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

项目概要 根据数据，SARS-CoV-2（导致 COVID-19 的病毒）已感染美国至少 94 只宠物猫 美国农业部确诊病例。许多猫的感染都是无症状的，只有少数是持续存在的 对伴侣动物进行的监测研究，因此猫的病例数可能更高。猫被感染了 SARS-CoV-2 来自人类主人，但实验表明该病毒可以在猫与猫之间传播。 一旦感染，至少在实验上，该病毒通过基因漂变和阳性反应在猫体内迅速适应。 选择刺突蛋白（一种用于细胞附着的蛋白质）内的重要残基。这些改编的 然后病毒会传播给其他猫并维持在群体内。这可能会导致加速 如果病毒能够重新感染人类，则确定可能与人类有关的变异。 此外，猫可能会根据其特征将变异病毒引入野生动物种群。 狩猎行为。因此，基于这些考虑，有必要对猫进行 SARS-CoV-2 监测。 有针对性的监视应涉及人类和动物的接触面，因为这最有可能是这些接触点 将会发生事件（人类感染动物，并有可能从动物传染给人类）。宠物 已知 SARS-CoV-2 阳性家庭中的猫有感染风险，应将其纳入其中 一项涉及家猫的有针对性的主动监测计划。此外，有些猫会出现呼吸道症状 当感染 SARS-CoV-2 时，因此将 SARS-CoV-2 检测纳入其中，并检测更有可能的病例 引起猫呼吸道疾病的病原体，允许进行额外的被动监测。猫已提交 尸检诊断实验室也可以轻松纳入监测计划。解决监视问题 根据需要，普渡大学动物疾病诊断实验室建议将 SARS-CoV-2 引物组添加到 用于检测狗和猫的传染病的靶向下一代测序面板。修订后的 将使用一组已测序的阳性样本来验证面板对 SARS-CoV-2 的检测，其中 包含 CDC 定义的所有当前感兴趣和关注的 SARS-CoV-2 变体。另外， 根据上述标准，将从猫身上采集鼻腔和口咽拭子进行监测检测。 这些样本将通过经批准的 SARS-CoV-2 RT-PCR 和目标 NGS 组合进行测试，以 确定 SARS-CoV-2 检测组合的诊断敏感性/特异性。此外，任何 我们从猫身上获得的阳性样本将被测序，以评估与感染相关的变异。 将这种病毒添加到常用的传染病检测组合中将允许持续被动 无需专门请求并获得测试批准即可进行监督。这应该增强 我们在猫身上检测到这种病毒，有可能防止不必要的引入或传播到新的国家 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.