Surveillance genome sequencing to detect SARS-CoV-2 virus variants in Montana

项目摘要 蒙大拿州是一个拥有大量农村和部落人口的州。这两个群体在 SARS-CoV-2变异株和蒙大拿州的全基因组测序明显落后于 在从感染SARS-CoV-2的患者获得的测序数据中，中国是一个整体。给定 出现危险的SARS-CoV-2变异株，具有更高的病毒传播率和对 在单抗治疗和疫苗疗效方面，缺乏测序数据是一个关键问题 蒙大拿州公共卫生和公共服务部(DPHHS)在制定适当的 应对大流行。此外，测序数据对于理解病毒尤为重要 在部落国家的传播，这些国家受到大流行的不成比例的影响。本副刊 对生物分子结构和动力学中心的资助将允许全基因组测序和 从蒙大拿州患者中分离的&gt；3000 SARS-CoV-2病毒分析 农村和部落社区。一般测序结果将公之于众，部落除外 除非得到部落批准，否则通过GenBank和GISAID提供样本，以促进对 在美国出现了关注的变体(VOC)和感兴趣的变体(VOI)，并将 直接与蒙大拿州国土安全部和参与部落国家沟通，以便他们可以调整他们的 应对大流行。我们利用CLIA认证的SARS-CoV-2检测设施在 蒙大拿大学校区，我们在全基因组测序方面的专业知识和我们建立的关系 与蒙大拿州的部落国家合作，以实现这一SARS-CoV-2测序补充方案的目标。这个 对这些数据的分析将侧重于三个具体目标： 特定目标1：蒙大拿州社区中SARS-CoV-2变异株的遗传结构是什么 这种变异与地区、国家和全球SARS-CoV-2的多样性相比如何？ 特定目标2：农村和农村之间流行的SARS-CoV-2变异株的基因组成是否有所不同 蒙大拿州的大都市和部落社区还是非部落社区？ 特定目标3：特定的疫情是否与已知的或假定的新的感兴趣的变种有关 和/或担忧？ 总体而言，该项目将提供关键的新见解，了解更危险的SARS-CoV-2变异是如何产生的，以及 在一个农村州和蒙大拿州受不成比例影响的部落国家中传播，这将允许 为这些群体更好地应对大流行。

Project Summary Montana is a state with large rural and Tribal Nations populations. Both groups have been underrepresented in whole genome sequencing of SARS-CoV-2 variants and the state of Montana lags significantly behind the country as a whole in sequencing data available from patients infected with SARS-CoV-2. Given the emergence of dangerous SARS-CoV-2 variants with higher viral transmissibility and reduced response to monoclonal antibody therapy and vaccine efficacy, lack of sequencing data is a critical problem for the Montana state Department of Public Health and Human Services (DPHHS) in mounting an appropriate response to the pandemic. Furthermore, sequencing data will be particularly important for understanding viral transmission in Tribal Nations, which have been disproportionately affected by the pandemic. This supplement to the Center for Biomolecular Structure and Dynamics COBRE grant will allow whole genome sequencing and analysis of >3000 SARS-CoV-2 viruses isolated from patients in the state of Montana, including those living in rural and Tribal communities. General sequencing results will be made publicly available, except Tribal samples unless Tribal approval is given, through GenBank and GISAID to facilitate broader analysis of the emergence of variants of concern (VOC) and variants of interest (VOI) in the United States and will be communicated directly to the Montana DPHHS and participating Tribal Nations so that they can adjust their responses to the pandemic. We take advantage of the CLIA-certified SARS-CoV-2 testing facility on the University of Montana campus, our expertise in whole genome sequencing and our established relationships with Tribal Nations in Montana to accomplish the goals of this SARS-CoV-2 sequencing supplement. The analysis of these data will focus on three specific aims:  Specific Aim 1: What is the genetic structure of SARS-CoV-2 variants across Montana communities and how does this variation compare to regional, national, and global SARS-CoV-2 diversity?  Specific Aim 2: Does the genetic composition of circulating SARS-CoV-2 variants differ between rural versus metropolitan and Tribal versus non-Tribal communities in Montana?  Specific Aim 3: Are specific outbreaks associated with known or putative novel variants of interest and/or concern? Overall, the project will provide critical new insight into how more dangerous variants of SARS-CoV-2 arise and spread in a rural state and among the disproportionately-effected Tribal Nations in Montana that will allow for better response to the pandemic for these groups.