COVID-19 Research at the CDI
An Update from Dr. David Perlin, the CDI’s chief scientific officer
The CDI was formally established in May 2019 with a fundamental mission to conduct “science with clinical impact” by translating in real-time insights from molecular and cellular science to improve patient outcomes, especially in cancer and infectious diseases. CDI science is guided by unmet medical need and is intended to address clinical urgency. There has been no greater threat to patient and community health than COVID-19 and CDI’s scientists and staff members, including experts in global infectious diseases, embraced this unprecedented challenge. They have played a critical role in impacting clinical care through development of novel diagnostics, improved antiviral therapy, and support of numerous clinical trial regimens. CDI scientists are also studying the biology and genomics of the SARS-CoV-2 virus, host factors that impact disease progression, and discovery and development of novel drug candidates. These programs have resulted in more than 20 publications and attracted more than $12 million in research support for CDI scientists with numerous grants pending.
Rapid Molecular Testing of Virus. Yanan Zhao, M.D., Ph.D., and David Perlin, Ph.D., developed a highly accurate molecular assay for the rapid detection of COVID-19, which captured the best detection elements of tests developed by the CDC and WHO. This novel test was implemented in the Clinical Laboratory Improvement Amendments (CLIA)-approved high complexity molecular laboratory at Hackensack University Medical Center. It was approved for use with patients on March 12, 2020 by the NJ Department of Health under the FDA Emergency Use Authorization for COVID-19. Importantly, at the time, implementation of this test reduced delays in reporting sample results from 5-7 days to just a few hours, and it proved critical to diagnose and properly triage critically ill patients. Most prominently, it allowed emergency staff to triage patients more effectively by mobilizing the critical care infrastructure, especially negative-pressure isolation rooms, and helping healthcare professionals manage patients safely. It was the first rapid test to be approved and implemented by a hospital system in New Jersey during the pandemic. The test, which was licensed to T2 Diagnostics, has now been used to diagnose more than hundreds of thousands of hospitalized patients. This rapid bench-to-bed approach, which involved molecular assay development, test validation, implementation and operationalization, was a team effort between CDI scientists, David Chow, M.D., (Pathology and CDI) and members of the HUMC molecular lab. In addition to the clinical lab staff, more than a dozen CDI researchers volunteered to help run the test in the hospital. The test was licensed for commercial development to T2 Diagnostics. The media covered the developments:
- CNBC: “Hackensack Meridian Health on its Coronavirus Test”
- Yahoo Finance: “Hackensack Meridian Health Center’s David Perlin discusses effectively diagnosing COVID-19”
- The Record: “New coronavirus test at Hackensack Meridian sites across NJ can get results in hours”
- The announcement of the T2 licensing agreement
Rapid Evaluation of Virus Variants. A hallmark of SARS-Co-V2 has been the evolution of the virus in response to the human immune system resulting in virus variants that show enhanced transmissibility and ability to evade primary antibody therapies and escape vaccine action. Tracking the spread of these emerging virus variants in our region has important clinical and epidemiological consequences for the patients, hospitals, and public health authorities. The “gold standard” for assessing virus variants is genomic sequencing of its RNA. But this is a cumbersome, long (>22 hours) and expensive process. To accelerate the detection of virus variants,
Dr. Yanan Zhao developed a rapid, high throughput molecular detection system that could reliably identify major circulating virus variants in less than 2 hours. In partnership with Quest Diagnostics, it was possible to capture in real time a comprehensive picture of virus variants infected HMH hospitalized patients and more broadly epidemiology trends in the State, which were reported to the NJ Department of Health. The CDI team members Jose Mediavilla, Annie Lee, Elizabeth Titova, Veronica Kan, Liang Chen, Ph.D., David Perlin, Ph.D., and Barry Kreiswirth, Ph.D. have profiled nearly ten thousand virus variants and in partnership with the NYGC and NJDOH have subsequently sequenced many thousands looking at detailed virus evolution in the NJ population.
Convalescent Therapy Program (CTP). For most COVID-19 patients, successful clinical outcome requires control of viral replication and prevention or control of destructive inflammatory responses (cytokine storm) that may arise following tissue damage. In the early phase of the pandemic, the lack of an effective and reliable antiviral agent led to the use of convalescent therapy to control viral replication. This classical approach to control infection in the absence of an effective treatment has been used in recent decades to treat infections in patients due to Ebola, SARS-CoV-1, MERS, and now SARS CoV-2. The basic principle is that patients who recover from infection do so because they mount a strong antibody response that ‘neutralizes’ the infecting pathogen. These neutralizing antibodies can be measured in the serum of blood from recovered patients and are presumed to kill or block the pathogen from further damage to the body. This killing potential, and in the case of SARS-CoV-2 antiviral activity can be transferred from a recovered donor in the form of blood plasma by transfusing a seriously ill patient to help the body fight off the disease. This type of antiviral therapy is safe, but its efficacy very much depends on clinical disease manifestation, the antiviral potential of antibodies in the transferred plasma, and the status of the host immune system. One problem with this approach is that we don’t know what the correct threshold level is for a successful clinical outcome, as each recovered patient/donor mounts a different antibody response in terms of quantity and antiviral potency.
Our approach has been to attack the problem of antiviral therapy as we would drug treatment for any infectious agent. The drug must be delivered to the site of infection at the appropriate drug level and potency for a sustainable duration to have a successful outcome. Many drugs fail in clinical trials because they are not properly dosed to reach this target level. To address this treatment principle for our patients, Michele Donato, M.D., at Hackensack Meridian Health’s John Theurer Cancer Center, and CDI’s David Perlin, Ph.D. developed an alternative protocol that maximizes the amount and potency of antiviral antibodies delivered to each patient. The protocol was approved under an Investigational New Drug (IND) designation from the FDA.
- Frequently Asked Questions about Convalescent Plasma
- The New York Times: “He Beat Coronavirus. Now His Blood May Help Save Lives.”
- 60 Minutes: “Inside a Convalescent Plasma Therapy Program Treating Coronavirus Patients”
A key component of this therapy is the identification of recovered patients/donors with high titers of neutralizing antibodies that kill or disable the virus. The CDI screening program, led by David Perlin, Ph.D. and Steven Park, has been actively evaluating potential donors by performing a detailed assessment of Immunoglobin G (IgG) and Immunoglobin M (IgM) antibodies to identify the best donors for Convalescent Plasma therapy trials. We evaluated >1100 donors who were observed with a range of titers from weak or no antibody responses to highly neutralizing IgG at dilutions exceeding 1:10:000 and some >1:50,000.
In this program, we were looking for a subset of donors with supra-high levels of neutralizing antibodies based initially on titers directed against the SARS-CoV-2 Spike receptor binding domain (RBD) region. This initial screening work was greatly aided by the support of colleagues from the group of Dr. Florian Krammer at the Mount Sinai School of Medicine. Once high-titer sera was identified, we performed detailed antibody neutralization (protection) assays in a cytopathic virus challenge assay involving high exposures of SARS-CoV-2 with susceptible cells under biosafety level 3 (BSL-3) containment.
This pilot approach was highly successful and resulted in nearly 90% success in preventing hospitalized patients in the ICU from progressing to more severe disease requiring mechanical ventilation. This promising result led to a $5.5 million grant to pursue this approach more broadly.
Advancing COVID-19 Science
Drug Discovery. Pharmaceutical, biotech companies and academic discovery groups have partnered with CDI to develop new drug candidates against COVID-19, and other coronaviruses. Utilizing a semi-automated SARS-CoV-2 viral cytopathic screening assay that mimics viral infection of host cells in our Biosafety Level 3 lab suite, David Perlin, Ph.D. and Steven Park in partnership with Merck, other Pharma and Biotechs, and academic labs have evaluated more than 1500 compounds representing approved drugs, drug candidates in late-stage clinical development as antivirals, and as well as new chemical classes. The most promising compounds were profiled in animal pharmacodynamic animal models of infection to determine their potential suitability for human application. This work was partially funded by an NIH Center of Excellence in Translational Research (CETR) focused on novel anti-infective development.
Biorepository (Bio-R). It was recognized at the earliest stage of the COVID-19 epidemic that organized collection and processing of biological specimens from hospitalized patients linked to clinical data would be essential to understand this disease. The Bio-R, led by David Chow, M.D. and Ya’el Kramer, has been diligently collecting thousands of specimens from patients after obtaining informed consent for those specimens to be used for research purposes. Basic categories of patient specimens based on clinical disease states have been collected and include patients who were hospitalized, critically-ill and in the ICU with or without mechanical ventilation. Specimen types include: nasal and oropharyngeal swabs, extracted nucleic acid, blood, serum, respiratory fluids, stool and indwelling devices. The hard work of consenting and collecting specimen has been performed by the Bio-R team, the team of Chinwe Ogedegbe, M.D., group in the Emergency Department at HUMC and Marygrace Zetkulic, M.D., and Medical Residents within the HUMC ICU. The BioR has consented nearly 2,900 COVID patients and collected and cataloged >73,000 specimens.
Genomics and Beyond. The CDI has partnered with the New York Genome Center (NYGC) as part of a large consortium of mostly New York metropolitan area universities and hospitals. The objective is to share data in real-time about emerging science related to COVID-19, and to exploit genomics and genetic sequencing to explore key questions of virus microevolution, host susceptibility and disease progression. In addition, we are exploring the impact of the microbiome and the adipome on COVID-19, and opportunistic bacterial and fungal infections in COVID-19 patients.
Specific CDI programs include:
- Large scale full-length viral sequencing to determine viral evolution, molecular epidemiology of outbreaks, spread across the community and within individual patients (e.g. oral, nasal, lung, GI tract) Barry Kreiswirth, Ph.D., and Liang Chen, Ph.D.
- Whole-genome germline sequencing and immune repertoire sequencing of affected individuals, focused on extreme phenotypes to examine host factors and immune responses – Benjamin Tycko, M.D., Ph.D.
- Lung and GI tract microbiome of disease cohorts – Rena Feinman, Ph.D.
- Evaluation of secondary bacterial and fungal infections in COVID-19 patients – Barry Kreiswirth, Ph.D. and Milena Kordalewska, Ph.D.
- Assessment of exosomes and microRNA populations in COVID-19 patients –Olivier Loudig, Ph.D., and Meghan Mitchell, Ph.D.
- Role of adipocytes in harbor SARS-CoV-2 as an unexplored virus reservoir and promoter of cardiovascular disease – Jyothi Nagajyothi, Ph.D.
- Clinical evaluation of anti-LIGHT monoclonal antibody, novel drug candidate, in COVID-19 acute respiratory distress syndrome- David Perlin, PhD and Avalo Therapeutics
- Randomized, double-blind, controlled trial of human anti-LIGHT monoclonal antibody in COVID-19 acute respiratory distress syndrome.
Perlin DS, Neil GA, Anderson C, Zafir-Lavie I, Raines S, Ware CF, Wilkins HJ.J Clin Invest. 2021 Dec 6:e153173. doi: 10.1172/JCI153173. Online ahead of print.PMID: 34871182
- Postvaccination SARS–COV–2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study.
Mathema B, Chen L, Chow KF, Zhao Y, Zody MC, Mediavilla JR, Cunningham MH, Composto K, Lee A, Oschwald DM, Germer S, Fennessey S, Patel K, Wilson D, Cassell A, Pascual L, Ip A, Corvelo A, Dar S, Kramer Y, Maniatis T, Perlin DS, Kreiswirth BN.Microbiol Spectr. 2021 Dec 22;9(3):e0188221. doi: 10.1128/Spectrum.01882-21. Epub 2021 Nov 17.PMID: 34787439
- Elevated cytokines and chemokines in peripheral blood of patients with SARS–CoV–2 pneumonia treated with high-titer convalescent plasma.
Fanning SL, Korngold R, Yang Z, Goldgirsh K, Park S, Zenreich J, Baker M, McKiernan P, Tan M, Zhang B, Donato ML, Perlin DS.PLoS Pathog. 2021 Oct 29;17(10):e1010025. doi: 10.1371/journal.ppat.1010025. eCollection 2021 Oct.PMID: 34714894
- Sepsis leads to lasting changes in phenotype and function of memory CD8 T cells.
Jensen IJ, Li X, McGonagill PW, Shan Q, Fosdick MG, Tremblay MM, Houtman JC, Xue HH, Griffith TS, Peng W, Badovinac VP.Elife. 2021 Oct 15;10:e70989. doi: 10.7554/eLife.70989.PMID: 34652273
- Emergence of Multiple SARS–CoV–2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment.
Chen L, Zody MC, Di Germanio C, Martinelli R, Mediavilla JR, Cunningham MH, Composto K, Chow KF, Kordalewska M, Corvelo A, Oschwald DM, Fennessey S, Zetkulic M, Dar S, Kramer Y, Mathema B, Germer S, Stone M, Simmons G, Busch MP, Maniatis T, Perlin DS, Kreiswirth BN.mSphere. 2021 Aug 25;6(4):e0048021. doi: 10.1128/mSphere.00480-21. Epub 2021 Aug 25.PMID: 34431691
- Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID–19 Patients.
Kordalewska M, Guerrero KD, Garcia-Rubio R, Jiménez-Ortigosa C, Mediavilla JR, Cunningham MH, Hollis F, Hong T, Chow KF, Kreiswirth BN, Perlin DS.J Fungi (Basel). 2021 Jul 11;7(7):552. doi: 10.3390/jof7070552.PMID: 34356931
- Mechanistic Analysis of Age-Related Clinical Manifestations in Down Syndrome.
Chen XQ, Xing Z, Chen QD, Salvi RJ, Zhang X, Tycko B, Mobley WC, Yu YE.Front Aging Neurosci. 2021 Jul 1;13:700280. doi: 10.3389/fnagi.2021.700280. eCollection 2021.PMID: 34276349
- Pervasive but Neglected: A Perspective on COVID–19-Associated Pulmonary Mold Infections Among Mechanically Ventilated COVID–19 Patients.
Ghazanfari M, Arastehfar A, Davoodi L, Yazdani Charati J, Moazeni M, Abastabar M, Haghani I, Mirzakhani R, Mayahi S, Fang W, Liao W, Nguyen MH, Perlin DS, Hoenigl M, Pan W, Hedayati MT.Front Med (Lausanne). 2021 Jun 14;8:649675. doi: 10.3389/fmed.2021.649675. eCollection 2021.PMID: 34195207
- Extracellular Vesicle Capture by AnTibody of CHoice and Enzymatic Release (EV-CATCHER): A customizable purification assay designed for small-RNA biomarker identification and evaluation of circulating small-EVs.
Mitchell MI, Ben-Dov IZ, Liu C, Ye K, Chow K, Kramer Y, Gangadharan A, Park S, Fitzgerald S, Ramnauth A, Perlin DS, Donato M, Bhoy E, Manouchehri Doulabi E, Poulos M, Kamali-Moghaddam M, Loudig O.J Extracell Vesicles. 2021 Jun;10(8):e12110. doi: 10.1002/jev2.12110. Epub 2021 Jun 3.PMID: 34122779
- A novel diagnostic test to screen SARS–CoV–2 variants containing E484K and N501Y mutations.
Zhao Y, Lee A, Composto K, Cunningham MH, Mediavilla JR, Fennessey S, Corvelo A, Chow KF, Zody M, Chen L, Kreiswirth BN, Perlin DS.Emerg Microbes Infect. 2021 Dec;10(1):994-997. doi: 10.1080/22221751.2021.1929504.PMID: 33977858
- Candidemia among Iranian Patients with Severe COVID–19 Admitted to ICUs.
Arastehfar A, Shaban T, Zarrinfar H, Roudbary M, Ghazanfari M, Hedayati MT, Sedaghat A, Ilkit M, Najafzadeh MJ, Perlin DS.J Fungi (Basel). 2021 Apr 8;7(4):280. doi: 10.3390/jof7040280.PMID: 33917967
- Diagnosis, clinical characteristics, and outcomes of COVID–19 patients from a large healthcare system in northern New Jersey.
Zhao Y, Cunningham MH, Mediavilla JR, Park S, Fitzgerald S, Ahn HS, Li X, Zhan C, Hong T, Munk G, Chow KF, Perlin DS.Sci Rep. 2021 Feb 23;11(1):4389. doi: 10.1038/s41598-021-83959-7.PMID: 33623090
- Clinical and laboratory evaluation of patients with SARS–CoV–2 pneumonia treated with high-titer convalescent plasma.
Donato ML, Park S, Baker M, Korngold R, Morawski A, Geng X, Tan M, Ip A, Goldberg S, Rowley S, Chow K, Brown E, Zenreich J, McKiernan P, Buttner K, Ullrich A, Long L, Feinman R, Ricourt A, Kemp M, Vendivil M, Suh H, Balani B, Cicogna C, Sebti R, Al-Khan A, Sperber S, Desai S, Fanning S, Arad D, Go R, Tam E, Rose K, Sadikot S, Siegel D, Gutierrez M, Feldman T, Goy A, Pecora A, Biran N, Leslie L, Gillio A, Timmapuri S, Boonstra M, Singer S, Kaur S, Richards E, Perlin DS.JCI Insight. 2021 Mar 22;6(6):e143196. doi: 10.1172/jci.insight.143196.PMID: 33571168 Clinical Trial.
- Little to no expression of angiotensin-converting enzyme-2 on most human peripheral blood immune cells but highly expressed on tissue macrophages.
Song X, Hu W, Yu H, Zhao L, Zhao Y, Zhao X, Xue HH, Zhao Y.Cytometry A. 2020 Dec 6. doi: 10.1002/cyto.a.24285. Online ahead of print.PMID: 33280254
- COVID–19-Associated Candidiasis (CAC): An Underestimated Complication in the Absence of Immunological Predispositions?
Arastehfar A, Carvalho A, Nguyen MH, Hedayati MT, Netea MG, Perlin DS, Hoenigl M.J Fungi (Basel). 2020 Oct 8;6(4):211. doi: 10.3390/jof6040211.PMID: 33050019 Review.
- Rapid and quantitative detection of SARS–CoV–2 specific IgG for convalescent serum evaluation.
Tan X, Krel M, Dolgov E, Park S, Li X, Wu W, Sun YL, Zhang J, Khaing Oo MK, Perlin DS, Fan X.Biosens Bioelectron. 2020 Dec 1;169:112572. doi: 10.1016/j.bios.2020.112572. Epub 2020 Sep 3. PMID: 32916610
- Levels of the TNF-Related Cytokine LIGHT Increase in Hospitalized COVID–19 Patients with Cytokine Release Syndrome and ARDS.
Perlin DS, Zafir-Lavie I, Roadcap L, Raines S, Ware CF, Neil GA.mSphere. 2020 Aug 12;5(4):e00699-20. doi: 10.1128/mSphere.00699-20.PMID: 32817460
- Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID–19.
Jiang M, Pan W, Arasthfer A, Fang W, Ling L, Fang H, Daneshnia F, Yu J, Liao W, Pei H, Li X, Lass-Flörl C.Front Cell Infect Microbiol. 2020 Jun 16;10:331. doi: 10.3389/fcimb.2020.00331. eCollection 2020.PMID: 32626666
- COVID–19 Associated Pulmonary Aspergillosis (CAPA)-From Immunology to Treatment.
Arastehfar A, Carvalho A, van de Veerdonk FL, Jenks JD, Koehler P, Krause R, Cornely OA, S Perlin D, Lass-Flörl C, Hoenigl M.J Fungi (Basel). 2020 Jun 24;6(2):91. doi: 10.3390/jof6020091.PMID: 32599813 Review.