Assessing the Risk of SARS-CoV-2 Remdesivir Resistance

评估 SARS-CoV-2 瑞德西韦耐药性风险

基本信息

批准号：
10442701
负责人：
Judd F Hultquist
金额：
$ 20万
依托单位：
NORTHWESTERN UNIVERSITY AT CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-01 至 2023-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10442701
关键词：
2019-nCoV Active Sites Animal Model Antiviral Agents Antiviral Therapy Antiviral resistance Binding Binding Sites Biochemical Biological Assay COVID-19 COVID-19 monitoring COVID-19 pandemic COVID-19 patient COVID-19 treatment Cell Culture Techniques Cells Cessation of life Clinic Clinical Collection Complement Coronavirus Data Dexamethasone Disease Dyspnea Ebola virus Emergency Situation Enrollment Evolution FDA Emergency Use Authorization Funding General Population Genetic Variation Goals Grant Haplotypes Hospitalization Hospitals In Vitro Infection Lead Measures Mediating Medical Records Middle East Respiratory Syndrome Coronavirus Monitor Monoclonal Antibodies Mutation Nature Nucleotides Oligonucleotides Outcome Patients Persons Pneumonia Polymerase Population Population Dynamics Probability Prodrugs RNA Viruses RNA-Directed RNA Polymerase Recording of previous events Recovery Reporting Research Personnel Resistance Respiratory distress Risk SARS coronavirus Sampling Seeds Series Specimen Symptoms Testing Therapeutic Time Variant Viral Viral Load result Virus Work biobank deep sequencing design genome sequencing global health in silico mimicry molecular sequence database mutant nasal swab nasopharyngeal swab nucleotide analog online repository pandemic disease pathogen patient population pressure remdesivir research clinical testing resistance mutation respiratory pathogen response severe COVID-19 therapeutic evaluation treatment comparison treatment strategy viral RNA viral resistance virology whole genome

项目摘要

PROJECT SUMMARY The rapid spread of the SARS-CoV-2 pandemic around the globe has led to an urgent and ongoing evaluation of therapeutic strategies for the treatment of Coronavirus Disease 2019 (COVID-19). While a handful of host- directed therapies are being used for the treatment of severe disease, including monoclonal antibodies and dexamethasone, there is only one antiviral with emergency use authorization, the nucleotide analog remdesivir (GS-5734). Remdesivir is thought to inhibit the viral RNA-dependent RNA polymerase, Nsp12, through nucleotide mimicry and early chain termination. As use of remdesivir for the treatment of COVID-19 escalates, it is essential to understand the nature and risk of developing antiviral resistance. We hypothesize that intra-host variation in Nsp12 could allow for the evolution of remdesivir resistance. In this exploratory grant, we propose to test this hypothesis by quantifying the SARS-CoV-2 viral diversity that arises in hospitalized patients over time with and without remdesivir treatment (Aim 1), and by determining the impact of known Nsp12 mutations on polymerase activity and sensitivity to remdesivir (Aim 2). In Aim 1, we will leverage a biobank of longitudinally collected nasopharyngeal swabs from hospitalized COVID-19 patients at Northwestern Memorial Hospital. Specimens were collected every 4 days after enrollment for up to one month, including specimens from 8 patients given remdesivir. We are continuing to collect specimens and intend to enroll an additional 50 COVID-19 patients over the coming months. Deep, whole genome sequencing of SARS-CoV-2 viruses from each specimen will be performed to classify the viral variants detected within each patient over time. The nature and extent of variation will be compared by time point, viral load, and treatment course as determined from medical record data. These studies will be complemented with deep sequencing of viruses produced ex vivo in the presence of varying concentrations of remdesivir. Overall, this work will determine the nature and extent of SARS-CoV-2 intra-host variation that develops in hospitalized patients and will determine the impact of remdesivir treatment on that variation. In Aim 2, in vitro oligonucleotide extension assays will be used to assess the impact of previously described Nsp12 mutations on polymerase activity and remdesivir efficacy. Documented mutations near the remdesivir binding pocket and Nsp12 active site, newly documented haplotypes arising in our patient population, and Nsp12 mutants found to be under selective pressure will be assessed first for polymerase activity followed by remdesivir sensitivity. The phylodynamic histories of impactful mutations and haplotypes will be followed to look for evidence of selection in the population. Together, these results will assess the risk of emergent remdesivir resistance and additionally identify potential resistance mutations for active monitoring.

项目概要 SARS-CoV-2 大流行在全球范围内迅速蔓延，导致需要进行紧急且持续的评估 2019 年冠状病毒病 (COVID-19) 的治疗策略。虽然少数主机- 定向疗法被用于治疗严重疾病，包括单克隆抗体和地塞米松，只有一种具有紧急使用授权的抗病毒药物，即核苷酸类似物瑞德西韦（GS-5734）。瑞德西韦被认为通过抑制病毒 RNA 依赖性 RNA 聚合酶 Nsp12 核苷酸模拟和早期链终止。随着瑞德西韦治疗 COVID-19 的使用不断升级，对于了解产生抗病毒耐药性的性质和风险至关重要。我们假设主机内 Nsp12 的变异可能导致瑞德西韦耐药性的进化。在这项探索性拨款中，我们建议通过量化住院患者随时间推移出现的 SARS-CoV-2 病毒多样性来检验这一假设使用和不使用瑞德西韦治疗（目标 1），并通过确定已知 Nsp12 突变对聚合酶活性和对瑞德西韦的敏感性（目标 2）。在目标 1 中，我们将利用纵向生物库从西北纪念医院住院的 COVID-19 患者身上收集了鼻咽拭子。入组后每 4 天采集一次标本，持续长达 1 个月，其中包括 8 名患者的标本给予瑞德西韦。我们正在继续收集样本，并打算招募另外 50 名 COVID-19 患者在接下来的几个月里。对每个样本中的 SARS-CoV-2 病毒进行深度全基因组测序随着时间的推移，对每位患者体内检测到的病毒变异进行分类。变异的性质和程度将根据病历数据确定的时间点、病毒载量和治疗过程进行比较。这些研究将通过对在不同环境下产生的离体病毒进行深度测序来补充。瑞德西韦的浓度。总体而言，这项工作将确定 SARS-CoV-2 宿主内的性质和程度住院患者中发生的变异将决定瑞德西韦治疗对其的影响变化。在目标 2 中，将使用体外寡核苷酸延伸测定来评估先前的影响描述了 Nsp12 突变对聚合酶活性和瑞德西韦疗效的影响。记录在案的突变附近瑞德西韦结合袋和 Nsp12 活性位点，我们患者群体中出现的新记录的单倍型，发现处于选择压力下的 Nsp12 突变体将首先评估聚合酶活性，然后评估通过瑞德西韦敏感性。将跟踪有影响的突变和单倍型的系统动力学历史寻找人群中选择的证据。这些结果将共同评估紧急情况的风险瑞德西韦耐药性，并另外识别潜在的耐药突变以进行主动监测。

项目成果

期刊论文数量（3）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Has Omicron Changed the Evolution of the Pandemic?

Omicron 改变了疫情的演变吗？

DOI：
发表时间：
2022-01-31
期刊：
影响因子：
0
作者：
Lundberg, Alexander L;Lorenzo;Ozer, Egon A;Hawkins, Claudia A;Hultquist, Judd F;Welch, Sarah B;Prasad, P V Vara;Oehmke, James F;Achenbach, Chad J;Murphy, Robert L;White, Janine I;Havey, Robert J;Post, Lori Ann
通讯作者：
Post, Lori Ann

Overlapping Delta and Omicron Outbreaks During the COVID-19 Pandemic: Dynamic Panel Data Estimates.

COVID-19 大流行期间 Delta 和 Omicron 疫情重叠：动态面板数据估计。

DOI：
发表时间：
2022-06-03
期刊：
影响因子：
0
作者：
Lundberg, Alexander L;Lorenzo;Hultquist, Judd F;Hawkins, Claudia A;Ozer, Egon A;Welch, Sarah B;Prasad, P V Vara;Achenbach, Chad J;White, Janine I;Oehmke, James F;Murphy, Robert L;Havey, Robert J;Post, Lori A
通讯作者：
Post, Lori A

Covid-19: is omicron less lethal than delta?

Covid-19：omicron 的致命性比 Delta 低吗？