report 264 viral genomes from 242 individuals (both staff and patients) with associated clinical features and outcomes, as well as longitudinal samples, technical replicates and the first publicly disseminated SARS-CoV-2 genomes in Quebec. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades that evaded supervised lineage assignment methods, including Pangolin, and identified certain symptoms (headache, myalgia and sore throat) that are significantly associated with favorable patient outcomes. We also address certain limitations of standard SARS-CoV-2 bioinformatics procedures, notably when presented with multiple viral haplotypes.