RAPID: A Course-based Undergraduate Research Experience on the Interaction between the Nasal Microbiome and SARS-CoV-2 Coronavirus Infection

无症状的SARS-CoV-2冠状病毒携带者可能在不知不觉中传播新冠肺炎。本科生经常聚集在校园里上课和其他活动，他们接触呼吸道感染的风险更高。然而，作为一般较年轻的成年人群，他们进展到新冠肺炎的风险也相对较低。因此，学生可能是这种病毒的携带者，从而增加了将病毒传播给其他人的风险。这个快速项目将扩大休斯顿-克利尔湖大学现有的微生物学本科生课堂研究体验(CURE)的范围。目前参加治疗的学生在以课程为基础的环境中参与真实的研究，以研究鼻部微生物组。该奖项提供的支持将使学生能够将有关他们的SARS-CoV-2状态的信息添加到研究中。这种治疗方法将使他们了解研究是如何进行的，并有可能产生关于SARS-CoV-2病毒如何工作的新知识。学生还将开发和使用虚拟现实工具，学习如何使用MALDI-TOF对DNA片段进行测序，为他们提供对临床和研究实验室有价值的技能。参加治疗的学生已经在2020年春季学期的早些时候收集了自己的鼻拭子样本。这些标本被培养以筛选葡萄球菌属的细菌。在家里工作时，学生们将参与远程数据收集，通过高通量MALDI-TOF分析16S rRNA基因产生的带有细菌结构域的特定引物的PCR扩增产物。这些数据将确定哪些细菌分离株是表皮葡萄球菌。此外，这批学生中的志愿者将被邀请返回校园，提供鼻拭子样本，用于检测SARS-CoV-2的存在。为此，将使用要求学生始终留在车内的免下车测试设施。在该设施，注册护士将调查学生可能出现的新冠肺炎症状。根据FDA的指导方针，学生们随后将自拭子，将拭子放入装有灭活病毒的试剂的试管中，然后将试管放入二次容器。因此，只有个别学生处理他们的样本。Co-Pi Alexander将收集所有的二次容器，将它们放入第三个容器，并将其运送到商业实验室进行SARS-CoV-2检测，使用不能用于临床的仅供研究的检测试剂盒。学生将通过一种保密协议收到他们的SARS-CoV-2状态，确保只有个别学生知道他们的状态。来自该课程的已确定的数据将被汇集起来，以检查鼻部微生物群和SARS-CoV-2存在之间的关系。探索表皮葡萄球菌对SARS-CoV-2感染的保护作用可能有助于更好地了解SARS-CoV-2的毒力。因此，迫切需要立即收集数据。在收集和分析数据的同时，该项目打算开发用于教授MALDI-TOF的虚拟模块，为学生提供因校园关闭而无法获得的培训机会。这一快速奖项是由本科教育部门(教育和人力资源局)的改善本科STEM教育项目，使用冠状病毒援助、救济和经济安全(CARE)法案的资金颁发的。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Asymptomatic carriers of the SARS-CoV-2 coronavirus can unknowingly spread COVID-19. Undergraduate students, who routinely congregate on campuses for classes and other activities, have an elevated risk of exposure to respiratory infections. However, as a generally younger adult population, they also have a relatively low risk of progressing to COVID-19. As a result, it is possible that students could be carriers of this virus, posing increased risk of spreading it to others. This RAPID project will expand the scope of an existing Classroom-based Undergraduate Research Experience (CURE) in microbiology at the University of Houston – Clear Lake. Students currently enrolled in the CURE participate in authentic research in a course-based setting to study the nasal microbiome. Support provided by this award will enable students to add information about their SARS-CoV-2 status to the research. The CURE will allow them to learn both how research is conducted and to potentially generate new knowledge about how the SARS-CoV-2 virus works. Students will also develop and use a virtual reality tool to learn how to use MALDI-TOF to sequence DNA fragments, providing them with skills that are valuable in clinical and research laboratories. The students enrolled in the CURE have already collected their own nasal swab specimens earlier in the Spring 2020 semester. These specimens were cultured to select for bacteria in the Staphylococus genus. Working at home, students will participate in remote data collection from high-throughput MALDI-TOF analysis of PCR amplicons generated from the 16S rRNA gene with bacterial-domain specific primers. These data will identify which bacterial isolates are Stapthlococcus epidermis. In addition, volunteers from this group of students will be invited to return campus to provide nasal swab samples to be tested for the presence of SARS-Cov-2. A drive-through testing facility that requires students to remain in their vehicles at all times will be used for this purpose. At the facility, registered nurses will survey the students about possible CoVID-19 symptoms. Following FDA guidelines, students will then self-swab, place the swab into a tube containing reagents that inactivate viruses, then place the tube into a secondary container. Thus, only the individual student handles their sample. Co-PI Alexander will collect all of the secondary containers, place them into a third container, and deliver it to a commercial lab to be tested for SARS-CoV-2, using research-only test kits that cannot be used clinically. Students will receive their SARS-CoV-2 status via a blinded protocol that ensures that only the individual student will know their status. The deidentified data from the class will be pooled to examine the relationship between the nasal microbiome and the presence of SARS-CoV-2. Exploring the potential of S. epidermis to protect against SARS-CoV-2 infection might provide greater understanding of the virulence of SARS-CoV-2. Thus, there is a urgent need for immediate data collection. In parallel with data collection and analysis, the project intends to develop virtual modules for teaching MALDI-TOF, providing students with training opportunities that would be otherwise unavailable due to campus closure. This RAPID award is made by the Improving Undergraduate STEM Education program in the Division of Undergraduate Education (Education and Human Resources Directorate), using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.