'COVID-19' Incorporation of SARS-CoV-2 primers into a targeted NGS panel for surveillance use in cats

项目摘要 SARS-CoV-2是COVID-19的病毒原因，根据美国的数据， 美国农业部确认的病例许多猫的感染是无症状的，只有少数正在进行中 在伴侣动物中进行的监测研究，因此猫的病例数量可能更高。猫被感染 SARS-CoV-2从它们的人类主人身上分离出来，但实验表明这种病毒可以在猫与猫之间传播。 一旦感染，至少在实验上，病毒很快适应猫通过遗传漂变和阳性 在刺突蛋白（一种用于细胞附着的蛋白质）内的重要残基上进行选择。这些适应 然后病毒传播给其他猫并保持在群体中。这可能导致加速 如果病毒能够再次感染人类，则可以固定人群中可能相关的变异。 此外，猫可以作为将变异病毒引入野生动物种群的手段，这是基于它们的 狩猎行为因此，基于这些考虑，有必要对猫进行SARS-CoV-2监测。 有针对性的监测应涉及人类和动物的界面，因为这是最有可能的地方， 将发生事件（动物从人类感染，并可能从动物返溢至人类）。宠物 SARS-CoV-2阳性家庭中的猫已经知道有感染的风险，应包括在 一项针对家猫的主动监控计划此外，一些猫显示呼吸道症状 当感染了SARS-CoV-2，所以纳入SARS-CoV-2检测，沿着检测的可能性更大 在猫中产生呼吸道疾病的病原体，允许额外的被动监测。猫提交 到诊断实验室进行尸检也可以很容易地包括在监测计划中。为了解决监视问题 根据需要，普渡动物疾病诊断实验室建议将SARS-CoV-2引物组添加到 用于检测犬和猫传染病的下一代靶向测序板。经修订的 将通过使用一组测序阳性样本对检测SARS-CoV-2的面板进行验证， 包含CDC定义的所有当前感兴趣和关注的SARS-CoV-2变体。此外，本发明还 将根据上述标准从猫中采集鼻和口咽拭子进行监测检测。 这些样本将通过已批准的SARS-CoV-2 RT-PCR和靶向NGS面板进行检测， 确定检测SARS-CoV-2的试剂盒的诊断灵敏度/特异性。此外，任何 我们将对从猫身上获得的阳性样本进行测序，以评估与感染相关的变异。 将该病毒添加到用于传染病的常用面板中将允许继续被动检测。 监督，而不需要特别要求和获得批准的测试。这将增强 我们在猫中检测到这种病毒，可能会防止不必要的引入或传播到新的 人口。

Project Summary SARS-CoV-2, the viral cause of COVID-19, has infected at least 94 pet cats in the United States, based on confirmed cases by the USDA. Many infections in cats are asymptomatic, and there are only a few ongoing surveillance studies in companion animals, so the number of cases in cats is likely higher. Cats are infected by SARS-CoV-2 from their human owners but have been shown experimentally to transmit the virus cat-to-cat. Once infected, at least experimentally, the virus quickly adapts in cats through genetic drift and positive selection at important residues within the spike protein, a protein used for cellular attachment. These adapted viruses are then spread to additional cats and maintained within the group. This can lead to accelerated fixation of potentially concerning variants for the human population if the virus is then able to re-infect humans. Additionally, cats may serve as a means for introducing variant viruses into wildlife populations based on their hunting behavior. Therefore, surveillance of cats for SARS-CoV-2 is warranted based on these considerations. Targeted surveillance should involve the interface of humans and animals, as this is most likely where these events will occur (infection of animals from humans with a potential of spillback to humans from animals). Pet cats in positive SARS-CoV-2 households are already known to be at risk for infection and should be included in a targeted active surveillance program involving domestic cats. Additionally, some cats show respiratory signs when infected with SARS-CoV-2, so the inclusion of SARS-CoV-2 testing, along with testing for the more likely pathogens that produce respiratory disease in cats, allows for additional passive surveillance. Cats submitted to diagnostic labs for necropsies can also easily be included in a surveillance program. To address surveillance needs, the Purdue Animal Disease Diagnostic Laboratory proposes to add SARS-CoV-2 primer sets to the targeted next-generation sequencing panel for detection of infectious diseases of dogs and cats. The amended panel will be validated for the detection of SARS-CoV-2 by using a set of sequenced positive samples, which contains all the current SARS-CoV-2 variants of interest and concern, as defined by the CDC. Additionally, nasal and oropharyngeal swabs will be collected from cats for surveillance testing based on the above criteria. These samples will be tested by both an approved RT-PCR for SARS-CoV-2 and the targeted NGS panel to determine the diagnostic sensitivity/specificity of the panel for detection of SARS-CoV-2. Additionally, any positive samples we obtain from the cats will be sequenced to evaluate variants associated with infection. Addition of this virus to commonly used panels for infectious diseases will allow for continued passive surveillance without the need to specifically request and obtain approval for the testing. This should enhance our detection of this virus in cats, potentially preventing the unwanted introduction or spread into new populations.