The United States just passed a very ominous milestone in the COVID-19 pandemic. As almost every state struggles to contain a dramatic rise in COVID-19 cases, the United States has now lost more than 250,000 people to this virus. The abject incompetence and dereliction of duty at the federal government level notwithstanding, the scientific and medical communities are working tirelessly to understand the virus and develop effective treatments and vaccines. One company, Adaptive Biotechnologies is approaching the problem from a unique angle and harnessing the power of Microsoft Azure to help them.
Focusing on T Cells
From the beginning of the COVID-19 pandemic, there has been a focus on antibodies. Doctors and scientists want to understand what the immune response is to a COVID-19 infection and how the body creates the antibodies to fight it. That information is also an essential element of developing an effective vaccine—since the purpose of the vaccine is to induce your body to create those same antibodies to guard against the virus.
Antibodies can also help determine who has already been exposed or previously had COVID-19. However, antibodies in the system wane over time, and studies of COVID-19 have found that there are also many instances where people who tested positive for COVID-19 never developed enough antibodies to be detectable. Adaptive Biotechnologies researchers have found that this may be the result of different immune cells, T cells, fighting off the infection before the antibodies are developed.
A blog post from Adaptive Biotechnologies explains, “The study also found that T-cell response differed and was considerably higher in individuals with greater disease severity, whereas there was no correlation between disease severity and antibody levels in these recovered patients. Taken together, these data add to the growing body of evidence that T cells are critical in understanding our immunity to the novel coronavirus.”
The Adaptive Biotechnologies research focuses on T cell receptors (TCRs) and B cell receptors (BCRs). Adaptive has built a platform that sequences these receptors, maps the TCRs to the antigens to which they bind, and can characterize TCRs and BCRs to identify the ones that are the most promising therapeutically.
Based on the research they have done; Adaptive Biotechnologies is also bringing the first T cell diagnostic through the FDA. The T-Detect COVID test has outperformed commercial antibody testing as an indicator of past SARS-CoV-2 infection, with 99.8% specificity.
The Power of Microsoft Azure
One of the silver linings of the explosive spread of the COVID-19 pandemic is that there is virtually unlimited data to aggregate and parse. Processing all of that data takes a powerful platform, and that is where Microsoft Azure comes in.
Erin Chapple, Corporate Vice President for Azure Compute at Microsoft, told me that the partnership between Adaptive and Microsoft—and leveraging Azure Cloud—is essential. The process is managed on Azure end-to-end. Clinicians and researchers submit samples, which are processed to generate sequencing data. The data is sent to a bio informatics pipeline running on Azure virtual machines (VMs), and processed on a data science workbench running on Azure Kubernetes Service (AKS). Having the processing and data in Azure also makes it accessible to various teams regardless of where they are located in the world and facilitates collaboration.
I had an opportunity to speak with Julie Rubinstein, President of Adaptive Biotechnologies. She told me that they needed a partner with world class machine learning (ML), artificial intelligence (AI) and cloud computing capabilities. They selected Microsoft Azure a few years ago because they felt that Microsoft shared a similar vision for how to generate large scale genetic information and use it for practical clinical purposes.
Mark Adams, Chief Technical Officer for Adaptive Biotechnologies, shared in a Microsoft customer case study on Adaptive Biotechnologies, “We use Azure cloud computing resources and machine learning capabilities to power our immune medicine platform, so we can rapidly map the adaptive immune system to the many different diseases it recognizes. Armed with this map, we can develop novel diagnostics for diseases, including COVID-19, and fuel the next generation of diagnostics.”
Microsoft Azure allows Adaptive to apply machine learning to exponentially accelerate their ability to extract insights from the immune medicine platform. The scalability of Azure enables them to computationally map trillions of TCRs to millions of disease-specific antigens. Ultimately, the efforts of Adaptive Biotechnologies, combined with the power of Microsoft Azure may potentially enable new approaches to diagnose disease earlier and more accurately than is possible today.
Things don’t look so great right now—especially in the United States. With new record levels of cases and deaths from COVID-19 almost every day, the holiday season is not going to be as joyous as it is most years. However, there are promising breakthroughs on the vaccine front, and work like this research from Adaptive Biotechnologies that will help us get this under control soon.
In the meantime, stay home if you can. Limit your interaction outside of your own family. Wear a mask, social distance, and wash your hands.