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。这两个群体的代表性都不足， SARS-CoV-2变异体的全基因组测序和蒙大拿州明显落后于 从SARS-CoV-2感染患者获得的测序数据中，鉴于 出现危险的SARS-CoV-2变异体，具有更高的病毒传播性和对 单克隆抗体治疗和疫苗效力，缺乏测序数据是一个关键问题， 蒙大拿州公共卫生和人类服务部（DPHHS）在安装一个适当的 应对疫情。此外，测序数据对于理解病毒 在部落民族中传播，这些部落民族受到大流行病的影响不成比例。这种补充剂 生物分子结构和动力学中心的COBRE赠款将允许全基因组测序， 分析了从蒙大拿州患者中分离的>3000株SARS-CoV-2病毒，包括生活在 农村和部落社区。一般测序结果将公开提供，部落除外 样本，除非部落批准，通过基因库和GISAID，以促进更广泛的分析， 关注变体（VOC）和感兴趣变体（VOI）在美国的出现， 直接与蒙大拿州DPHHS和参与部落民族沟通，以便他们能够调整他们的 应对大流行病。我们利用CLIA认证的SARS-CoV-2测试设施， 蒙大拿大学校园，我们在全基因组测序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SARS-CoV-2测序补充的目标。的 对这些数据的分析将侧重于三个具体目标： 具体目标1：蒙大拿州社区SARS-CoV-2变异体的遗传结构是什么 这种变异与区域、国家和全球SARS-CoV-2多样性相比如何？ 具体目标2：农村和农村地区之间传播的SARS-CoV-2变异体的遗传组成是否不同 蒙大拿州的大都市和部落与非部落社区的对比 特定目标3：特定疫情是否与已知或推定的新变异相关 或者担心？ 总的来说，该项目将为SARS-CoV-2的更危险变体如何产生提供关键的新见解， 在一个农村州和蒙大拿州的部落国家中传播， 更好地应对这些群体的流行病。

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.