Surveillance of SARS-CoV-2 in Alaska

项目摘要：到目前为止(3/23/21)，阿拉斯加已经有超过58,000例新冠-19病例， 1318人住院，306人死亡。阿拉斯加是指定的初级保健健康 专业人才短缺地区。可能是由健康差距推动的，新冠肺炎的死亡率 在美国印第安人/阿拉斯加原住民(AI/AN)中，阿拉斯加居民的比例几乎高出两倍 超过整个阿拉斯加的人口(每10万人中有71人对47人；阿拉斯加DHSS Bull。1/29/21)，a 在全国人工智能/AN人口中观察到的模式(CDC MMWR 12/11/20)。即使有了这些 挑战，阿拉斯加是总体上新冠肺炎住院率和死亡率最低的州之一， 也是新冠肺炎疫苗接种率最高的国家之一。 SARS-CoV-2基因组测序已成为分析传播的关键技术 SARS-CoV-2谱系，包括检测可能导致更快传播的VOC，更多 严重疾病，或降低疫苗效力。重要的是，通过联合国的早期能力建设 阿拉斯加DHSS公共卫生实验室(PHL)，与阿拉斯加和阿拉斯加大学合作 INBRE，已对500多个SARS-CoV-2基因组进行了测序并发布(GISAID)， 包括最近的B.1.1.7、B.1.429和P.1变种(VOC)病例。因此，它是 了解SARS-CoV-2在中国的地理和时间传播很重要 国家，特别是在人工智能/人工智能人口中。 作为对NIGMS nosi的回应，阿拉斯加INBRE(IDEA)计划建议延长 阿拉斯加SARS-CoV-2谱系和变异的基因组监测，与一个大学团队 阿拉斯加研究人员(在UA-费尔班克斯和UA-Anclage)与 中南部基金会(SCF)和阿拉斯加土著医疗中心(ANMC)AI/AN Health 网络，以及包括阿拉斯加DHSS PHL和CDC北极在内的其他合作伙伴的支持 调查。该项目的目标是(1)VOC和VOI的预期基因组测序 阿拉斯加及其与其他地区的比较；(2)阿拉斯加VOC/VOI的前瞻性基因组测序 AI/AN卫生网络，以了解新冠肺炎差异；以及(3)地理和时间 对阿拉斯加SARS-CoV-2病毒的分析，以了解流行病学。我们将利用 短读(Illumina)和长读(纳米孔)测序平台，以及生物信息学 阿拉斯加INBRE建立的专业知识，用于分析SARS-CoV-2基因组，样本由 阿拉斯加DHSS/PHL，特别是在AI/AN(SCF和ANMC服务)人群中。数据将是 发布用于荟萃分析，以提供基因组学角度来追踪疫情，了解 新血统的传播，以及健康差距的影响。

Project Summary: To date (3/23/21), Alaska has suffered over 58,000 cases of COVID-19, 1,318 hospitalizations, and 306 deaths. Alaska is a designated Primary Care Health Professional Shortage Area. Likely driven by health disparities, the COVID-19 fatality rate among American Indian/Alaska Native (AI/AN) residents of Alaska is nearly two times higher than the population of Alaska as a whole (71 v. 47 per 100,000; Alaska DHSS Bull. 1/29/21), a pattern observed in AI/AN population nationwide (CDC MMWR 12/11/20). Even with these challenges, Alaska has one of the lowest COVID-19 hospitalization and fatality rates overall, and one of the highest rates of COVID-19 vaccination. Sequencing of SARS-CoV-2 genomes has emerged as the key technology for analyzing spread of SARS-CoV-2 lineages, including detection of VOC that may cause more rapid spread, more severe disease, or reduce vaccine efficacy. Importantly, through early capacity-building by the Alaska DHSS Public Health Lab (PHL), in partnership with the University of Alaska and Alaska INBRE, over 500 SARS-CoV-2 genomes have been sequenced and released (GISAID), including recent cases of B.1.1.7, B.1.429, and P.1 variants of concern (VOC). Thus, it is important to understand the geographical and temporal spread of SARS-CoV-2 lineages in the state, and specifically in the AI/AN population. In response to this NIGMS NOSI, the Alaska INBRE (IDeA) program is proposing to extend the genomic surveillance for SARS-CoV-2 lineages and variants in Alaska, with a team of University of Alaska researchers (at UA-Fairbanks and UA-Anchorage), in collaboration with the Southcentral Foundation (SCF) and Alaska Native Medical Center (ANMC) AI/AN health networks, and support from other partners including the Alaska DHSS PHL and CDC Arctic Investigations. The project goals are (1) Prospective genomic sequencing of VOC and VOI in Alaska and comparison to other regions; (2) Prospective genomic sequencing of VOC/VOI in AI/AN health networks to understand COVID-19 disparities; and (3) Geographic and temporal analysis of SARS-CoV-2 in Alaska to inform epidemiological understanding. We will leverage both short-read (Illumina) and long-read (Nanopore) sequencing platforms, and bioinformatics expertise built by Alaska INBRE, to analyze SARS-CoV-2 genomes with samples provided by Alaska DHSS/PHL, and specifically in AI/AN (SCF and ANMC served) populations. Data will be released for meta-analyses to provide genomics perspective to epidemic tracing, understanding of spread of novel lineages, and impact of health disparities.