Surveillance of wildlife and livestock for novel and emerging coronaviruses

项目摘要 迫切需要对野生动物和牲畜进行冠状病毒（CoV）监测。 正如反复看到的那样，冠状病毒倾向于从蝙蝠、啮齿动物和 在感染之前，通常感染到包括牲畜在内的中间物种 人类我们对野生动物物种中的北美冠状病毒的了解很少， 牲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， 蝙蝠和野生动物很少被监控。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狂犬病测试超过12个月 期间，由合并的肺、脾和肠组织匀浆组成。同时， 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， 呼吸道疾病 我们的第二个目标是进一步描述冠状病毒的基因组， 病毒分离株，系统发育和重组分析将与 组装CoV基因组。具体而言，组装的基因组将被注释， 提交给Genbank并立即公开。系统发育分析 将确定SARS-CoV-2、与SARS-CoV-2相似的CoV或新的CoV是否具有 出现在非人类物种中。接下来将使用 SARS-CoV-2和组装的CoV基因组，以确定SARS-CoV-2或相关 冠状病毒经历了自然重组，并贡献了遗传物质， 地方性冠状病毒这一目标的另一个组成部分是分离和传播检测到的 细胞培养中的CoV。后一个目标对于进一步研究糖尿病的发病机制至关重要。 自然宿主和模式生物。 这个R21探索性项目满足了在全球范围内进行CoV监测的迫切需要。 人与动物之间的相互作用，包括野生动物和牲畜。这项研究的结果将 确定新出现的疾病威胁，并开发关键工具，包括序列， 检测方法和细胞培养适应的病毒，这将使进一步的研究 可能的人畜共患病并采取先发制人的行动

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.