Jacobs School researchers collecting COVID-19 data

Researchers in the Jacobs School of Medicine and Biomedical Sciences continue to spearhead a number of projects related to the COVID-19 global health pandemic.

Peter L. Elkin, professor and chair of biomedical informatics, says several current studies are focused on data collection that can be used to better understand how to combat COVID-19.

Much of the work is being completed through the Clinical and Translational Science Awards (CTSA) consortium, of which UB is a member. It is one of more than 50 medical research institutions across the nation currently receiving CTSA program funding from the National Institutes of Health.

One such project is the launch of the National COVID Cohort Collaborative (N3C), a joint program between the National Center for Data to Health and the National Center for Advancing Translational Sciences.

Elkin says the project’s aim is to build a warehouse of COVID-19 data for the entire CTSA consortium and for other interested contributing health care organizations.

“This is intended to hold all patient data (inpatient and outpatient) on COVID-tested patients from all of the CTSA hubs,” he says. “It entails a cloud-based method for data collection on the COVID-19 pandemic.

“We are working closely with N3C to see how this can be designed and implemented in a standardized and timely fashion.

“The goal of developing a national-level COVID-19 database is to facilitate research and improve recruitment to clinical trials,” he says.

N3C is looking to address the many difficult questions raised by the COVID-19 global emergency, such as:

• Who is infectious?
• Who may need hospital care and at what level?
• What are the key risk factors?
• What are the best prognostic indicators?
• What are best practices for ethical resource allocation?
• Which drugs are the most viable candidates for patients?

UB is also a member of COMBATCOVID, a New York State initiative to save case report forms on all hospital admissions for upper respiratory infections, including all patients tested for COVID-19 or patients who are suspected to have COVID-19.

The statewide consortium will collect and analyze the results from all the CTSA institutions in the state.

“It is being run out of New York University, and I am participating from our site as our CTSA informatics core director,” Elkin says. “I am working on the design and data governance.

“The data use agreements are being signed, and the database design and data definitions are being built,” he adds. “This larger row-level dataset will allow us to ask questions that would not be possible at any one institution.”

In UB’s Department of Biomedical Informatics, Elkin and Frank D. LeHouillier, senior programmer and analyst, are involved in the project.

Clinical researchers in the Jacobs School who are involved include:

• Omar S. Alibrahim, clinical associate professor of pediatrics and chief of the Division of Critical Care.
• Teresa R. Hennon, clinical assistant professor of pediatrics in the Division of Allergy/Immunology and Rheumatology.
• Mark D. Hicar, assistant professor of pediatrics in the Division of Infectious Diseases.
• Manoj J. Mammen, associate professor of medicine in the Division of Pulmonary, Critical Care and Sleep Medicine.
• Timothy F. Murphy, SUNY Distinguished Professor of medicine in the Division of Infectious Diseases and senior associate dean for clinical and translational research.
• Sanjay Sethi, professor of medicine and chief of the Division of Pulmonary, Critical Care and Sleep Medicine.

Researchers in the Department of Biomedical Informatics have also developed a validated microbiome platform that finds infected persons with COVID-19 — whether symptomatic or not — using deep sequencing of stool microbiome samples.

Elkin is working with postdoctoral associate Sapan Mandloi in using a National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to collect and process metagenomics data for the organism classified as “human gut metagenome.”

The more than 300,000 samples are divided into 3,464 projects, according to Mandloi.

“We are performing comparison of all samples’ raw sequences with SARS-Cov-2 genome using a NCBI SRA Taxonomy Analysis Tool (STAT), which utilizes precomputed k-mer dictionary databases and gene-specific profiling,” Mandloi says. “This allows us to perform geographic mapping of samples identified across the world.”

Some 9,720 samples were identified as potential cases of colonization for COVID-19, which were mostly from the U.S., China, Australia and the U.K., he adds.

“The ability to identify and track this trafficking of genetic material is vital as a public health topic,” he says. “As of now, this large pool of genetic data remains largely untapped for clinical surveillance using the combined strategy of gene-based profiling and k-mer-based classification on raw genomic data.”