Surveillance of wildlife and livestock for novel and emerging coronaviruses

项目摘要 迫切需要对野生动物和家畜进行冠状病毒(CoV)监测。 正如反复看到的那样，Cov有从蝙蝠、啮齿动物和 禽类宿主，通常在感染之前传染给包括家畜在内的中间物种 人类。我们对北美野生动物物种的Cov的了解很少， 家畜冠状病毒的常规测序是有限的。 在我们的第一个目标中，检测和测序野生动物和牲畜中的冠状病毒， 我们将利用一种泛冠状病毒RT-PCR来筛选一个独特的样本集，该样本集包括 蝙蝠和野生动物很少受到监视。样本集由大约500只动物组成 在12个月内提交给我们的兽医诊断实验室进行狂犬病检测 由肺、脾、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材料。 呼吸道疾病。 我们的第二个目标，进一步确定冠状病毒基因组的特征 病毒分离、系统发育和重组分析将与 组装好的冠状病毒基因组。具体地说，组装的基因组将被注释并 提交给Genbank并立即公开。系统发育分析 将确定SARS-CoV-2、类似SARS-CoV-2的CoV或新型CoV是否有 出现在非人类物种中。接下来将使用以下工具执行重组分析 SARS-CoV-2及组装的冠状病毒基因组以确定SARS-CoV-2或相关病毒 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。该目标的另一个组件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是至关重要的。 自然宿主和模式生物。 这个R21探索性项目满足了在 人与动物的界面，在野生动物和牲畜中都是如此。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、 检测方法和细胞培养适应的病毒将使进一步的研究成为可能 关于可能的人畜共患病，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.