Posted on 05/03/2003 6:17:56 AM PDT by Lessismore
Every week brings new questions about SARS--and sometimes, glimmers of answers. Last week, many of the questions centered on the genome of the new coronavirus believed to be the culprit. Since a Canadian research group first posted its entire sequence online on 13 April, genome information for nine other virus isolates has become available on the Web. Researchers around the world have devoured the genetic code like a pack of wolves, searching for clues to the virus's origins, behavior, and future.
After press time this week, Science was set to publish online a paper analyzing the genome from the BCCA Genome Sciences Centre in Vancouver, as well as one from the Centers for Disease Control and Prevention (CDC) in Atlanta (www.sciencemag.org/feature/data/sars). But as these papers neared completion, researchers in other labs had their computers parse all the available genomes for themselves, and on the Internet, subtle variations among the 30,000-nucleotide genomes were the subject of intense speculation.
Now that sequencing technology has become cheap and widely available, almost every country affected by SARS is sequencing its own version, says coronavirologist Willy Spaan of Leiden University Medical Center in the Netherlands. Shortly after the U.S. and Canadian teams, two groups in Hong Kong and one in Singapore posted online the sequences of their SARS virus isolates. But the big surprise was the flood of data produced by the Beijing Genomics Institute (BGI), together with the Academy of Military Medical Sciences.
Well known for its role in sequencing the rice genome, BGI was eager to work on SARS from the start, says director Yang Huanming--but lacking the government's blessing, it had a hard time obtaining samples. The researchers finally got them on 15 April, and within days they had posted in GenBank partial sequences of five isolates--with minimal fanfare to avoid offending authorities. Recognition came only after the Chinese government's about-face and the sacking of top health officials; on 20 April, Chinese Vice President Hu Jintao visited BGI to praise its contribution. "Now we are all welcome to contribute to SARS research," says deputy director Wang Jian.
In the analyses set for publication this week, CDC and the Canadian group confirm earlier findings, based on the sequence of small snippets of the genome, that the new virus is distantly related to all known coronaviruses and deserves to be placed in a new group of its own (Science, 18 April, p. 413). Both groups also show the genome organization is similar to that of known coronaviruses, and both identify a number of putative viral genes. But neither of the groups had a coronavirologist in its midst, says Spaan, who believes a more expert analysis of the two genomes--which his laboratory is currently undertaking--may reveal intriguing additional details about the viral machinery.
Whereas the two North American isolates differ in only eight nucleotides, a broader comparison across the 10 genomes now available shows much more variation. Although some variations may be due to sequencing errors, the data do suggest that the virus is mutating quite rapidly, says coronavirologist Luís Enjuanes of the Autonomous University of Madrid; variations occur both in the enzymes that help it replicate and the proteins that sit on its outer surface. That could mean the virus will prove adept at eluding drugs and vaccines, Enjuanes warns.
A close reading of the variation hints at other fascinating trends, says Henry Niman, a Harvard surgery instructor who operates an increasingly popular mailing list about SARS science. Last week, Niman and others were speculating how differences of a single amino acid among viruses isolated from different patients might explain variations in pathogenicity and infectivity. Others are skeptical, however. To show such correlations, you need data from many more patients, or animal tests, says Spaan. "There's a lot of nonsense going around at the moment," he says. To get a better handle on the problem, the World Health Organization (WHO) in Geneva has plans to set up a SARS genetic diversity databank, linked to a clinical databank, says WHO virologist Klaus Stöhr.
It could swell quickly, because new genomes are churned out almost daily. The Genome Institute of Singapore alone has four more ready but not yet posted on its Web site, says executive director Edison Liu. After all, in the SARS era, says Liu, "it's just a hop, skip, and jump" from a patient's bedside to another sequence.
--------------------------------------------------------
With reporting by Dennis Normile in Hong Kong and Ding Yimin in Beijing.
Are you saying that you think there might be a connection between SARS and HIV??
Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.