Study & PI
SARS-CoV-2 Sample Type and Diagnostic Test Performance: RadX

PI: Yukari Manabe
Contact: Agha Mirza 443-301-8572

Primary objectives of this study are to determine the sensitivity of SARS-CoV-2 antigen testing for symptomatic and asymptomatic persons in midturbinate or nasal swabs and saliva specimens compared to reference nucleic acid testing and viral culture and to prospectively establish a biorepository of clinical specimens for validation of SARS-CoV-2 diagnostic assays in symptomatic and asymptomatic individuals. All study participants will undergo nucleic acid testing and will receive results within 48 hours. Potential participants must either be a symptomatic person suspected of having COVID-19 or an asymptomatic close contact of a person diagnosed with COVID-19. Participants who enroll will undergo nasopharyngeal sampling as well as nasal and saliva sample collection.
Validation of a COVID-19 Test Using the TagPath™ COVID-19 Combo Kit (Applied Biosystems)

PI: Karen Carroll
The purpose of this effort is to validate testing of the recently approved TaqPath™ COVID-19 Combo Kit (Applied Biosystems). Results of this testing will be applied as a quality check for additional validation of the Johns Hopkins laboratory developed assay.
Assessment of Serum Antibodies Against the SARS CoV-2 Virus and Serum Cytokines: Use for Validation of Clinical Assay and Subsequent Publication

PI: Patrizio Caturegli
Residual sera from patients who test positive and negative in a PCR assay for SARS CoV-2, will be used to validate commercially available assays to detect serum antibodies against COVID-19 antigens (i.e. the spike protein or the nucleoprotein), and serum cytokines (to include IL-1 beta, IL-6, IL-8, and TNF-alpha).
Clinical Evaluation of Point of Care Testing Kits for SARS-CoV-2 Antibodies

PI: William Clarke
Multiple lateral flow point-of–care test kits for detecting IgG and IgM associated with SARS-CoV-2 infection will be evaluated to better understand the reproducibility and analytical sensitivity of these assays. All results will be compared to measurements obtained by ELISA testing.
Impact and Performance of a Rapid Diagnostic Platform for SARS-CoV-2 under Pandemic Conditions

PI: Jeremiah Hinson
The primary objective of this study is to evaluate the clinical impact of a SARS-CoV-2 standard and rapid testing algorithm used by the Johns Hopkins Health System on resource allocation and care delivery, for patients who do and do not have COVID-19. The algorithm incorporates two FDA EUA approved diagnostic tests, the Johns Hopkins-developed SARS-CoV-2 RT-PCR and Cepheid’s Xpert® Xpress SARS-CoV-2 test platform, with turnaround times of 24-36 hours and 45 minutes, respectively. The predictive performance of these 2 assays for COVID-19 related clinical outcomes will also be assessed.
Identification of Unrecognized HIV Infection and Other Bloodborne Pathogens in Emergency Department (ED) Patients, 2015-2016

PI: Yu-Hsiang Hsieh
The main objective of the proposed research is to collect remnant, residual blood product from samples obtained as part of routine ED clinical care, to determine population-level, epidemiologic measurements of incidence, prevalence, and undiagnosed SARS-CoV-2 infection in patients presenting to the Emergency Department. This study will be conducted as an amendment to an ongoing study that uses the same blind seroprevalence study methodology.
Evaluation of Chest Imaging Characteristics for Patients with COVID-19 Pneumonia: Imaging Diagnosis and Association with Outcomes

PI: Cheng Lin
Clinical, diagnostic, and imaging (chest radiographs and computed tomography scans) characteristics of patients suspected or confirmed to have COVID-19 will be assessed to test 2 hypotheses: 1) characteristic chest CT features of COVID-19 pneumonia can be diagnostic for the disease and predictive of severe disease; and 2) radiomic features can be utilized to improve the sensitivity and specificity of COVID-19 diagnosis, as well as allow for an automated method of quantifying and characterizing lung abnormalities.
Diagnostic Performance of Lung Point of Care Ultrasound (POCUS) for COVID-19

PI: Gigi Liu
The purpose of this study is to assess the ability of Lung Point of Care Ultrasound (POCUS) to diagnose COVID-19. COVID-19 RT-PCR will be used as the standard against which the sensitivity, specificity, positive predictive and negative predictive values associated with lung POCUS will be assessed. This study will be retrospective in an observational case series of adults who present to the Johns Hopkins Hospital with respiratory symptoms suggestive of COVID-19.
Analytical and Clinical Performance of COVID-19 Molecular Diagnostic Methods

PI: Heba Mostafa
To enable the publication of validation results that will assist other laboratories seeking to develop their own diagnostic assays for SARS-CoV-2, this project will analyze the performance of 3 different molecular assays for COVID-19 diagnosis. Samples will be deidentified for testing and will include leftover, discarded SARS-CoV-2 positive and negative specimens sent to the clinical virology lab for standard of care diagnosis, as well as archived specimens for use as negative controls.
Development of a Rapid Molecular Test for Point-of-Care Detection of SARS-CoV-2

PI: Heba Mostafa
This study will enable the use of deidentified samples remaining after standard of care testing is completed to assess two point of care methods for detecting SARS-CoV-2. In collaboration with external researchers, positive and negative samples will be used to evaluate new testing technologies.
Evaluation of the BioRad Digital Droplet PCR (ddPCR) for the Molecular Detection of SARS-CoV-2

PI: Heba Mostafa
This study is designed to evaluate the BioRad digital droplet PCR as a diagnostic tool for the molecular detection of SARS-CoV-2 infections in patients at Johns Hopkins. Upon successfully completing this project, which will only provide aggregate de-identified laboratory data with basic patient demographic information, and BioRad receiving regulatory approval for their assay, our institution will gain the advantage of early infection control through more sensitive testing, especially very early in the disease.
Evaluation of the Research Use Only (RUO) Gene Xpert SARS-CoV-2 Assay

PI: Heba Mostafa
The goal of this study is to use de-identified patient samples to help assess the performance of a real-time PCR COVID-19 assay that is being developed by Cepheid Diagnostics for FDA Emergency Use Authorization. Upon successfully completing this project, which will only provide aggregate de-identified laboratory data with basic patient demographic information, and achieving regulatory approval, COVID-19 testing capacity will increase throughout the Johns Hopkins Medicine System as all hospitals will have this FDA-cleared platform in their labs.
Genomic Evolution of Viral Pathogens: Impact on Clinical Severity and Molecular Diagnosis

PI: Heba Mostafa
The purpose of this study is to conduct viral surveillance using partial and whole genome sequencing. The applications of this study include understanding viral evolution and monitoring the effect of viral polymorphisms, particularly at common primer binding sites, on the sensitivity of diagnostic molecular assays and on the severity of the disease. Particularly in the setting of SARS-CoV-2, these data will help to better understand the emergence of highly pathogenic and transmissible strains of coronaviruses.
Recognition of Secondary Fungal Infections in Patients with COVID-19: Clinical Characterization and Rapid Laboratory Diagnosis

PI: Sean Zhang
Clinical and laboratory data will be collected from hospitalized COVID -19 patients to determine the presence and better understand the clinical course of fungal infections developed in this population. In addition, a recently developed urinary galactofuranose (galF) enzyme immunoassay for the rapid and early diagnosis of aspergillosis will be validated and subsequently evaluated in these study subjects.
Real-Time Screening for SARS-CoV-2 Virus Infection with DigitalMALDI Analysis

PI: Marek Mirski
The major aim of this study is to test and validate a new technique utilizing Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry to rapidly diagnose COVID-19 respiratory infections. With the ultimate goal of developing a “Point-of-Care” test in both the hospital and ambulatory settings, this protocol will initially analyze ventilator expired air as a source of concentrated breath samples from mechanically ventilated ICU patients diagnosed with COVID-19. The samples will be analyzed for SARS-CoV-2 viral components, as well as other cellular elements and biomarkers, by mass spectrometry and correlated with other validated diagnostic techniques.
Subgenomic RNA SARS-CoV-2 Assay Development

PI: Chloe Thio
Better data on the duration of active viral replication after SARS-CoV-2 infection would be useful to help inform public health guidelines. For this reason, an assay using droplet digital PCR for subgenomic RNA of SARS-CoV-2 is being developed to attempt to determine the presence of replication competent virus in biospecimens.
Validation of a Salivary-Based Assay for SARS-CoV-2 in Long-term Care Facilities

PI: Morgan Katz
A novel salivary-based approach to SARS-CoV-2 sampling and laboratory analysis will be evaluated as a potentially more feasible means of enabling frequent testing of residents and staff in long-term care (LTC) facilities. As a first step, this study will validate salivary sampling for detecting SARS-CoV-2 viral RNA, IgG, IgA and viable virus. This will be achieved by first obtaining nasopharyngeal, blood and saliva samples from LTC facility residents and staff, and then comparing the results from salivary testing to those obtained with nasopharyngeal swabs and serum.