Center for Translational Pediatric Research (CTPR)

项目总结 SARS-CoV-2变种的持续出现和随后在世界各地的传播令人担忧 为控制冠状病毒病(COVID)-19大流行的全球努力。尽管有很高的 疾病总体而言，阿肯色州在对与该州感染相关的病毒进行测序方面一直进展缓慢。为了这个 建议，我们的转化儿科研究中心(CTPR)生物医学研究卓越中心 (Cobre)和阿肯色州IDEA生物医学研究卓越网络(INBRE)合作 为阿肯色州提供可持续的SARS CoV-2基因组监测数据和分析。在核心 在这项提议中，我们建立了一个强大的合作伙伴，名为阿肯色州测序(ArkSeq)联盟 其中包括阿肯色州医学大学(UAMS)、阿肯色州儿童医院(ACH)、 包括阿肯色州儿童西北分校和UAMS西北分校，小石城的浸信健康(BH)， 由阿肯色州卫生部(ADH)和阿肯色州经营的全州免下车中心 儿童研究所(ACRI)。该联盟提供残留病毒传输介质(VTM) 已被确认为SARS-CoV-2阳性。我们的目标是持续监测这些样本中是否有SARS- CoV-2序列多样性和病毒系统动力学，并向ADH和CDC提供可操作的数据 关于变种。这项提案的目标1是为阿肯色州提供基因组监测。为了实现这一目标，我们 将使用基于Illumina的平台对我们ArkSeq财团的至少12288个样本进行变种测序 值得关注的问题(VOCs)在明年，目标是扩大到所有患者。我们将获得有关的临床信息 这些样本，包括受试者的人口统计数据(年龄、性别、种族、民族、居住地和邮编 代码)、采集日期、采样时的症状、当时存在的其他呼吸道病毒 阳性结果和接种情况(疫苗类型和接种日期)。这种方法将使我们能够 回答研究问题：“不同变种在阿肯色州的相对水平是多少？” 这种变化是随着时间的推移而变化的吗？阿肯色州不同的变种如何分布在不同的地理位置 地区之间以及种族、民族、性别和/或年龄组之间的差异？“与美国疾病控制与预防中心和美国疾病控制与预防中心合作 我们将把阿肯色州的VOCs和其他血统整合到国家数据库中。我们计划提供可行的 阿肯色州目前流行的SARS-CoV-2毒株的测序信息。为了满足这一点 Goal，我们目前正在与CDC参加每周一次的SPERES电话会议，我们正在与ADH合作 和ArkSeq合作伙伴每月就已确定的变体举行会议。在成功完成此操作后 提议，我们将从阿肯色州向数据库提供比目前多21倍的序列 可从我们州获得，并保留了许多其他样品以供将来评估。

PROJECT SUMMARY The continuing emergence and subsequent circulation of SARS-CoV-2 variants across the world is of concern for the global effort of controlling the Coronavirus Disease (COVID)-19 pandemic. Despite a high-burden of disease overall, Arkansas has been slow to sequence viruses associated with infections in the state. For this proposal, our Center for Translational Pediatric Research (CTPR) Center of Biomedical Research Excellence (COBRE) and Arkansas IDeA Network of Biomedical Research Excellence (INBRE) have partnered together to deliver sustainable SARS CoV-2 genomic surveillance data and analyses for the State of Arkansas. At the core of this proposal, we have built a powerful collaboration named the Arkansas Sequencing (ArkSeq) Consortium which includes the University of Arkansas for Medical Sciences (UAMS), Arkansas Children’s Hospital (ACH), including Arkansas Children’s Northwest and UAMS Northwest extensions, Baptist Health (BH) in Little Rock, drive-through centers across the State run by the Arkansas Department of Health (ADH), and Arkansas Children’s Research Institute (ACRI). This consortium provides remnant viral transport media (VTM) that have been identified as positive for SARS-CoV-2. Our objective is to continuously monitor these samples for SARS- CoV-2 sequence diversity and viral phylodynamics and to provide actionable data back to the ADH and CDC regarding variants. Aim 1 of this proposal is to provide genomic surveillance for Arkansas. To fulfill this aim, we will use Illumina-based platforms to sequence at least 12288 samples from our ArkSeq Consortium for variants of concern (VoCs) over the next year with a goal to scale to all patients. We will obtain clinical information on these samples, including the subject’s demographics (age, sex, race, ethnicity, county of residence, and zip code), date of collection, symptoms at the time of sampling, other respiratory viruses present at the time of positive result, and vaccination status (vaccine type and date of vaccination). This approach will allow us to answer the research questions: “What are the relative levels of the different variants in Arkansas?”; “How does this change over time?” and “How are different Arkansas variants distributed across different geographical regions, as well among racial, ethnic, gender, and/or age groups?” In collaboration with the ADH and the CDC, we will integrate VoCs and other lineages from Arkansas into national databases. We plan to provide actionable sequencing information on current strains of SARS-CoV-2 that are circulating within Arkansas. To meet this goal, we are currently participating in the weekly SPHERES calls with CDC, and we are partnering with ADH and ArkSeq partners to have monthly meetings regarding identified variants. Upon successful completion of this proposal, we will have provided ~21 times more sequences from Arkansas to the databases than are currently available from our State, with many other samples maintained for future evaluation.