COVID-19 Research at the CDI

COVID-19 News 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.

Clinical Support

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:

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.

CNN: “Meet the Doctor Who Hunts New COVID-19 Variants”

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.

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.

Yahoo Finance: “Hackensack Meridian Health Awarded $5.5 Million by Department of Defense to Continue Convalescent Plasma Work for COVID-19”

JCI Insight: “Clinical and laboratory evaluation of patients with SARS-CoV-2 pneumonia treated with high-titer convalescent plasma”

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


  • Emergence of Multiple SARSCoV2 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
  • Clinical and laboratory evaluation of patients with SARSCoV2 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.