MADISON, WI-JUNE 4, 2004-Scientists from the Genome Institute of Singapore (GIS) have developed a new technology to quickly and accurately identify different strains of the Severe Acute Respiratory (SARS) virus. Should SARS return, their method will halve the time required to determine the genetic origins of the virus, an essential part of contact tracing, thereby reducing the risk of a second SARS epidemic.

In 2003, the Severe Acute Respiratory (SARS) virus wreaked havoc across Asia. The epidemic demonstrated the importance of accurate and timely contact tracing for the control of viral spread.

However, contact tracing is a very slow process, requiring much tedious questioning of the patient as well as a molecular test to determine the genetic origins of the infecting virus. The molecular test required that the virus be carefully extracted and grown in cell culture for a week before that test could be administered.

GIS partnered with NimbleGen Systems Inc., a US-based private biotechnology firm, to develop a fast, reliable and cost-effective alternative. Their new method allows the molecular test to be completed in three days and will be used to complement existing methods. Currently clinicians will use two to three tests to verify the SARS virus.

The new "genetic fingerprinting" technique relies on the use of an oligonucleotide microarray, a tiny glass surface containing hundreds of thousands of pieces of genetic material from the SARS virus.

GIS used data obtained from its previous sequencing of five SARS virus strains (See ref 1) to derive a single consensus sequence for the SARS virus. That sequence was then used to produce a SARS-specific detection chip.

Said Dr. Edison Liu, Executive Director at the GIS, "This chip allows us to identify very small changes in the genetic make-up of the SARS coronavirus. These changes happen as the virus spreads through a population and can serve as a 'fingerprint' to distinguish different strains. So, it can help to tell where and when an infected individual may have contracted the disease, hence allowing a rapid public health response."

Dr. Stanley Rose, CEO of NimbleGen, commented, "GIS scientists, Chris Wong and Lance Miller have leveraged NimbleGen's unique combination of array density and flexibility to demonstrate an important advance in SARS monitoring. NimbleGen's ability to implement new array designs within hours of new mutations being discovered should prove beneficial to a broad range of public health research and screening programs. This is a perfect example of how NimbleGen's technology is being used to study genomes of disease."

In addition to its flexibility, the microarray can process up to 50 samples at a time, meaning that, potentially, a large number of SARS patients can be effectively screened at the same time. It also lends itself to large-scale studies of the evolution of the genetic makeup of the SARS virus over time. This method can also be adapted for use with other diseases.

Ref 1:

Ruan, Y.J., Wei, C.L., Ee, A.L., Vega, V.B., Thoreau, H., Su, S.T., Chia, J.M., Ng, P., Chiu, K.P., Lim, L. et al; 2003. Comparative full length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet 361: 1779-1785.

Notes to the Editor:

The research findings described in this press release can be found in the March issue of the scientific journal Genome Research (14, 398-405) under the title "Tracking the Evolution of the SARS Coronavirus using high-throughput, high-density resequencing arrays".

Authors: Christopher W. Wong, Thomas J. Albert, Vinsensius B. Vega, Jason E. Norton, David J. Cutler, Todd A. Richmond, Lawrence W. Stanton, Edison T. Liu and Lance D. Miller.
Genome Institute of Singapore, S'pore 138672

The work is also quoted in online version of Nature Methods (05 April 2004) under the title "Taking the Strain Out of Viral Genotyping" by Michael Eisenstein.
http://www.nature.com/cgi-taf/dynapage.taf?file=/nmeth/journal/v1/n1/full/nmeth005.html

Useful websites:

The Virus Hunters: Singapore Researchers Part of a Global Force against SARS
http://www.biomed-singapore.com/bms/sg/en_uk/index/research_resources/research_highlights/2003/the_virus_hunters.html

The Singapore Government SARS Website
http://www.sars.gov.sg/

About the Genome Institute of Singapore (GIS)

The Genome Institute of Singapore (GIS) is a member of the Agency for Science, Technology and Research (A*STAR). Established in 2001, the research institute's mission is to be a world-class genomics institute and a centre for genomic discovery. GIS pursues the integration of technology, genetics, and biology towards the goal of individualised medicine. The genomics infrastructure at GIS is utilized to train new scientific talent, to act as a bridge between academic and industrial research, and explore scientific questions of high impact.

For more information on GIS please visit: www.gis.a-star.edu.sg
For more information on A*STAR, please visit: www.a-star.edu.sg

About NimbleGen Systems Inc.

NimbleGen Systems is the leading supplier of customized high-density microarray products and services, offering unprecedented flexibility for genomics research. NimbleGen's Maskless Array Synthesis (MAS) technology combines photo-deposition chemistry with digital light projection to shorten array fabrication from months to hours. Customers benefit from extreme flexibility, optimized array design, highly reproducible array fabrication and statistically robust results-all with low cost and quick turnaround. NimbleGen is working with scientists around the world to develop and deploy a wide range of new microarray applications.