Inquiry in Action
Improving Virus Detection
Tim Rose and his colleagues are developing sensitive virus assays that have broad specificity and are fast, portable and inexpensive.
Recent outbreaks of respiratory viruses — SARS, “bird flu,” and H1N1 (swine flu) — highlight the need for quick diagnosis to prevent the spread of disease. However, laboratories are still only able to detect virus in about 50% of samples from people with respiratory illnesses.
Tim Rose, PhD, and his colleagues at the Center for Childhood Infections and Prematurity Research at Seattle Children’s Research Institute want to increase that detection rate.
Identifying novel viruses
Typically, diagnostic labs use assays that target respiratory viruses known to cause disease in humans. So viruses that have yet to be identified or that are not considered human pathogens are generally not detected in current diagnostic assays. Rose and his team are developing assays with broad specificity to detect both known and unknown viruses within different families of respiratory viruses. These assays are designed to detect not only existing viruses, but viruses that have mutated or recombined from existing viruses — as in the case of avian and pig influenza viruses.
Unique technique amplifies unknown but related viral sequences
A low level of virus in a sample is another reason test detection rates are low. A process called PCR (polymerase chain reaction) amplification enables scientists to increase virus levels in a sample for detection. PCR uses DNA primers specific to a viral gene sequence to copy a portion of the viral genome. Multiple cycles of gene copying lead to a million-fold increase in the amount of the viral DNA in the sample.
In general, this type of amplification depends on knowing the sequence of the virus targeted in the assay. The PCR assay can detect low levels of virus, but only the virus from which the DNA primers were obtained. Rose and his colleagues have developed a unique technique to design PCR primers that can amplify unknown, but related viral sequences.
The assays developed by Tim Rose and his team are designed to detect existing viruses as well as those that have mutated or recombined from existing viruses — as in the case of avian and pig influenza viruses.
Known as consensus-degenerate hybrid oligonucleotide primer method, or CODEHOP, the process enables lab tests to detect low levels of virus while preserving the ability to detect known, unknown and mutated members of a virus family. Rose hopes that in the future, CODEHOP can be used to monitor virus outbreaks.
Partnering to develop “point of care” molecular diagnostic assays
Not only do Rose and his colleagues hope to create assays for respiratory viruses that boast broad specificity and high sensitivity — their ultimate goal is to create nucleic acid amplification tests that are fast, portable and affordable.
To make that happen, his team has joined forces with Redmond-based Micronics, Inc., a company that is developing “point of care” PCR-based assays on a lightweight, easy to use, sample-to-result platform known as the PanNAT™ system. This project combines Rose’s CODEHOP technology with Micronics’ microfluidics methods and assay integration technology, which makes it possible to incorporate all reagents into a disposable cartridge and to greatly reduce the sample and reagent volumes — and time to result — required.
“Assays that would normally take three hours or more could be done in the timeframe of a patient being in the doctor’s office,” says Rose.
His CODEHOP technology has caught the eye of other researchers, who are also looking at ways to prevent localized virus outbreaks from erupting into epidemics. “The CDC is also developing assays based on our technique to identify novel viruses,” says Rose.