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
基本信息
- 批准号:10381408
- 负责人:
- 金额:$ 9.44万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 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:
- 关键词:2019-nCoVAdministratorAgreementAmerican IndiansAmino AcidsAreaArizonaAwardBrazilCOVID testingCOVID-19 pandemicCaliforniaCessation of lifeClinicalCollaborationsCommunitiesComplementary DNACoronavirusDataEarly DiagnosisEngineeringFacultyFutureGeneral PopulationGenesGenetic PolymorphismGenomeGenotypeGoalsHealthHourIndividualInfrastructureLeadMapsMentorshipMethodologyMissionModelingMutagenesisMutationNative American Research Center for HealthNucleotidesOwnershipPopulationProcessProtein RegionProteinsRNARaceReportingResearchResearch InfrastructureSARS-CoV-2 genomeSARS-CoV-2 variantSamplingSouth AfricanTeacher Professional DevelopmentTestingTimeTrainingTranslatingTranslationsTribesUniversitiesUpdateVariantWorkcaucasian Americanclinical sequencingcoronavirus diseasedata disseminationepidemiology studyexperiencein silicointerestintertribalmeetingsmembermortalitymutantnovelpandemic diseaserecruitresponsetrendtribal Nationtribal communitytribal healthvaccine distributionviral RNAwastewater epidemiologywastewater sampleswastewater surveillance
项目摘要
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。
项目成果
期刊论文数量(1)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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