In the middle of the COVID-19 epidemic, flaws in the SARS-CoV-2 diagnostic
test were identified by the impending supply shortages of nasopharyngeal swabs and nucleic acid isolation and purification kits. The ASU Biodesign Clinical Testing Lab (ABCTL), which converted from a research lab to SARS-CoV-2 testing lab, was not an exception to these shortages, but the consequences were greater due to its significant testing load in the state of Arizona. In response to the shortages, researchers at The Department of Epidemiology of Microbial Diseases, at the Yale School of Public Health created SalivaDirect method, which is an epidemic effective test, that accounts for limitations of materials, accessibility to specialized lab equipment, time per test, and cost per test. SalivaDirect simplified the diagnostic process by collecting samples via saliva and skipping the nucleic acid extraction and purification, and did it in a way that resulted in a highly sensitive limit of detection of 6-12 SARS-CoV-2 copies/μL with a minimal decrease in positive test agreement.
The ASU Biodesign Clinical Testing Laboratory began in March 2020 after the severe acute respiratory syndrome, coronavirus 2, began spreading throughout the world. ASU worked towards implementing its own efficient way of testing for the virus, in order to assist the university but also keep the communities around it safe. By developing its own strategy for COVID-19 testing, ASU was on the forefront of research by developing new ways to test for the virus. This process began when research labs at ASU were quickly converted into clinical testing laboratories, which used saliva testing to develop swift COVID-19 diagnostic tests for the Arizona community. The lab developed more accurate and time efficient results, while also converting Nasopharyngeal tests to saliva tests. Not only did this allow for fewer amounts of resources required, but more individuals were able to get tested at faster rates. The ASU Biodesign Clinical Testing Laboratory (ABCTL) was able to accomplish this through the adaptation of previous machines and personnel to fit the testing needs of the community. In the future, the ABCTL will continue to adapt to the ever-changing needs of the community in regards to the unprecedented COVID-19 pandemic. The research collected throughout the past year following the breakout of the COVID-19 pandemic is a reflection of the impressive strategy ASU has created to keep its communities safe, while continuously working towards improving not only the testing sites and functions, but also the ways in which an institution approaches and manages an unfortunate impact on diverse communities.
This thesis project is part of a larger collaboration documenting the history of the ASU Biodesign Clinical Testing Laboratory (ABCTL). There are many different aspects that need to be considered when transforming to a clinical testing laboratory. This includes the different types of tests performed in the laboratory. In addition to the diagnostic polymerase chain reaction (PCR) test that is performed detecting the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), antibody testing is also performed in clinical laboratories. Antibody testing is used to detect a previous infection. Antibodies are produced as part of the immune response against SARS-CoV-2. There are many different forms of antibody tests and their sensitives and specificities have been examined and reviewed in the literature. Antibody testing can be used to determine the seroprevalence of the disease which can inform policy decisions regarding public health strategies. The results from antibody testing can also be used for creating new therapeutics like vaccines. The ABCTL recognizes the shifting need of the community to begin testing for previous infections of SARS-CoV-2 and is developing new forms of antibody testing that can meet them.
This thesis project is the result of close collaboration with the Arizona State University Biodesign Clinical Testing Laboratory (ABCTL) to document the characteristics of saliva as a test sample, preanalytical considerations, and how the ABCTL utilized saliva testing to develop swift COVID-19 diagnostic tests for the Arizona community. As of April 2021, there have been over 130 million recorded cases of COVID-19 globally, with the United States taking the lead with approximately 31.5 million cases. Developing highly accurate and timely diagnostics has been an important need of our country that the ABCTL has had tremendous success in delivering. Near the start of the pandemic, the ABCTL utilized saliva as a testing sample rather than nasopharyngeal (NP) swabs that were limited in supply, required highly trained medical personnel, and were generally uncomfortable for participants. Results from literature across the globe showed how saliva performed just as well as the NP swabs (the golden standard) while being an easier test to collect and analyze. Going forward, the ABCTL will continue to develop high quality diagnostic tools and adapt to the ever-evolving needs our communities face regarding the COVID-19 pandemic.
Methods: We have designed a multiplexed magnetics programmable bead ELISA (MagProBE) to profile the immune responses of the proteins from 11 high-risk HPV types and 2 low-risk types—106 genes in total. HPV genes were optimized for human expression and either built with PCR or commercially purchased, and cloned into the Gateway-compatible pANT7_cGST vector for in vitro transcription/translation (IVTT) in a MagProBE array. Anti-GST antibody (Ab) labeling was then used to measure gene expression.
Results: 53/106 (50%) HPV genes have been cloned and tested for expression of protein. 91% of HPV proteins expressed at levels above the background control (MFI = 2288), and the mean expression was MFI = 4318. Codon-optimized genes have also shown a 20% higher expression over non-codon optimized genes.
Conclusion: Although this research is ongoing, it suggests that gene optimization may improve IVTT expression of HPV proteins in human HeLa lysate. Once the remaining HPV proteins have been expression confirmed, the cDNA for each gene will be printed onto slides and tested in serologic assays to identify potential Ab biomarkers to CIN3.
Recent studies suggest a role for the microbiota in autism spectrum disorders (ASD), potentially arising from their role in modulating the immune system and gastrointestinal (GI) function or from gut–brain interactions dependent or independent from the immune system. GI problems such as chronic constipation and/or diarrhea are common in children with ASD, and significantly worsen their behavior and their quality of life. Here we first summarize previously published data supporting that GI dysfunction is common in individuals with ASD and the role of the microbiota in ASD. Second, by comparing with other publically available microbiome datasets, we provide some evidence that the shifted microbiota can be a result of westernization and that this shift could also be framing an altered immune system. Third, we explore the possibility that gut–brain interactions could also be a direct result of microbially produced metabolites.