Scientists break SARS genetic code

B.C. Doctor Caroline Astell believes that a vaccine is possibility in the near future

Developing a vaccine will take years, but the information we've collected will help us obtain the right antigen." Doctor Caroline Astell, chief of laboratory projects at the Michael Smith Genome Sciences Centre, harbours little doubt about the genetic sequence of the coronavirus that could be the agent of SARS. The announcement of the Vancouver lab, directed by Marco Marra and referring to the BC Cancer Research Centre, had a vast echo all over the world, also because the mapping of the virus could lead to therapies and treatments and, later, to a vaccine.
"Everything began with a conversation I had with Dr. Marco Marra," continued Astell. "We were attending a conference at the University of British Columbia when we decided to take the first steps, i.e. request permission to obtain DNA samples from SARS patients. One week later we received samples taken from an unnamed Toronto patient."
The samples were delivered to Winnipeg's National Microbiology Lab, which studies the deadliest infective agents, including the West Nile virus and anthrax. The cultures were purified, inactivated and sent to the BC Centre for Disease Control, directed by Doctor Robert C. Brunham. That's when the staff of the Genome Sciences Centre, founded in 1999 by Nobel Laureate chemist Michael Smith, began cracking the code.
"We obtained the data we needed to create a library of nucleotide sequences. Five weeks and a half later, sleeping 2 or 3 hours per night, we succeeded in completing the mapping," says Dr. Astell, a member of the research team since last year, following 25 years in teaching.
"In the laboratory we cloned the virus to obtain many identical copies: larger chunks were broken down in simpler components, with a procedure that takes almost 16 hours, in sequences of between 200 and 6000 units." By Thursday night the Vancouver team, some 30 researchers, had isolated the DNA of the various samples: a 3,000-piece puzzle that was fed into highly sophisticated computer programs that reassembled all the gene bases and reconstructed the folding sequence of the virus.
"The job was done by 4am, Saturday night," remembers Astell.
"We kept staring at the computer screen, not believing our eyes, and the coronavirus was really there, completely sequenced: the virus that could be the cause of the Severe Acute Respiratory Syndrome. However, the genetic sequence is not final yet, we might say this is a draft. We need to carry out more controls to avoid errors, albeit there could be two or three at most. We need very few elements more in order to define the typical specimen of the virus. I can say that we have over 30,000 gene bases, and that this is the sequence of the coronavirus. There is no doubt that the coronavirus is associated with SARS, many results clearly point to this, but we cannot positively declare that this the one cause of the disease. That's why I insist we need additional studies."
The whole world turns its eyes - and hopes - on the Canadian team of researchers. The scientists at the Michael Smith Genome Sciences Centre called their project "TOR2" with reference to the origin of the samples, while the U.S. Centre for Disease Control, in Atlanta, is working on "Urbani", named after Italian doctor Carlo Urbani, killed last month in Bangkok by the disease. The U.S. researchers announced that they too had sequenced the virus a few hours after the Canadians.
"Actually, until a few days ago I was unaware of the fact that they were trying to map the coronavirus," says Caroline Astell. "I got in touch with a researcher in Atlanta, an acquaintance of mine, and we compared notes. They are working on the same virus. Theirs was isolated from Carlo Urbani, while ours came from a patient in Toronto: they're technically different, as they were taken from different sources, but they are virtually identical. This seems to confirm that, before Dr. Urbani and before the Toronto patient, someone else has caught the virus from another source. Epidemiology will track the origin of this disease."
A few days ago Dr. Brunham of the BC Centre for Disease Control, in an interview to CBC, confirmed that the two viruses are identical and that they appear to be mutated forms of viruses commonly found in mammals or birds.
"The next steps, in fact, will concern an analysis of China's animal population to find out which species was hosting the virus," continues Dr. Astell, "and if it turns out that the host species was the chicken we shall have to prepare to slaughter them to stop the epidemics. On the other hand we shall prepare sophisticated diagnostic tests with samples taken from other SARS patients in order to verify the link between coronavirus and SARS. This will not be done exclusively at the Genome Science Centre, and we put all the information on the Internet, allowing researchers all over the world the opportunity to collaborate in the studies. This will be the way for understanding the causes of this disease, looking for a therapy and developing a vaccine."
Caroline Astell concludes: "Developing a vaccine will take years, but the information we've collected will help us obtain the right antigen. After all, we've been working on a vaccine for AIDS for a decade now. This is a completely different virus, of course, but still proving the effectiveness of a vaccine will take time."

Publication Date: 2003-04-20
Story Location: http://tandemnews.com/viewstory.php?storyid=2634