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Canadian Team Leader: SARS Coronavirus Genome Has 11 Novel ORFs

Note: This article has been edited from the original version to correct a typographical error.


NEW YORK, April 15 - The sequenced coronavirus believed to cause Severe Acute Respiratory Syndrome has eleven open reading frames, and these predicted coding regions lack significant homology to sequence in existing gene databases, Steven Jones, director of bioinformatics at the British ColumbiaCancerCenter, said today.


"People were thinking that [the SARS virus] was some kind of hybrid virus between a fairly well studied human virus, recombined with a non-human virus," he said. "A lot of those Asian flus have been associated with avian viruses." But the ORFs that Jones' group is finding all have consistent phylogeny. "They all look like they have been in the same organism for a long period of time," he said. And they are "only modestly similar to [ORFs in] other coronaviruses."


Jones led an all-night effort last Friday night to assemble the sequence of this viral pathogen, after the raw reads began coming off of the center's ten ABI 3700s and 3730 sequencers at . "We were continuously doing assemblies through the night as more and more virus accrued," he said. As a result, the small team beat the US Centers for Disease Control to the finish line for the draft sequence (although nobody says there was a race).


The process began six days earlier, when the group received a microgram sample of virus from the Canadian National Microbiology lab in Winnipeg, Manitoba -- a small sample to work with. They spent the first four days making the cDNA library out of the RNA virus, Jones said. "On Thursday we were able to pick enough colonies to start doing DNA prep on the clones, and by Friday virtually the entire genome's worth of sequence was loaded up."


There were no real bumps in the road once the sequencing machines got going. The shotgun sequencing was at a 20-30-fold level of redundance, Jones said, "because we didn't want to do any iterative finishing steps."


The only problem with sequencing this deep was that the group began finding single-base mutations in different copies of the viral genome. Though mutations in the virus are of potential research interest, Jones said the level of mutation found was not surprising given the rapid rate at which viruses mutate, and the fact that the group had grown the virus in primate cells to produce more sample. Still, they have to further analyze the sequence for mutation sites.


Now Jones' team is redesigning PCR primers to confirm the sequence, and is doing further sequence analysis, including comparing its draft to that released yesterday by the US Centers for Disease Control, Jones said.


The BC Cancer Center team is also in touch with the Canadian Centers for Disease Control, which is involved in efforts to establish reliable tests for SARS, along with the US CDC and other bodies around the world. 


Separately, the Singapore News reported Tuesday that the Genome Institute of Singapore has also sequenced the SARS coronavirus, and has prepared a test kit for SARS which it plans to make available to local laboratories and hospitals this week.