Identification and Dynamics of SARS-CoV-2 Sequence Variants in Idaho

摘要 发表的第一个SARS-CoV-2序列为所有目前批准的检测提供了基础。 方法和疫苗已经开发出来。然而，携带多种变化的SARS-CoV-2变体， 它们的基因组可以使病毒逃避检测和逃避天然或疫苗诱导的免疫， 阻碍了当前的减排努力。此外，增加遗传性的变异， 严重性和改善对治疗剂的耐药性也是控制全球 2019冠状病毒病疫情。因此，仍然迫切需要快速鉴定SARS-CoV-2变体 在所有人群中，包括监测工作滞后的服务不足地区的人群。一年 在COVID-19被宣布为大流行后，来自美国的SARS-CoV-2基因组不到350个， 爱达荷州已被排序，排名倒数6个州。为了满足这一需求，博伊西VA 采购Illumina NextSeq 500 Dx测序平台， 本地和全州样本的测序。利用现有的技术，我们的新兴和再新兴 传染病COBRE调查人员与爱达荷州实验室局和博伊西 VA病理学和实验室医学服务的理想定位，以解决以下紧迫的优先事项： (1)在研究人群中是否存在不同的变异，以及 研究人群中不同的变体随时间变化;（2）不同变体感染的病例 与特定爆发事件、地理位置或特定时间相关;（3） 变异体分布于不同种族、民族、性别和/或年龄组;（4）是特异性变异体 与COVID-19症状的不同表现水平相关;（5）对于正在接受治疗的研究人群， 接种疫苗，在第一次接种疫苗之前，参与者中SARS-CoV-2阳性的百分比是多少;以及 (6)接种疫苗的研究参与者是否仍然会感染SARS-CoV-2病毒，如果是，他们会感染哪些变体？ 携带.通过大量的合作努力，我们预计将对5,000个SARS-CoV-2病毒基因组进行测序， 从2020年3月开始，在整个爱达荷州收集样本，并将继续收集 通过拟议的研究时间轴。所得到的SARS-CoV-2共有序列数据将存放在 原始序列数据（FASTA）将保存在NCBI SRA上，如NCBI GenBank、Nextstrain和GISAID。 允许，并将报告给提供样本访问的SARS-CoV-2计划。这些努力将 大大改善爱达荷州的SARS-CoV-2监测，跟踪传播的变体，并通知地方和国家 卫生领导人指导大流行病应对工作。

ABSTRACT The first SARS-CoV-2 sequence published provided the foundation by which all currently approved detection methods and vaccines have been developed. However, variants of SARS-CoV-2 that carry multiple changes to their genome may enable the virus to evade detection and escape natural or vaccine-induced immunity, thwarting current abatement efforts. Additionally, variants that increase transmissibility, enhance disease severity, and improve resistance to therapeutic agents are also of significant concern in controlling the global COVID-19 pandemic. Thus, there remains a critical need for the rapid identification of SARS-CoV-2 variants among all populations, including those in underserved areas where surveillance efforts are lagging. One year after COVID-19 was declared a pandemic, fewer than 350 SARS-CoV-2 genomes originating from the state of Idaho have been sequenced, ranking among the bottom 6 IDeA states. To address this need, the Boise VA procured an Illumina NextSeq 500Dx sequencing platform to enable high capacity SARS-CoV-2 genome sequencing of local and statewide samples. With this existing technology, our Emerging and Reemerging Infectious Diseases COBRE investigators, in collaboration with the Idaho Bureau of Laboratories and the Boise VA Pathology and Laboratory Medicine Service are ideally positioned to address the following urgent priorities: (1) Are there different variants present in the study population, and how has the number of cases caused by different variants changed over time in the study population; (2) Are cases of infection by different variants associated with particular outbreak events, geographic locations, or specific times; (3) How are different variants distributed among different racial, ethnical, gender, and/or age groups; (4) Are specific variants associated with different levels of manifestation of COVID-19 symptoms; (5) For study populations undergoing vaccination, what percentage of the participants were SARS-CoV-2 positive prior to the first vaccine shot; and (6) Do vaccinated study participants still acquire the SARS-CoV-2 virus, and if so, what variants do they carry. With a large collaborative effort, we expect to sequence 5,000 SARS-CoV-2 viral genomes from samples collected throughout the state of Idaho, beginning in March of 2020 and collection will continue through the proposed study timeline. Resulting SARS-CoV-2 consensus sequence data will be deposited on NCBI GenBank, Nextstrain, and GISAID, while raw sequence data (FASTA) will be deposited on NCBI SRA, as permitted, and will be reported back to SARS-CoV-2 programs providing sample access. These efforts will vastly improve SARS-CoV-2 surveillance in Idaho, track circulating variants, and inform local and national health leaders to guide the pandemic response.