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

SARS-CoV-2冠状病毒的无症状携带者可以在不知不觉中传播COVID-19。 本科生经常聚集在校园里上课和参加其他活动，他们接触呼吸道感染的风险很高。 然而，作为一个普遍较年轻的成年人群，他们发展为COVID-19的风险也相对较低。 因此，学生可能是这种病毒的携带者，增加了将其传播给他人的风险。 这个快速项目将扩大现有的基于课堂的本科生研究经验（CURE）在休斯敦大学-清澈的湖水微生物学的范围。 目前就读于CURE的学生在基于课程的环境中参与真实的研究，以研究鼻腔微生物组。 该奖项提供的支持将使学生能够将有关其SARS-CoV-2状态的信息添加到研究中。 CURE将使他们能够了解研究是如何进行的，并可能产生关于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来学习如何使用MALDI-TOF对DNA片段进行测序，为他们提供在临床和研究实验室中有价值的技能。 参加治愈的学生已经在2020年春季学期早些时候收集了自己的鼻拭子标本。 培养这些标本以选择葡萄球菌属的细菌。 在家里工作，学生将参与远程数据收集从16 S rRNA基因与细菌结构域特异性引物产生的PCR扩增子的高通量MALDI-TOF分析。这些数据将确定哪些细菌分离株是表皮葡萄球菌。 此外，这批学生的志愿者将被邀请返回校园，提供鼻拭子样本，以检测是否存在SARS-Cov-2。 一个驱动器通过测试设施，要求学生留在他们的车辆在任何时候都将用于此目的。 在该设施，注册护士将调查学生可能的COVID-19症状。 根据FDA的指导方针，学生将自己拭子，将拭子放入含有病毒检测试剂的试管中，然后将试管放入二级容器中。 因此，只有个别学生处理他们的样本。Co-PI亚历山大将收集所有二级容器，将其放入第三个容器中，并将其交付给商业实验室进行SARS-CoV-2检测，使用的是不能用于临床的仅供研究的检测试剂盒。 学生将通过一个盲法协议获得他们的SARS-CoV-2状态，该协议确保只有个别学生知道他们的状态。 将汇总来自该类别的去识别数据，以检查鼻微生物组与SARS-CoV-2存在之间的关系。 探索S.表皮对SARS-CoV-2感染的保护作用可能有助于进一步了解SARS-CoV-2的毒力。 因此，迫切需要立即收集数据。 在数据收集和分析的同时，该项目打算开发用于教学MALDI-TOF的虚拟模块，为学生提供由于校园关闭而无法获得的培训机会。 该奖项由本科教育部（教育和人力资源局）的改进本科STEM教育计划颁发，使用冠状病毒援助，救济和经济安全（CARES）法案的资金。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值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.