ITCA ASU-Sequencing of Tribal Wastewater to Assess Coronavirus Variants

ITCA ASU 对部落废水进行测序以评估冠状病毒变异体

• 批准号: 10381408
• 负责人: Maria Dadgar
• 金额: $ 9.44万
• 依托单位: INTER TRIBAL COUNCIL OF ARIZONA, INC.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-14 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10381408
• 关键词: 2019-nCoV; Administrator; Agreement; American Indians; Amino Acids; Area; Arizona; Award; Brazil; COVID testing; COVID-19 pandemic; California; Cessation of life; Clinical; Collaborations; Communities; Complementary DNA; Coronavirus; Data; Early Diagnosis; Engineering; Faculty; Future; General Population; Genes; Genetic Polymorphism; Genome; Genotype; Goals; Health; Hour; Individual; Infrastructure; Lead; Maps; Mentorship; Methodology; Mission; Modeling; Mutagenesis; Mutation; Native American Research Center for Health; Nucleotides; Ownership; Population; Process; Protein Region; Proteins; RNA; Race; Reporting; Research; Research Infrastructure; SARS-CoV-2 genome; SARS-CoV-2 variant; Sampling; South African; Teacher Professional Development; Testing; Time; Training; Translating; Translations; Tribes; Universities; Update; Variant; Work; caucasian American; clinical sequencing; coronavirus disease; data dissemination; epidemiology study; experience; in silico; interest; intertribal; meetings; member; mortality; mutant; novel; pandemic disease; recruit; response; trend; tribal Nation; tribal community; tribal health; vaccine distribution; viral RNA; wastewater epidemiology; wastewater samples; wastewater surveillance

PROJECT SUMMARY The COVID pandemic has been particularly detrimental for Tribal communities across the U.S., who have experienced mortality rates greater than any other race: American Indians have 256 deaths per 100,000 people compared to 150/100,000 for white Americans. Several factors have been suggested as contributors to elevated infectivity, including inadequate infrastructure and underlying health conditions. An additional consideration is the presence of SARS-CoV-2 variants within Tribal communities, of which little is known as COVID testing and vaccine distribution have been the priorities of Tribal Health Departments and COVID Response Teams. To determine if variants are present in Tribal communities, we propose to assess wastewater for excreted coronavirus variants, a non-invasive approach that will capture community-wide mutations more efficiently than sequencing clinical samples. Untreated wastewater samples (24-hour composites) will be processed and quantified for coronavirus using RT-qPCR for the E-gene of SARS-CoV-2. After confirmation of the presence of coronavirus, extracted RNA will be converted to cDNA and sequenced with primers that cover the entire 30kb genome. While we are particularly interested in the U.K., South African, and Brazil strains, we will also report if other U.S. and novel variants are detected in the selected Tribal communities. Nucleotide mutations will be translated and modelled in silico to determine if the polymorphism(s) result in amino acid mutagenesis and/or are mapped to key protein regions. Results will be returned to Tribal health administrators to determine if additional testing of clinical biospecimens is necessary. This NARCH project will provide critical and timely pandemic information to sensitive populations through scientific translation and collaboration with Tribal communities.

项目概要 新冠疫情大流行对美国各地的部落社区尤其不利，他们 死亡率高于任何其他种族：美洲印第安人每年有 256 人死亡 100,000 人，而美国白人则为 150/100,000。提出了几个因素 导致传染性上升的因素，包括基础设施不足和潜在的健康状况 状况。另一个考虑因素是部落中是否存在 SARS-CoV-2 变种 社区，但鲜为人知的是，新冠病毒检测和疫苗分发一直是社区的首要任务 部落卫生部门和新冠疫情应对小组。确定是否存在变体 部落社区，我们建议评估废水中排泄的冠状病毒变种，这是一种非侵入性的 比对临床样本进行测序更有效地捕获社区范围内的突变的方法。 未经处理的废水样本（24 小时复合样本）将被处理并量化冠状病毒 使用 RT-qPCR 检测 SARS-CoV-2 的 E 基因。在确认存在冠状病毒后， 提取的 RNA 将转化为 cDNA，并使用覆盖整个 30kb 的引物进行测序 基因组。虽然我们对英国、南非和巴西菌株特别感兴趣，但我们也会 报告是否在选定的部落社区中检测到其他美国变种和新变种。核苷酸 突变将被翻译并在计算机中建模，以确定多态性是否导致氨基 酸诱变和/或定位到关键蛋白质区域。结果将返回至 Tribal health 管理员确定是否有必要对临床生物样本进行额外测试。这个NARCH 项目将通过科学的方式向敏感人群提供关键和及时的流行病信​​息 翻译以及与部落社区的合作。