AWS Diagnostic Development Initiative helps nonprofits harness the cloud to research and combat COVID-19

Nonprofits play a vital role in improving quality of life for individuals worldwide. At no time has this been more evident than over the last year. COVID-19 has created extraordinary demand for nonprofit services and these organizations are stepping up to make a meaningful impact in their communities, even as the pandemic takes a massive toll on their own operations.

One subset of the sector doing crucial work behind the scenes is nonprofit research organizations. These institutions are using science and technology to better understand the virus, speed diagnostics, develop new, innovative testing methods, and more.

Solving these types of large scientific problems requires researchers to have access to massive computing power, which can sometimes be unattainably expensive for resource-strapped nonprofits. AWS understands the crucial role that nonprofit research institutions play in improving public health overall. That’s why we’ve helped multiple nonprofit research organizations advance their COVID-19 research through our Diagnostic Development Initiative, first launched in March 2020. Through this initiative, AWS committed $20 million over two years in computing credits and customized expertise from the AWS Professional Services team to support customers using the cloud to drive diagnostic innovations.

The next round of funding opens today. As we launch the next phase, we are excited to broaden the AWS Diagnostic Development Initiative’s scope and distribute the remaining $12 million this year. Starting today, we are expanding the scope to three new areas in addition to diagnostics: 1) early disease detection to identify outbreaks at the individual and at the community level, 2) prognosis to better understand disease trajectory, and 3) public health genomics to bolster viral genome sequencing worldwide. While AWS will prioritize COVID-19 projects, we will also evaluate projects focused on other infectious diseases. We will accept applications through the end of the year, with priority consideration given to applications received before July 31. Interested organizations can apply here.

Following are a few examples of the nonprofit research projects supported by the AWS Diagnostic Development Initiative.

Institute for Systems Biology uncovers diagnostic clues in blood samples

The Institute for Systems Biology (ISB) is uncovering clues about how COVID-19 can present in individuals and why those infected with COVID-19 have drastically different outcomes.

The nonprofit’s COVID-19 Immune Response Study examined serial blood draws from 139 COVID-19 patients of all severities. Researchers used novel computational methods powered by AWS to merge data together to provide an integrated view of COVID-19 infection during the week following initial diagnosis. They found that mild COVID-19 cases produce a very distinct immune response compared to moderate or severe forms of disease. In moderate and severe COVID-19 cases, ISB discovered that inflammation caused by the virus promoted a stronger immune response—while at the same time key nutrients in the blood required for building that response were depleted. This leads to unusual and dysfunctional immune responses. Understanding COVID impacts based on these characteristics can help future diagnoses that include information on expected disease progression and expected severity of outcomes for the patient. ISB has now expanded their study to over 300 patients, including a study of the phenomena of long COVID – a condition wherein people continue to experience symptoms for longer than usual after initially contracting the virus.

“We discovered that moderate or severe COVID-19 creates a stressed environment which can be correlated to the emergence of immune system dysfunction. Using the AWS cloud, we have been able to move quickly to gather data from over seven hospitals and mobile phlebotomy units. AWS has also helped us share data with multiple scientific and clinical collaborators around the globe, and to facilitate end-to-end coordination to help manage various data flows, starting with distributed patient enrollment to clinical data collection, and scalable data processing and public release.”

– Jim Heath, PhD, ISB President and Professor

Chan Zuckerberg Biohub quantifies the silent spread of COVID-19

One thing that makes COVID-19 challenging to track is that not all individuals who have it exhibit symptoms. In early 2020, researchers at Chan Zuckerberg Biohub (CZB) were interested in estimating the true number of infections. They created a mathematical model to estimate the number of undetected infections at 12 locations in Asia, Europe, and the U.S. over the course of the pandemic. The study found that there was a very wide range of infections that were undetected across these locations. Researchers also found that there was significant change over time in the probability of detecting a case. When the virus was first transmitted to these 12 locations, over 98% of infections were undetected during those initial couple of weeks, indicating that the epidemic was already taking off by the time that intense testing started happening.

For each of the 12 data sets that CZB worked with, they had to test thousands of different parameter sets and use those parameters to simulate what the epidemic should look like using those parameters, while also comparing it to the data they had at hand. That process can take hours or sometimes days. With support from AWS, CZB was able to better parallelize a process so that they could conduct work in a reasonable time frame, and could report on the data in a matter of days, rather than months. AWS provided computational support through credits and also offered the expertise of the AWS Professional Services team, who helped scale up this analysis using Amazon Elastic Compute Cloud (Amazon EC2) and AWS Batch.

Gladstone Institutes develops CRISPR-based test using a smartphone camera

Scientists at Gladstone Institutes—in partnership with the University of California, Berkeley (UC Berkeley) and the University of California, San Francisco (UCSF)—have developed a CRISPR-based test for COVID-19 that uses a smartphone camera to provide accurate results in under 30 minutes. In the new test, the Cas13 protein is combined with a reporter molecule and mixed with a patient sample from a nasal swab. The sample is placed in a device that attaches to a smartphone. If the sample contains RNA from SARS-CoV-2 (the virus that causes COVID-19), Cas13 will be activated and will cut the reporter molecule, causing the emission of a fluorescent signal. Then, the smartphone camera, essentially converted into a microscope, can detect the fluorescence and report that a swab tested positive for the virus.

The assay that Gladstone developed could provide rapid, low-cost testing to help control the spread of COVID-19. To develop this assay, Gladstone researchers designed guide RNAs that can target COVID-19 sequence for quick diagnosis. A critical part of that is making sure that the guide RNAs are sensitive (catch as many positives as possible) and specific (to ensure that a positive test is not a spurious match to RNA from another virus, bacteria, or the person themselves). To that end, they need to run homology (sequence similarity) assessments against large amounts of sequencing data. This process of identifying guide sequences to improve the assay requires massive amounts of computing power, provided by AWS.

CVPath Institute conducts first systematic cardiac autopsy study of COVID-19 victims, revealing new understanding of how the virus injures the heart

CVPath Institute, a premier cardiovascular research and education institute, is working to better understand cardiac injury in COVID-19 patients. Studies indicate about 30% of COVID-19 patients have evidence of cardiac injury, and those patients have a substantially higher mortality rate than those without. However, the effect of COVID-19 on the heart and how this contributes to morbidity and mortality is still not completely understood. CVPath Institute is conducting the first systematic cardiac autopsy study of COVID-19 victims who died during the early pandemic in Italy to understand the pathology and genetic risk factors of cardiac injury in these patients.

For this research, CVPath uses the American Heart Association’s® Precision Medicine Platform (PMP)—which is powered by AWS. The PMP provides search and filtering capabilities for data discovery; automated data access; secure workspaces equipped with artificial intelligence tools and cloud computing; and a set of collaboration services, empowering scientists to collaborate and focus on the research without getting tangled in the details of managing the data. CVPath used the PMP to upload, store, and analyze large genetic data sets, and analyzed the patients’ genetic data to discover new risk variants in the DNA that could be associated with cardiovascular disease.

Initial findings from CVPath’s work revealed that microvascular thrombi are common in patients dying of COVID-19—these are tiny blood clots seen in the heart tissue itself. This is novel because myocardial infarction (commonly known as a heart attack) caused by microvascular thrombosis in the absence of significant coronary artery disease has not been previously reported. This type of discovery will allow scientists and researchers to begin looking at how to prevent this type of injury using targeted treatments. In future phases of this research, CVPath plans to explore genetic risk factors that might predispose subjects to excess clotting after COVID-19 infection, as well as explore long-term effects of COVID-19 infection on the heart. These studies could lead to the development of an accurate and potentially lifesaving diagnostic method to distinguish the most vulnerable patients who might die from severe COVID-19 infection and cardiac injury.

Learn more

The AWS Diagnostic Development Initiative is open to organizations including nonprofits, research institutions, startups, and private organizations. Nonprofits interested in applying can do so here. For any questions, contact aws-ddi@amazon.com. Learn more about AWS for nonprofits.