ITCA ASU-Sequencing of Tribal Wastewater to Assess Coronavirus Variants

项目摘要 新冠疫情对美国各地的部落社区尤其不利，谁 美国印第安人的死亡率比其他任何种族都高：美国印第安人每年有256人死亡， 10万人，而白色美国人为150/10万。已经提出了几个因素 导致传染性升高，包括基础设施不足和基础健康状况不佳 条件另一个考虑因素是部落中存在SARS-CoV-2变体。 社区，其中鲜为人知的是新冠病毒检测和疫苗分发一直是优先事项 部落卫生部门和新冠疫情应对小组的成员。为了确定是否存在变异， 部落社区，我们建议评估废水中排泄的冠状病毒变体，这是一种非侵入性的 这种方法将比测序临床样本更有效地捕获社区范围的突变。 未经处理的废水样本（24小时复合物）将被处理和量化的冠状病毒 用RT-qPCR方法检测SARS冠状病毒2型E基因。在确认存在冠状病毒后， 将提取的RNA转化为cDNA，并使用覆盖整个30 kb的引物进行测序 基因组虽然我们对英国特别感兴趣，南非和巴西的菌株，我们也将 报告是否在选定的部落社区中检测到其他美国和新型变体。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突变。 酸诱变和/或定位于关键蛋白质区域。结果将返回给部落卫生部 管理员确定是否需要对临床生物标本进行额外检测。这个仙女 该项目将通过科学方法向敏感人群提供关键和及时的大流行病信息， 翻译和与部落社区的合作。

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.