Hepatitis C virus (HCV)
Scientists in the Molecular Diagnostics Laboratory at UW Hospital and Clinics are now providing doctors and patients much more information about virus type and subtype than before. No other hospital or laboratory in the country routinely offers this level of detail.
“We hope this new information will help clinicians make better judgments about the best course of treatment for each patient,” says Dr. William Rehrauer, head of the Molecular Diagnostics Laboratory and assistant professor of pathology and laboratory medicine at UW School of Medicine and Public Health (SMPH).
Rehrauer and colleagues have developed a test that more accurately defines HCV type and subtype than before by looking at multiple locations on the viral genome instead of just one, as was done in the past.
In the process, the scientists also discovered, to their great surprise, a new type of hepatitis C virus never before seen in the United States. The strain, similar to one found in Russia, is probably very rare in North America, they say.
HCV is the most common chronic blood-borne disease in the United States, infecting approximately 3.2 million people. The World Health Organization estimates that 130 million to 170 million people worldwide carry the virus. The infection can cause several kinds of liver diseases, including cirrhosis and cancer.
The hepatitis C virus is divided into six or seven genotypes, or types, each defined by specific genetic information. Each type is further divided into many subtypes, with new types and subtypes being identified regularly. Type 1, subtype a (1a) is by far the most common form of hepatitis C virus in patients in the United States.
Genotype and subtype can significantly influence how, and even if, a patient will be treated.
“Patients with genotype1 do not respond all that well to standard therapies of alpha interferon or the combination of alpha interferon and ribavirin,” says Dr. Robert Striker, a UW Hospital infectious disease specialist who sees many hepatitis C virus-infected patients.
The newest drugs have much better response rates but are expensive and produce side effects.
“They work well for genotype 1 viruses in general,” says Striker. “While they do work for 1as, the effectiveness is not as high as for 1bs, where they work great.”
Called protease inhibitors, the new drugs specifically target the area in the center of the virus genome called the protease, which is responsible for important steps in virus replication.
Genotype is determined by analyzing sequences in the viral genome. Laboratory technologists typically use commercially available tests that focus on a sequence at one end of the hepatitis C virus genome, referred to as 5 prime.
“The 5 prime tests don’t provide much information on newly identified types and subtypes,” says Striker, a professor of medical microbiology and immunology at the SMPH. “They don’t tell you how the protease will respond to treatment.”
Rehrauer and his team set out to provide additional sequence information that could be used to better guide treatment. Scientists in the Molecular Diagnostics Laboratory, a division of the hospital’s clinical laboratories, are experts at doing this.
Dr. Molly Accola, who leads the efforts, scanned the scientific literature and viral sequence databases for an additional region to test. She found a good candidate at the opposite end of the HCV genome, called 3 prime, which could provide a distinguishing sequence that was better than 5 prime at identifying HCV genotype and subtype.
Accola developed a method to test 3 prime and validated it against the old test. She found that the combination of both regions was more effective at identifying hepatitis C virus types and subtypes than the historical 5 prime sequence alone. The lab began using the new test clinically about two years ago.
“Now, not only do we have a more informative region to test, we can add it to the old information,” says Accola. “The combination is much richer in data.”
With a molecular profile of the two ends of the genome in hand, Striker’s team, which does genomic research on HCV, filled in the rest of the sequence.
Over a year, the scientists analyzed 133 samples with their two-site method and unexpectedly found one patient with type 2b genetic information in the 5 prime area and type 1a in the 3 prime area-a new kind of hepatitis C virus. Such a combined form of two related viruses–in this case a 2b/1a–is called a recombinant.
“HCV-infected patients are frequently exposed to multiple forms of the virus, but very few recombinants between two HCV genotyes have been found,” says Rehrauer.
The place where 2b/1a combined–the cross-over point–was at the center of the genome, next to the hepatitis C virus protease where the new drugs work.
“While the 2b/1a recombinant finding was very interesting, the real value of testing the viral genome in two places, in my opinion, is that it lets us be more confident about the subtype determination,” Striker says.
Over time, with new medications expected on the market in coming years, such details will matter more and more, he adds.
“The complexity of these viruses has not been appreciated,” Striker says.
The recombinant work was published in the Virology Journal.
University of Wisconsin School of Medicine and Public Health