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New Abbott, UCSF Dx Center Will Use ViroChip and Second-Gen Sequencing to ID Viruses

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Abbott and the University of California, San Francisco, this week said a new diagnostic center they jointly created will use UCSF's ViroChip pathogen-identification screening tool to ID and study viruses in acute and chronic human illnesses, including rare and unusual organisms responsible for outbreaks.

Opened this week, the UCSF Viral Diagnostics and Discovery Center, located near the school’s Mission Bay, Calif., campus, will employ the chip as its "core technology." Other genomic technologies, including an Illumina Genetic Analyzer II, will also be used at the center, according to its director.

"This center will enable ViroChip testing, and testing with other platforms, as well as high-throughput sequencing analyses on clinical specimens at a scale that would not be possible in a single academic laboratory," Charles Chiu, an assistant professor at UCSF and director of the new center, told BioArray News this week.

Abbott is the primary funding source for the center, which will also be used as a resource for processing clinical specimens provided by Abbott and the partners' collaborators worldwide, Chiu said.

According to an Abbott spokesperson, the company will also help develop downstream technologies, such as serological assays for novel viruses. This component of the center could enable Abbott to identify new infectious agents that could eventually lead to new tests, particularly in screening blood supplies.

Abbott currently markets blood-screening assays and tests for a variety of infectious diseases, including HIV. According to the spokesperson, Abbott has a staff of its own scientists who will be working on center projects from the company's headquarters in Illinois. Their role will include providing "technical expertise for such activities as diagnostic assay development, primer and probe development expertise, sourcing specimens from persons with specified diseases to screen for new infectious agents, and sourcing samples from various parts of the world through Abbott's Global HIV Surveillance Program and other resources," the spokesperson told BioArray News this week.

It will be Abbott's responsibility to translate any new infectious agent discovery into assays that will become part of standard practice of care, the spokesperson said. These assays will "include both immunoassays on Abbott platforms such as Architect as well as genetically based tests on molecular instruments such as the m2000 and systems based on Abbott’s newly acquired Ibis technology," he added.

According to the spokesperson, the licensing structure of the firm's relationship with UCSF is "somewhat complex and depends on a number of factors, including sourcing of specimens, [and] extent of technological input by each party."

Technology Toolbox

John Hackett, manager of Abbott's Virus Discovery Program and the person responsible for managing Abbott's contributions to the center, said in a statement that the use of new technologies like the ViroChip and second-generation sequencing could" lead to the development of new diagnostics and therapeutics."

UCSF researchers Joe DeRisi and Don Ganem developed the ViroChip in 2002 and used it to identify the pathogen responsible for severe acute respiratory syndrome during the SARS outbreak the following year (see BAN 4/4/2003).

ViroChip contains around 30,000 viral sequences that are used to identify rare and unusual viruses and to monitor their genetic mutations. BioArray News interviewed DeRisi about the chip during a site visit in 2007 (see BAN 7/3/2007).

Chiu, DeRisi, and Ganem are all affiliated with QB3, a cooperative effort among private industry and more than 200 scientists at UCSF, UC Berkeley, and UC Santa Cruz. UCSF's Mission Bay campus acts as the headquarters for QB3.

During the site visit, DeRisi said his lab had used ViroChip to analyze "over a thousand clinical samples" that have become the foundation for a "large database" of information that could be used to support "increased clinical use." He added that the database could be used by Abbott and others to develop new assays, and could eventually be used by physicians to ID rare or unusual sources of infection and prescribe treatments against them.

"If the identity of the pathogen is known, experimental therapies may be possible, or, in the absence of an experimental therapy, the supportive care can be customized," DeRisi said. For example, proof of a viral infection would preclude physicians from prescribing antibiotics or antifungals because they do not work against viruses.

To date, the ViroChip has been validated at UCSF for its ability to diagnose viral respiratory infections and gastroenteritis. For those blinded validation studies the technology was compared against conventional testing methods such as culture direct fluorescent antibody testing and PCR, said Chiu. He said that the center is "currently in the process of validating the ViroChip for clinical diagnostic use."

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Chiu said that the demand for the ViroChip from QB3 members and others necessitated the creation of a larger center that could make the expertise at QB3 and Abbott available for more projects.

According to Chiu, the new center is "unique" in that it offers "both viral discovery as well as serving as a diagnostic resource for clinical researchers and physicians." Since the ViroChip platform was launched, two centers at Cold Spring Harbor Laboratory in New York and the Genome Institute of Singapore have used it to test patient samples.

QB3 has seen "tremendous demand for better and more comprehensive diagnostics for viral pathogens," said Chiu. "In acute illnesses, 20 to 40 percent of respiratory infections and more than 80 percent of encephalitis [cases] remain undiagnosed despite extensive conventional testing.

"This center, by utilizing the latest genomics technologies [including] microarrays and high-throughput sequencing, will serve as a resource for researchers and clinicians to rapidly identify viral pathogens in both acute and chronic disease states," Chiu added.

Currently, the center consists of a director, a research associate and administrator, and a bioinformatics specialist, Chiu said, adding that the number of personnel should "expand rapidly." The ViroChip is the "main platform" on offer, and Chiu said that new versions will be introduced into the lab as they are designed and validated.

While ViroChip is central to its offering, the center has access to other technology platforms. According to QB3, the center houses an Agilent 2 µm DNA microarray scanner, Biosafety Level 2-tissue culture suite, Stratagene 3005P real-time PCR instrument, several thermocyclers, and an 8-core compute cluster. The center also has access to an Illumina Genetic Analyzer II for deep sequencing through the UCSF Center for Advanced Technology.

Two initial center projects showcase how it will use these technologies. In the first project, the center is using the ViroChip and Illumina's sequencer to study an undisclosed number of known influenza A (H1N1) specimens from medical centers in North America. For that study, researchers at the UCSF center hope to "analyze strain differences geographically and over time and to illustrate the utility of these technologies in outbreak investigation," Chiu said.

In its second project, the center is working with partners in the West African country of Cameroon to characterize rare and unusual strains of HIV "or other retroviruses," said Chiu.

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