Gian Sepulveda, PhD Candidate
Five days away from his PhD dissertation defense date, GMS doctoral candidate Richard Giadone spent early mornings in the lab to optimize and adapt CDC and WHO COVID-19 testing protocols for use at Boston Medical Center (BMC).
Under the supervision of his PI, Dr. George Murphy at the BU Center for Regenerative Medicine (CReM), and in collaboration with labs from the Broad Institute and the BU/BMC Department of Pathology and Laboratory Medicine, the team optimized methods for viral inactivation, viral RNA extraction, and quantitative PCR. The test is designed to detect two nucleocapsid genes, N1 and N2, from SARS-CoV-2, the virus responsible for the pandemic which affected more than a million people worldwide. Using an R-script to extract data from the qPCR machine, an algorithm developed by the CReM team calls whether the sample is positive, negative, or inconclusive.
The hardest part of developing the test was translating the standards of a basic research setting to the rigid requirement of the clinical realm, while simultaneously ensuring that all results are reported accurately and in a timely manner. The CReM testing platform went through multiple clinical validation steps, including a verification of 30 positive and 30 negative samples provided by the state. Though it is typical to use a viral RNA extraction kit, dwindling supplies pushed the team to adapt broad use RNA extraction kits, most of which have been donated by the BU and GMS research community. What started out in the Murphy Lab at the CReM, eventually became a collective effort across the entire BU Medical Campus. As more and more people joined in the cause, more structure had to be set in place and they had to find a way to make things run smoothly despite variations in people’s scientific backgrounds. “It was cool to see people from BU that you see in passing, and you see them coming in carrying all these mini kits. It was cool seeing everybody pitch in and doing what they can,” Richard said.
Collaborators in the BU/BMC Pathology and Laboratory Medicine department are implementing commercial kits. Assistant Professor Liz Duffy, the Master’s in Pathology Program Director, mentioned that there are two commercial COVID-19 testing platforms in their department. One is a rapid test and another is an automated high throughput machine that heat inactivates the samples before putting them through a thermocycler. The latter system is interfaced with the BMC medical record system but has a slower turnaround time compared to the CReM platform. According to Prof. Duffy, having these three platforms allows them to better assign a patient to a test depending on how quickly the results need to be received.
Prof. Duffy also is responsible for the regulatory affairs in the department and played a leading role in filing the Emergency Use Authorization (EUA) required for the CReM test. The EUA gives authorization for the COVID-19 test, stating that it is valid and can be used to test patient samples. She played a vital role in writing up the documents to the FDA regarding validation and making sure that the test is compliant with required guideline standards.
Though the platforms are now up and running, Prof. Duffy mentioned that the testing kits for sampling patients, which include a tube of viral transport media and a nasopharyngeal swab, are now in dwindling supply. She teamed up with interim GMS Associate Dean and Associate Professor of Pathology, Dr. Deborah Stearns-Kurosawa and Assistant Professor of Medicine, Dr. Sarah Mazzilli, to prepare viral transport media in-house.
“As Pathology has put forth efforts to procure the nasopharyngeal swab, our group has focused on making the needed viral transport media” said Dr. Mazzilli. She has been collaborating closely with Prof. Duffy and members of the Department of Pathology to expand the utility of the Biospecimen Repository at BMC. Following a CDC protocol, their team created 20 liter batches of sterile media and with the support of over 20 GMS PhD student volunteers, they aliquoted the viral transport media into over 10,000 sterile tubes ready to be deployed for testing in the hospital.
In discussing her motivation to involve her lab to aid in these efforts, Dr. Mazzilli said “Everyone in the BU and BMC community is doing what they can for this effort. The biggest highlight for me is the opportunity to be part of this team, where people are coming together that may not normally work together, and highlighting the strength our community has when we do so”
Though the initial weeks of craziness for test and kit production are behind them, these scientists are not done with their work to combat COVID-19. Prof. Duffy, who runs the Biospecimen Repository, has been busy in coordinating the research requests for blood and nasopharyngeal samples that will allow COVID-19 research to continue. “[This experience] has been amazing. It has really restored a lot of faith in humanity to see the way that everyone has come together and put all of their genius together to make sure that we get through this,” she said.
After successfully defending his dissertation, Richard is advancing the test and trying to multiplex it to have a one-step RT-qPCR reaction with multiple probes to increase sensitivity and increase the number of samples they will be able to run.
“Everybody cannot do everything, everyday,” said Richard. It is with this mentality that scientists all over BU and nearby institutions have collaborated and delegated tasks in a noble effort to combat the urgent need for COVID-19 testing, all the while putting their immediate work aside and their lives at potential risk.
If you would like to donate supplies to this effort, please contact Liz Duffy, firstname.lastname@example.org, 617-358-2677 or drop off supplies at 670 Albany St., 4th floor.
Abbreviations: Boston University (BU), Centers for Disease Control (CDC), World Health Organization (WHO), Center for Regenerative Medicine (CReM); Boston Medical Center (BMC; the teaching hospital for BU School of Medicine), Graduate Medical Sciences (GMS; Master’s and PhD academic and research community in the School of Medicine).
Kim Vanuytsel, PhD – Research Assistant Professor of Medicine, Murphy Lab, Section of Hematology/Oncology
George Murphy, PhD- Co-Director- CReM, Associate Professor Medicine, Director of Research, Section of Hematology/Oncology
Richard Giadone – PhD Candidate, Murphy Laboratory, CReM, Molecular and Translational Medicine
Nancy Miller, MD- Chief and Vice Chair Laboratory Medicine, Clinical Microbiology and Molecular Diagnostics; Associate Professor of Pathology and Laboratory Medicine, BUSM & BMC
Beverly Orr, MT (ASCP) – Operations Director for Pathology & Laboratory Medicine, BMC
Todd Dowry – Laboratory Manager, Murphy Laboratory, CReM
Christopher Andry, PhD – Chief and Chair, Department of Pathology & Laboratory Medicine, Professor of Pathology & Laboratory Medicine and Family Medicine, BUSM & BMC
Anthony Yeung – MD/PhD Candidate, Murphy Laboratory, CReM, Molecular and Translational Medicine
Greg Miller, PhD – Laboratory/Operations Manager, CReM
Rhiannon Werder, PhD – Postdoctoral Fellow, Wilson Laboratory, CReM
Aditya Mithal – MD/PhD Candidate, Mostoslavsky Laboratory, CReM, Department of Microbiology