COVID-19 Genomics

The network is aggressively moving forward to collect, sequence, and analyze 10,000 viral RNA and host genomic DNA samples to begin this important work. We will work on joint projects in four areas where we can make meaningful contributions:

LARGE SCALE VIRAL SEQUENCING

This technology will be used to determine viral evolution and spread across the community. Such data can be used to infer important factors for epidemiological models such as how many introductions of the virus have occurred in a specific region and the number of unique clusters of transmission. These data will also provide insights to the number of undetected cases that are currently transmitting in the population.

WHOLE GENOME HOST DNA SEQUENCING

The high mortality rates for COVID-19 have predominantly been attributed to the elderly and those with pre-existing immune, cardiovascular, or lung diseases; however, one striking observation is respiratory failure in some otherwise healthy young individuals. Greater insight into the genetic makeup of these severely infected individuals may explain some aspects of extreme response to the virus, which may in turn guide risk mitigation, drug development, and treatment. The insights obtained could be impactful in the current pandemic and also inform future pandemics.

SINGLE CELL AND IMMUNE REPERTOIRE SEQUENCING

Single cell sequencing will provide insight into both innate and adaptive immune responses to virus infection, including how the immune systems of those diagnosed with COVID-19 respond to virus, helping to inform therapeutic approaches and vaccine development. It will also allow us to examine tissue responses and provide a genome variation of expression context for viral responses.

DATA COMMONS FOR DATA INTEGRATION AND SHARING

Sharing data and working collaboratively is key to enabling scientists to quickly analyze genetic samples along with clinical data. Establishing a data commons will make all data and research from the Network broadly available to the scientific community locally, nationally, and internationally, allowing for a multitude of different analyses to provide useful insights into the spread, distribution, and scale of the pandemic.

When the coronavirus pandemic began to spread globally, there was some relief in the initial evidence that children were largely unaffected. However, in early May reports began to surface of a mysterious illness linked to COVID-19 that causes life-threatening inflammation in children. Now known as multi-system inflammatory syndrome in children (MIS-C), this rare disease shares common features with other pediatric inflammatory conditions including Kawasaki disease and toxic shock syndromes. Early on, NYGC leadership moved to direct our expertise to better understand the syndrome and swiftly engaged with our research partners and New York State Governor Andrew Cuomo’s office.

On May 9^th, Governor Cuomo announced that the NYGC, in partnership with the New York State Department of Health (DOH) and The Rockefeller University, will investigate the possible genetic basis of this rare COVID-19 associated pediatric syndrome. Utilizing NYGC’s NYS DOH-approved clinical constitutional whole genome sequencing test, the study involves genomic sequencing of samples from affected children and their parents in New York and the surrounding region to determine if these patients share rare genetic variants in common that affect their response to the virus. Through previous genomic studies, several susceptibility genes have been implicated to have association with Kawasaki disease. Knowledge of susceptibility genes involved in the pathogenesis of MIS-C is expected to provide new insights into diagnosis and treatment of the disease. 

A central part of the investigation is our collaboration with Jean-Laurent Casanova, head of the St. Giles Laboratory of Human Genetics of Infectious Diseases at The Rockefeller University, who has established an international consortium directed toward studying exceptional cases of COVID-19. Our research partnership will extend beyond our efforts in New York and New Jersey to include researchers around the world with the hope of increasing the statistical significance and confidence behind any finding.

Scientists agree that the most effective way to prevent infection is by breaking the chains of transmission.  This means that we must have more testing availability, followed by isolation and contract tracing. In addition to our COVID-19 research, NYGC also is helping local efforts to make testing more accessible by performing NYS DOH-approved diagnostic testing for SARS-CoV-2 in our clinical lab. Working together with Renegade Bio to implement the testing, we are now able to process 1,500 tests a day and gearing up to triple that number.