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Viral Genome Genomics World Rallies to Stop SARS in Tracks

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Genomics garnered worldwide attention recently as it became a crucial factor in the efforts to identify the new SARS virus and make a diagnostic for it. Researchers from all areas — public sector and private, RNAi to proteomics to sequencing, and around the globe — have used their specialties to help confront the spreading virus.

In the weeks leading up to GT’s press deadline, a number of companies announced diagnostic tools in development or ready to go. EraGen Biosciences of Madison, Wis., said it had designed a specific assay capable of detecting the genetic structure of SARS within an hour. The test was sent to the US Army Medical Research Institute of Infectious Diseases, the WHO Central Public Health Laboratory, and the British Columbia Center of Disease Control.

Earlier, Roche Diagnostics confirmed plans to launch a diagnostic test for the coronavirus by the end of July. That test will be based on the company’s real-time PCR technology.

Any test will likely have to be vetted by a number of disease institutes. The US Centers for Disease Control said they are still trying to determine, along with World Health Organization labs, the accuracy of PCR-based tests for SARS made by various labs.

“There is a lot of interest in getting good testing protocols available for this agent,” says Julie Gerberding, the CDC director. One stumbling block will be figuring out why some people get sicker than others: “We need to sequence more viruses,” she adds. This “will be a longer-term investigation.”

Nailing the virus in the first place prompted fast action from the genomics community. Steven Jones, director of bioinformatics at the British Columbia Cancer Center, led an all-night effort to assemble the sequence of the pathogen after the raw reads began coming off the center’s 10 ABI 3700s and 3730 sequencers at 9:30 pm. “We were continuously doing assemblies through the night as more and more virus accrued,” he says.

They weren’t the only ones trying to get the sequence. By the start of May, the CDC and teams in Hong Kong, Singapore, and Beijing had also completed the viral genome.

The sequenced coronavirus has 11 open reading frames, and these predicted coding regions lack significant homology to sequence in existing gene databases, Jones says.

Companies have also gathered to do what they can. CombiMatrix offered some of its new SARS microarrays to certain research centers free of charge, according to CEO Amit Kumar, “due to the public health and economic implications of SARS.”

Qiagen, too, has joined in by lending its RNAi expertise to scientists on the front lines of SARS research. The company will contribute its RNA interference design resource, along with its custom siRNA and other sample preparation and nucleic acid chemistry products, to laboratories in Hong Kong, China, Singapore, and Canada.

— Marian Moser Jones and Meredith Salisbury

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