Source: Amazon, UCSF Partner for COVID-19 Genome Sequencing Projects. 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.
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.