Amazon, UCSF Partner for COVID-19 Genome Sequencing Projects

May 15, 2020 - Amazon Web Services (AWS) is partnering with researchers at the University of California San Francisco (UCSF) to conduct genome sequencing on the viruses infecting hundreds of COVID-19 patients in the Bay Area.

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AWS is connecting with the laboratory of Charles Chiu, PhD, MD, to enable two projects using cloud computing and data.

“In today’s rapid-changing environment around the COVID-19 pandemic, cloud computing resources will accelerate our efforts to design the next-generation of diagnostic tests and provide real-time, actionable genomic data to inform the public health response,” said Chiu.

In the first project, Chiu and his team are performing transcriptome analysis of nasal swab and whole blood samples from patients with viral respiratory infection to identify specific biomarkers of the disease. To date, they have detected distinct signatures for influenza, RSV (respiratory syncytial virus), bacterial sepsis, Lyme disease, babesiosis.

The team hypothesizes that COVID-19 infection evokes a specific and distinct host response in infected patients that would be detectable by RNA sequencing, and that machine learning models can discriminate between respiratory viral infections on the basis of the host response.

Indirect diagnostic testing on the basis of the early host response could be critical to helping rapid response efforts, as recent data has indicated that SARS-CoV-2 is associated with asymptomatic infection and transmission.

For the second project, Chiu and his team developed a method that will supplement metagenomic libraries for COVID-19 genome sequences. The method complements other methods of viral genome sequence recovery, and is particularly valuable for analysis of nasopharyngeal swab samples with low viral concentrations.

Chiu and his research group have leveraged this method to conduct a genomic survey of SARS-CoV-2 strains circulating in California. The team showed that the strain that infected people on the Grand Princess cruise ship clusters with the WA1 strain that is predominantly circulating Washington State.

Now, the researchers are partnering with the CDC, the California Department of Public Health, and Santa Clara Department of Public Health to conduct real-time genomic surveillance of SARS-CoV-2 infection in California. This work will be essential for guiding public health interventions to contain further spread of the virus while residents are told to shelter-in-place.

AWS is supporting the projects through donated service credits provided by the AWS Diagnostic Development Initiative. Launched in March with an initial investment of $20 million, the program aims to support customers who are working to bring better and more accurate diagnostic solutions to market faster.

COVID-19 is the preliminary focus of the initiative, with subsequent projects concentrated on other infectious disease diagnostic projects.

“As COVID-19 continues to spread, we are acutely aware of the impact this is having on families, businesses, and communities. This is a global health emergency that will only be resolved by governments, businesses, academia, and individuals working together to better understand this virus and ultimately find a cure,” Teresa Carlson, vice president for AWS’s worldwide public sector, wrote in a blog post when the initiative was announced.

“In our AWS business, one area where we have heard an urgent need is in the research and development of diagnostics, which consist of rapid, accurate detection and testing of COVID-19. Better diagnostics will help accelerate treatment and containment, and in time, shorten the course of this epidemic.”

Through this partnership with UCSF, AWS will further promote innovative solutions for treating and controlling COVID-19.

“Data and computation are hallmarks of the newest paradigm of scientific research, and especially in this time of COVID-19, we need innovation to drive discovery. Technology is a key tool that is helping researchers work more effectively with data and support COVID data science projects,” UCSF researchers said.