Host-microbe interactions and SARS-CoV-2 susceptibility and symptoms in a novel human challenge model

摘要 SARS-CoV-2是COVID-19的病原体，已报告超过6亿人 感染和全球650万人死亡。虽然一些抗病毒药物，单克隆抗体， 尽管免疫调节治疗改善了患者预后，但COVID-19的死亡率仍然高得令人无法接受。 此外，尽管采取了缓解措施并开发了几种高效疫苗，但SARS-CoV-2仍 这种病毒继续在全球蔓延，几乎可以肯定，它将成为人类的地方病。 因此，迫切需要确定改变SARS-CoV-2易感性和严重性的宿主因素， 指导感染预防策略，并为未来的疫苗和治疗开发研究提供信息。SARS- CoV-2人类挑战实验为研究这些宿主因素提供了前所未有的机会， 使病毒接种物、病毒暴露的精确时间和环境条件标准化，从而 控制那些不可避免地混淆自然感染研究的因素。本建议的总体目标是 确定上呼吸道微生物组特征和宿主基因表达谱， 和SARS-CoV-2感染的症状。这项研究将利用以前收集的临床数据， 来自在健康成人中进行的首次人体SARS-CoV-2攻击研究的样本， 既往感染或接种疫苗的证据。我们将进行鸟枪宏基因组和RNA测序的系列 从34名接种野生型病毒（SARS-CoV， 2/human/GBR/484861/2020），其中18例（53%）发生PCR证实的感染。在目标1中，我们将使用鼻音 在基线和病毒接种后立即（第-1天至第+3天）采集样本，以鉴定微生物组 与SARS-CoV-2感染抗性相关的特征和宿主转录反应。在目标2中， 将使用在第-1天和第+14天之间收集的鼻样本来表征上呼吸道的变化， 在SARS-CoV-2感染期间发生的微生物组和宿主转录组以及相关的微生物组和 转录组谱与SARS-CoV-2感染的特定症状的存在和严重程度。无论是 目的是，我们将使用创新的多组学分析，以确定患者特征，上 呼吸道微生物组-转录组谱和SARS-CoV-2易感性和症状。这项研究将 确定与SARS-CoV-2易感性和症状相关的上呼吸道细菌种类 感染，并可能导致开发合理设计的益生菌，防止SARS-CoV-2感染。 此外，对SARS后上呼吸道发生的宿主反应的详细了解- CoV-2暴露和感染可以为鼻疫苗的开发提供信息，并确定宿主的新靶点。 指导诊断或治疗。最后，整合微生物组和宿主转录组数据的分析将 阐明上呼吸道微生物群和宿主免疫系统相互作用的机制， 对SARS-CoV-2和其他呼吸道病毒引起的感染的敏感性和严重程度。

ABSTRACT SARS-CoV-2, the etiological agent of COVID-19, has been responsible for more than 600 million reported infections and 6.5 million deaths globally. Although several antivirals, monoclonal antibodies, and immunomodulatory treatments improve patient outcomes, mortality from COVID-19 remains unacceptably high. Moreover, despite mitigation measures and development of several highly effective vaccines, SARS-CoV-2 has continued to spread globally, making it almost certain that the virus will become endemic in human populations. There is therefore a critical need to identify host factors that modify SARS-CoV-2 susceptibility and severity to guide infection prevention strategies and inform future vaccine and therapeutic development studies. SARS- CoV-2 human challenge experiments provide an unprecedented opportunity to study these host factors by standardizing the viral inoculum, the precise timing of viral exposure, and environmental conditions, thereby controlling for factors that inevitably confound natural infection studies. The overall objective of this proposal is to identify upper respiratory microbiome features and host gene expression profiles that modify susceptibility to and symptoms of SARS-CoV-2 infection. This research will leverage previously collected clinical data and samples from a first-in-human SARS-CoV-2 challenge study conducted in healthy adults without serological evidence of prior infection or vaccination. We will perform shotgun metagenomic and RNA sequencing of serially collected mid-turbinate nasal samples from 34 adults who were inoculated with a wild-type virus (SARS-CoV- 2/human/GBR/484861/2020), 18 (53%) of whom developed PCR-confirmed infection. In Aim 1, we will use nasal samples collected at baseline and immediately following viral inoculation (days -1 to +3) to identify microbiome features and host transcriptional responses associated with resistance to SARS-CoV-2 infection. In Aim 2, we will use nasal samples collected between days -1 and +14 to characterize changes in the upper respiratory microbiome and host transcriptome that occur during SARS-CoV-2 infection and correlate microbiome and transcriptome profiles with the presence and severity of specific symptoms of SARS-CoV-2 infection. In both Aims, we will use innovative multi-omics analyses to identify relationships between patient characteristics, upper respiratory microbiome-transcriptome profiles, and SARS-CoV-2 susceptibility and symptoms. This research will identify upper respiratory bacterial species associated with susceptibility to and symptoms of SARS-CoV-2 infection and could lead to development of rationally designed probiotics that prevent SARS-CoV-2 infection. Further, a detailed understanding of the host responses that occur in the upper respiratory tract following SARS- CoV-2 exposure and infection could inform development of nasal vaccines and identify novel targets for host- directed diagnostics or therapeutics. Finally, analyses integrating microbiome and host transcriptome data will elucidate mechanisms by which the upper respiratory microbiota and host immune system interact to influence susceptibility to and severity of infections caused by SARS-CoV-2 and other respiratory viruses.