Graphics Processing Units Tech to Accelerate COVID-19 Sequencing

Genome-sequencing software NVIDIA announced that it will provide a free 90-day license to Parabricks to any researcher worldwide for rapid  COVID-19 sequencing, according to a recent press release.

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Parabrick is based on the Genome Analysis Toolkit and uses graphics processing units (GPUs) to accelerate by nearly 50 times the analysis of sequence data. Parabricks joined NVIDIA back in December 2019 to speed up the process of analyzing genomes. 

“We recognize the pandemic is evolving, so we’ll monitor the situation and extend the offer as needed,” NVIDIA explained. 

Researchers are analyzing COVID-19 itself as well as the genomes of the individuals affected by the disease to understand the spread and who is most at risk. 

Studying the viral genomes will enhance the understanding of the origin of COVID-19 and how it fits into other related viruses such as severe acute respiratory syndrome (SARS) and middle-east respiratory syndrome (MERS.) Genomes also provide information into what the discovered virus physically looks like, how it’s changing, and how it can be stopped.

“One of the biggest takeaway messages is that there was a single introduction into humans and then human-to-human spread,” Trevor Bedford, bioinformatics specialist at the University of Washington and Fred Hutchinson Cancer Research Center said in a recent article.

COVID-19 currently has nearly 29,000 nucleotides that hold the genetic information to produce the virus, the article highlighted.  The sharing of genomic information by Chinese researchers allows public health systems to develop their own diagnostics for the virus.

When virus sequences like COVID-19 become available, researchers incorporate the sequence into a group of known coronaviruses that are notable and affect many species. The longer a virus spreads throughout countries, the more time it has to develop different mutations that affect different individuals. 

Despite the information experts have taken away about COVID-19 so far, it is still unclear where exactly the origin is.

“Until you consistently isolate the virus out of a single species, it’s really, really difficult to try and determine what the natural host is,” Kristian Andersen, an evolutionary biologist at Scripps Research said in the article.

A report released January 23 highlighted that COVID-19’s sequence has 79.5 percent similarity to the coronavirus that causes SARS. For this reason, experts and researchers turned to remdesivir as a potential treatment, an antiviral drug previously used to treat MERS and SARS.

Remdesivir mimics one of the natural building blocks of RNA synthesis that is vital for genome replication of COVID-19, according to a recent research from University of Alberta.

The virus is not able to be replicated once the enzymes in the virus synthesize with the RNA genome in the building blocks, experts stressed.

“We know the drug works against different coronavirus, like MERS and SARS, and we know the novel coronavirus is very similar to SARS. So I would say that I’m cautiously optimistic that the result our team found with remdesivir and MERS will be similar with COVID-19,” said Matthias Gotte, a virologist at the university.

Applications including Medaka, Racon, Raven, Reticulatus, and Unicycler currently have NVIDIA GPU acceleration built in, but for researchers working with Oxford Nanopore long-read data, GPU-accelerated tools are available on GritHub. 

Parabricks joined NVIDIA in December 2019 and provided the latest tool to analyze genomic sequences. It can reduce the time for variant calling on a whole human genome from days to less than an hour on a single server, the press release stated. 

Receiving COVID-19 results in hours versus days will enhance researchers efforts in understanding the virus’s evolution and the development of vaccines. 

The company is asking individuals and organizations with access to NVIDIA GPUs to fill out a form to request a Parabricks license and they are inviting partners to join them to tackle challenges in the research community. 

“We’re in discussion with cloud service providers and supercomputing centers to provide compute resources and access to Parabricks on their platforms,” NVDIA concluded.