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

项目摘要 新冠肺炎的病毒源SARS-CoV-2已经在美国感染了至少94只宠物猫，根据 美国农业部确认的病例。猫的许多感染都是无症状的，只有少数是持续的。 对同伴动物的监测研究，所以猫的病例数量可能更高。猫被感染了 SARS-CoV-2来自人类主人，但已被实验证明可将病毒在猫与猫之间传播。 一旦被感染，至少在实验上，病毒会通过基因漂移和阳性在猫身上迅速适应。 在用于细胞附着的蛋白质--尖峰蛋白内的重要残基的选择。这些改编自 然后，病毒会传播给其他猫，并在群体内维持。这可能会导致加速 如果病毒能够再次感染人类，对人类群体潜在的令人担忧的变异进行固定。 此外，猫可能是一种将变异病毒引入野生动物种群的手段，基于它们的 狩猎行为。因此，基于这些考虑，对猫进行SARS-CoV-2监测是必要的。 有针对性的监视应该涉及人和动物的界面，因为这是最有可能的地方 将会发生事件(从人类感染动物，并有可能从动物传染给人类)。宠物 SARS-CoV-2阳性家庭中的猫已经知道有感染风险，应该包括在 一项涉及家猫的有针对性的积极监测计划。此外，有些猫还会有呼吸道症状。 当感染SARS-CoV-2时，因此纳入SARS-CoV-2检测，与检测一起进行的可能性更大 导致猫呼吸道疾病的病原体允许进行额外的被动监测。已提交的猫 对尸检的诊断实验室也可以很容易地包括在监测计划中。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引物集添加到 有针对性的下一代测序面板用于检测狗和猫的传染病。经修订的 面板将通过使用一组已测序的阳性样本来验证对SARS-CoV-2的检测，这些样本 包含疾控中心定义的所有当前感兴趣和关注的SARS-CoV-2变种。另外， 根据上述标准，将从猫身上采集鼻咽拭子进行监测测试。 这些样本将通过批准的SARS-CoV-2 RT-PCR和目标NGS小组进行测试，以 确定检测SARS-CoV-2的试剂盒的诊断敏感性/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，以评估与感染有关的变异。 将这种病毒添加到常用的传染病小组中，将允许继续被动 监督，而不需要特别要求和获得测试的批准。这应该会增强 我们在猫身上检测到这种病毒，潜在地防止了不必要的传入或传播到新的 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.