SARS virus genetic map will lead to better tests, speed vaccine

Robert Roos

Apr 15, 2003 (CIDRAP News) Genetic sequencing of the virus believed to cause severe acute respiratory syndrome (SARS)an achievement announced by Canadian and US scientists in the past few dayshas set the stage for improving diagnostic tests and developing treatments and vaccines for the disease, according to health officials.

The British Columbia Cancer Agency in Vancouver, B.C., announced over the weekend that it had sequenced the genome of the coronavirus suspected as the cause of SARS. Yesterday, the US Centers for Disease Control and Prevention (CDC) announced that it had also sequenced the viral genome and found it nearly identical to the Canadian results.

Reporting the achievement at a briefing yesterday, CDC Director Julie Gerberding said, "We can now say with a great deal of confidence that the virus sequence at CDC is very similar to the virus sequence in Canada, with a difference of about ten base pairs, which is a trivial difference in a virus that's about 29,000 base pairs."

CDC said in a news release that the CDC-determined sequence has 15 additional nucleotides, "which provides the important beginning of the sequence."

"The nearly identical findings in the US and Canada are important because they were derived from different individuals who were infected in different countries," the CDC release said. "This suggests that the virus probably originated from a common source."

Gerberding said, "Having this information is critically important for developing even faster diagnostic tests, and certainly should help us in the development of antivirals and vaccine work down the road."

She said the most immediate use for the genome data is likely to be in improving diagnostic tests. "Once we have comprehensive information about the genome of the virus, we can make tests based on the PCR [polymerase chain reaction], where you take a piece of the virus and amplify it in the test tube, and it makes it easier to detect in patient tissue."

Gerberding called the sequencing, completed just 31 days into the SARS investigation, "a scientific achievement that I don't think has ever been paralleled in our history." She said the Canadian investigators deserve "enormous congratulations."

However, she cautioned that the sequencing "is not a magic bullet for dealing with SARS." She predicted that developing and testing a vaccine will still take at least a year.

CDC scientists sequenced the viral genome by taking cells from a SARS patient's throat culture and growing them in Vero (African green monkey kidney) cells, the agency said. A 10-member team completed the task in 12 days, working around the clock, according to the release.

The genome data support the view that the virus is a previously unknown member of the coronavirus family. "The new sequence has 29,727 nucleotides, which places it well within the typical RNA boundaries for coronaviruses," CDC said.

But the findings have not yet shed much light on the origin of the virus, according to Gerberding. "We can't say it's a mouse virus or a pig virus , or any other animal virus," she said. The CDC's Dr. Larry Anderson, who worked on the sequencing, said the virus is distinct from the three known antigenic groups of coronaviruses.

In other SARS developments, the World Health Organization (WHO) yesterday reported 213 new cases since the previous global count on Apr 12, for a cumulative total of 3,169 cases worldwide, with 144 deaths. The report showed 109 new cases in China and 82 new cases in Hong Kong, the two hardest hit areas.

Two Chinese provinces reported SARS cases for the first time, WHO reported. Inner Mongolia had 10 cases, and the Fujian Province had three. WHO officials said the reports indicate that China's new nationwide surveillance system is working, but the ability of some provinces to cope with SARS is still in doubt. They also said Chinese authorities had not permitted WHO experts to visit military hospitals, "which have been the focus of numerous rumours."

Gerberding said the United States had 193 suspected SARS cases as of yesterday. Most cases were in people who had traveled to Asia, but 15 cases involved travelers' family members, and 5 cases were in healthcare workers who had cared for SARS patients, she said.

Reports from Hong Kong, China, and Singapore suggest that containment measures there have not been entirely adequate, but containment steps in most other places, including the United States, Canada, and Taiwan, seem to be working, Gerberding said. Nonetheless, she said, "We have to remain vigilant, because it is only one highly transmissible patient that can infect a very large number of people. Even though we would like to be able to take a deep breath and relax a little bit here, this is absolutely the wrong time to do that."

WHO reported good news regarding a PCR diagnostic test developed by CDC. The test "has been shown to be ten times more sensitive than previous PCR tests for SARS," the WHO statement said. "WHO experts hope that the test will be ready for roll out by the end of this week."