Surveillance of wildlife and livestock for novel and emerging coronaviruses

监测野生动物和牲畜是否存在新型和新出现的冠状病毒

• 批准号: 10266305
• 负责人: Eric A Nelson
• 金额: $ 22.28万
• 依托单位: SOUTH DAKOTA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10266305
• 关键词: 2019-nCoV; Acute; Address; American; Animal Feed; Animal Model; Animals; Birds; COVID detection; Cattle; Cell Culture Techniques; Chiroptera; Communities; Coronavirus; Country; Data; Deltaretrovirus; Detection; Diagnostic; Disease; Enteral; Family suidae; Genbank; Genetic Materials; Genetic Recombination; Genome; Health; Human; Influenza D Virus; Intestines; Investigation; Knowledge; Laboratories; Livestock; Lung; Lung diseases; Methodology; North America; Pathogenesis; Pestivirus; Phylogenetic Analysis; Porcine circovirus; Prevalence; Publications; Rabies; Research; Reverse Transcriptase Polymerase Chain Reaction; Rodent; Sampling; Spleen; Stream; Testing; Tissues; Virus; Work; base; cross-species transmission; innovation; metagenomic sequencing; novel; novel coronavirus; pathogen; respiratory; screening; tool; virology; whole genome

Project Summary There is an urgent need for coronavirus (CoV) surveillance in both wildlife and livestock. As seen repeatedly, CoVs have a propensity to jump species from their bat, rodent and avian reservoirs, often to intermediate species including livestock, before infecting humans. Our knowledge of North American CoVs in wildlife species is sparse and routine sequencing of livestock CoVs are limited. In our first aim, to detect and sequence coronaviruses in wildlife and livestock, we will utilize a pan-coronavirus RT-PCR to screen a unique sample set consisting of bats and wildlife rarely surveilled. The sample set is comprised of ~500 animals submitted to our veterinary diagnostic laboratory for rabies testing over a 12-month period and consists of pooled lung, spleen and intestine tissue homogenate. In parallel, we will screen food animal diagnostic submissions from animals with acute enteric and respiratory disease. Our second aim, to further characterize coronavirus genomes and characterize virus isolates, phylogenetic and recombination analysis will be performed with the assembled CoV genomes. Specifically, assembled genomes will be annotated and submitted to Genbank and made publicly available immediately. Phylogenetic analysis will determine if SARS-CoV-2, CoVs similar to SARS-CoV-2 or novel CoVs have emerged in non-human species. Recombination analysis will next be performed using SARS-CoV-2 and the assembled CoV genomes to determine if SARS-CoV-2 or related CoVs have undergone natural recombination and contributed genetic material to endemic CoV. Another component of this aim is to isolate and propagate the detected CoVs in cell culture. This latter aim is critical for further pathogenesis studies in the natural host and model organisms. This R21 exploratory project meets an urgent need for CoV surveillance at the human-animal interface, both in wildlife and livestock. Results from this study will identify emerging disease threats and develop critical tools, including sequences, detection methodology and cell culture adapted viruses that will enable further studies on possible zoonosis and enable preemptive action.

项目概要 迫切需要对野生动物和牲畜的冠状病毒（CoV）进行监测。 正如反复观察到的，冠状病毒有一种从蝙蝠、啮齿动物和其他物种中跳跃的倾向。 在感染之前，禽类宿主通常是包括牲畜在内的中间物种 人类。我们对北美野生动物物种中的冠状病毒的了解很少，而且 家畜冠状病毒的常规测序是有限的。 我们的第一个目标是检测野生动物和牲畜中的冠状病毒并对其进行测序， 我们将利用泛冠状病毒 RT-PCR 筛选一组独特的样本，其中包括 蝙蝠和野生动物很少受到监视。样本集由约 500 只动物组成 提交给我们的兽医诊断实验室进行为期 12 个月的狂犬病检测 期并由汇集的肺、脾和肠组织匀浆组成。并联， 我们将筛选患有急性肠道疾病的动物提交的食用动物诊断报告 呼吸道疾病。 我们的第二个目标是进一步表征冠状病毒基因组并表征 病毒分离、系统发育和重组分析将与 组装了 CoV 基因组。具体来说，组装的基因组将被注释并 提交给 Genbank 并立即公开发布。系统发育分析 将确定 SARS-CoV-2、与 SARS-CoV-2 相似的 CoV 或新型 CoV 是否具有 出现在非人类物种中。接下来将使用进行重组分析 SARS-CoV-2 和组装的 CoV 基因组，以确定 SARS-CoV-2 或相关病毒是否 冠状病毒经历了自然重组并贡献了遗传物质 地方性冠状病毒。该目标的另一个组成部分是隔离和传播检测到的 细胞培养中的冠状病毒。后一个目标对于进一步的发病机制研究至关重要 天然宿主和模式生物。 这个 R21 探索性项目满足了冠状病毒监测的迫切需求 人与动物的界面，包括野生动物和牲畜。这项研究的结果将 识别新出现的疾病威胁并开发关键工具，包括序列、 检测方法和适应细胞培养的病毒将有助于进一步研究 可能的人畜共患病并采取先发制人的行动。