Ochsner Health and BioInfoExperts Complete First Genomic Sequences of COVID-19 from New Orleans
Scientists from BioInfoExperts LLC (BIE) and Ochsner Health have completed the first whole genome sequences of the SARS-CoV-2 coronavirus from the New Orleans area. By breaking down the virus to its most basic building blocks, researchers are one step closer to understanding viral spread across the state. One additional sequence originating from Baton Rouge has been released by the Centers for Disease Control.
Phylogenomic analysis revealed that the New Orleans and Baton Rouge genomes are closely related. The Louisiana genomes also group with other genomes mainly derived from the Northwest United States, highlighting the potential role of travel in the spread of COVID-19.
Using viral samples collected from COVID-19 infected patients in New Orleans, BIE and Ochsner teamed up to implement FoxSeq – a cloud-based software which uses bacterial genomes to track infection through a process called “Precision Epidemiology.” Based in Thibodaux, LA, BIE is funded to develop FoxSeq by the National Science Foundation Small Business Innovative Research Program.
“Together, our teams are utilizing high-throughput technology and advanced analytics that will enable us to better understand and treat COVID-19. Similarly to how Ancestry.com uses human DNA to find out where people come from, we are studying the building blocks or RNA of this specific virus to find out how it compares to the larger global epidemic,” said Susanna Lamers, CEO of BIE. “
After Ochsner research scientist Dr. Amy Feehan and Ms. Lamers met in February at a New Orleans BioInnovation Center event, and in considering the burgeoning pandemic, BIE quickly pivoted its existing technology in collaboration with Ochsner to better understand COVID-19 progression in critical care patients.
Unlocking the virus’ code provides researchers with a key puzzle piece needed to identify treatment therapies to help communities hit hard by the spread of COVID-19. In addition to experiencing some of the highest per-capita rates of COVID-19 infection, New Orleans has a high rate of comorbidities, including hypertension, diabetes and obesity, which are associated with significant health complications from COVID-19.
“Pathogen genomics is a powerful tool to learn how the viral epidemic evolved in our state and also how the virus impacts a patient’s innate microbial populations, which may be associated with immune failure,” said Lamers. “Researchers have found that many critical patients develop additional bacterial infections leading to pneumonia. There may be microbial markers present in those infected that will help identify which patients will progress to a more critical disease. New technologies and new ways to evaluate patients are required to understand the microbial landscape in patients, which may lead to novel therapies and testing strategies.”
Dr. Julia Garcia-Diaz, Director Clinical Infectious Diseases and Multispecialties Research at Ochsner Health added, “Through a rather phenomenal effort, our teams came together to launch this initiative. We have several strategies to generate predictive models, one of which will focus on viral quantification and genomics. This research can help us predict how COVID-19 may impact different patient populations, allowing us to treat patients with better targeted therapies.”
Dr. Garcia-Diaz and Dr. Feehan are the lead Ochsner researchers for this project. Key personnel at BIE include Mr. David Nolan, the pathogen sequencing expert for the BIE Laboratory at the University of Florida’s Sid Martin Biotech Incubator in Alachua, Florida, and Dr. Rebecca Rose, CTO at BIE who is responsible for FoxSeq technology development and data analytics. The sequences were generated on the Illumina NextSeq500 at the University of Florida’s Interdisciplinary Center for Biotechnology Research under the direction of Dr. David Moraga Amador.
Ochsner currently has more than 30 clinical studies and trials for COVID-19 treatment underway. Ochsner was the first organization in Louisiana to launch in-house testing capabilities in March. To learn more about Ochsner, please visit www.ochsner.org/coronavirus. To learn more about BIE, please visit www.bioinfox.com.
Phylogenetic tree and location of 239 SARS-CoV-2 genomes. Colored dots at branch tips represent samples colored by location of sample (according to map on right); branch lengths are scaled by genetic substitutions/site (scale bar at left). LA sequences in red.
BIE is funded through the National Science Foundation Small Business Innovative Research (NSF SBIR) program, also called, “America’s Seed Fund.” BIE’s historical focus technology is “bioinformatics,” which is a field of biology that uses computer technology to analyze large and complex biological data sets that can reveal global pathogen transmission patterns and dynamics of infectious diseases. In the SBIR program, they are developing a cloud-based information technology platform, called FoxSeqTM, that will be used in hospital infection control departments to identify infection sources.
About Ochsner Health
Ochsner Health is a system that delivers health to the people of Louisiana, Mississippi and the Gulf South with a mission to Serve, Heal, Lead, Educate and Innovate. Ochsner Health is a not-for-profit committed to giving back to the communities it serves through preventative screenings, health and wellness resources and partnerships with innovative organizations that share our vision. Ochsner Health healed more than 876,000 people from across the globe in 2019, providing the latest medical breakthroughs and therapies, including digital medicine for chronic conditions and telehealth specialty services. Ochsner Health is a national leader, named the top hospital in Louisiana and a top children’s hospital by U.S. News & World Report. As Louisiana’s leading healthcare educator, Ochsner Health and its partners educate thousands of healthcare professionals annually. Ochsner Health is innovating healthcare by investing in new technologies and research to make world-class care more accessible, affordable, convenient and effective. Ochsner's team of more than 26,000 employees and 4,500 providers are working to reinvent the future of health and wellness in the region. To learn more about Ochsner Health, please visit www.ochsner.org. To transform your health, please visit www.ochsner.org/healthyyou.