DAYTONA BEACH, Fla. (GenomeWeb) – Clinical diagnostics firm Quidel described improvements it has made to its Solana molecular testing platform, and outlined future menu goals and possible platform improvements during a company-sponsored corporate workshop at the Clinical Virology Symposium here this week.
In addition, independent researchers presented preliminary data on a clinical trial of Quidel's AmpliVue Trichomonas assay and described novel sample types that might be used with the company's tests in the future.
Quidel gained the base technology for the Solana isothermal nucleic acid detection system when it acquired BioHelix two years ago. The firm debuted the new platform, along with its larger Savanna system, at the American Association of Clinical Chemistry Lab Expo in Chicago last July.
The systems both rely on helicase-dependent amplification (HDA), an isothermal amplification technology that was developed by BioHelix President Huimin Kong.
During the Quidel workshop, Kong described HDA for attendees. The chemistry, which Kong began developing while he was at New England Biolabs, uses helicase to "mimic nature" and unwind the DNA, allowing access for Gst DNA polymerase, Kong said.
The technique uses one primer in three-fold excess of the other primer to obtain mostly single-strand DNA with a small tail of double strand. Primers are biotinylated, and via streptavidin and FITC binding, the pathogen nucleic acid is marked for detection. The tests can also use DNP or DIG for labeling, allowing flexibility.
The method ultimately has similar sensitivity to PCR, Kong said, and is now used in various Quidel applications: the AmpliVue line of manual, on-demand, single-use tests, several of which are cleared by the US Food and Drug Administration; the Solana platform, which is automated and runs 12 tests at a time; and Savanna, which has two bays, one of which runs an HDA cartridge in around 30 minutes and on of which runs traditional 90-minute PCR. Neither Solana nor Savanna is commercially available yet for clinical diagnostic use in the US, although Solana recently garnered CE marking along with a Group A Strep assay. Savanna, meanwhile, has been funded in part by the Bill and Melinda Gates Foundation, as Quidel is developing it initially for resource-poor areas of the world and eventually for other markets.
To date, Quidel has marched six AmpliVue assays through FDA clearance — Clostridium difficile, Group B Strep, HSV 1+2, Bordetella pertussis, Group A Strep, and, most recently, Trichomonas. Importantly, the core HDA-based assays seem to port between the platforms, so the firm may now have a jump on these targets for Solana and Savanna.
AmpliVue tests require separate lysis and amplification heating blocks, as well as single-use cassettes for the lateral flow detection. After amplification, the sample tube is locked into the detection cassette, which chops off the bottom of the tube and allows the product to wick through the detection pad. There are two test lines and one control line embedded in the filter.
Solana, meanwhile, uses the same basic chemistry but takes advantage of direct FITC fluorescence. The platform measures 9.4 x 9.4 x 5.9 inches, and consists of a heating block that executes the HDA isothermal steps, an automated LED-based fluorescence reader, an Ethernet port, and a USB drive, Kong said. Data is reported to a touchpad interface that is "similar in size to an iPhone 6," and can be uploaded to a network or cloud.
The system includes an internal battery pack, and a heated lid obviates the need for mineral oil, Kong noted. It also allows for bar coding of the entire process to help organize workflow.
Notably, Solana scans each tube every 30 seconds, and thus can compute changes in fluorescence that, via an algorithm, allow for real-time detection and read-out.
Kong described the system as "easy to use," and said instruments cost "a couple hundred dollars."
During the platform's development, Quidel has gradually decreased the hands-on time and total test time such that the Group A Strep test takes five minutes for lysis, 25 minutes for amplification, and one minute for data reporting.
Kong further noted that the GAS test in development shows no cross reactivity with other organisms. It has 98.2 percent sensitivity and 97.2 percent specificity and works for specimens stored up to six days in the refrigerator.
Quidel just completed a clinical study of the Group A Strep test and is "waiting for the FDA to review that assay," Kong said. The test shows no cross-reactivity with other organisms, has achieved 98.2 percent sensitivity and 97.2 percent specificity, and works with specimens that have been stored for up to six days in the refrigerator. The firm is also exploring the possibility of getting it CLIA waived by eliminating the need for accurate pipetting and making the lysis step enzymatic.
"We are very excited; we're developing a lot of assays on the Solana system and hopefully we can bring them to the market in the near future," he said.
An influenza A/B test in development will also likely be CLIA waived and will be designed for near-patient care in a physician's office.
Meanwhile, a combined herpes simplex virus 1+2/varicella-zoster virus test for Solana will be "the first isothermal triplex NAAT," he said.
Preliminary results from testing at Quidel have shown that assay detected all the archival HSV1 and VZV positive samples tested. It detected all but one HSV2, but Kong described that particular sample as frozen from a previous clinical trial and possibly too old.
Quidel is also developing a Solana Trichomonas test, which may possibly use swab specimens or urine. Total sample-to-result time for the trichomonas test is now 33 minutes, down from 45 minutes, Kong said, and the test has a sensitivity on neat urine of 35 cells per ml.
Finally, Kong said a project began last week to port the AmpliVue C. diff test to Solana, which should take 10 to 12 months.
All of these assays overcome PCR inhibitors via diluting sample, but up to 2 to 3 microliters of blood are tolerated by AmpliVue, Kong said. The fluorescence-based assays initially showed less tolerance, but the firm has gotten them to work by changing detection parameters.
Kong said given the throughput of 12 samples per run, a lab can process perhaps 100 tests per day on Solana. The device is not random access, but is random batch, in that different tests can be run at the same time. Once the lid is closed, it can't be opened, although, "a split lid is something we might think about in the future," Kong said.
AmpliVue Trichomonas
Also at this week's CVS workshop, Charlotte Gaydos, Director of the International Sexually Transmitted Diseases Research Laboratory and a professor at Johns Hopkins University School of Medicine, strongly endorsed molecular testing for Trichomonas vaginalis, and presented preliminary data on her lab's clinical trial of Quidel's AmpliVue Trichomonas test.
Gaydos noted that despite the clinical importance of the parasite, it is understudied in part due to the fact that there have been no good, inexpensive tests.
Gaydos' lab compared AmpliVue Trichomonas to microscopy, viral culture, and to Hologic's Aptima Trichomonas vaginalis (ATV) assay. Positive microscopy or culture were used to establish infected patient status.
In 1,126 women, Gaydos and colleagues found 90 percent positive agreement with culture in symptomatic patients, and 80 percent in asymptomatic. They also found a "very high" percent negative agreement.
Percent agreement versus ATV was 97.1 in symptomatic women, and 97.7 in asymptomatic women. Sensitivity for AmpliVue compared to ATV was 90.1 percent for symptomatic and 87.2 percent for asymptomatic women.
"The test is moderately complex, and is really pretty easy to perform," Gaydos said. "It also doesn't require any investment in expensive equipment."
Gaydos said she hopes that better tests will yield more attention to this infection and influence funding apportioned by public health officials and the National Institutes of Health.
In her STD clinic, she noted that only half of her male patients return for follow up, so point-of-care is ideal for them because she can also provide counseling while waiting 45 minutes for results.
Alternative sample types
Off-label sample type validation on a newly-cleared test might be one way to track whether a product is being embraced by the clinical lab community.
Gaydos noted that the standard methods to detect trichomonas — an assay called a 'wet prep' in which the lab looks for swimming parasites under the microscope — is very unreliable.
Molecular tests are ideal, especially for infection in men, she said, noting that there is some evidence linking trichomonas infection in men with prostate health. However, AmpliVue Trichomonas is currently only cleared for use with clinician-collected vaginal swabs.
At CVS, Gaydos' lab also presented preliminary results in a poster showing that self-collected penile swabs could be an effective sample type for detecting STDs.
Of 203 men at the Baltimore City Health Department STD Clinics recruited for that study — including 15 cases of trichomonas, 78 chlamydia, 58 gonorrhea, 9 herpes/HSV, and 13 syphilis cases — 90 percent of the men described the self-collection method as "easy" or "very easy" to perform, and 85 percent said they'd pay up to $20 if a swab test kit were available over the counter in the future.
At the corporate event, Gaydos said that self-collected penile swabs might make a nice addition to the AmpliVue sample types for trichomonas, although she did not describe any results of clinical testing.
Meanwhile, researchers from Children's Mercy Hospitals and Clinics in Kansas City, Mo., also presented a poster at CVS on an alternative specimen type for AmpliVue HSV 1+2.
Microbiology lab director Rangaraj Selvarangan explained that herpes infection in a mother can result in infection of an infant during delivery. This can cause HSV encephalitis, with very high morbidity and mortality. Suspected cases are usually given potent antivirals, which can be very toxic to newborns, so quickly ruling out infection would be very beneficial for patient management, he said.
Selvarangan's preliminary data showed that the AmpliVue test, which is approved for use on samples from open herpetic lesions, can also detect the virus from so-called 'surface cultures' of newborns.
Swabs were collected from different sites on the infants, and 96 swabs from 29 neonates were included in the study. Overall, 18 neonates had positive viral cultures, and AmpliVue accurately detected 16 of these 18 cases, with a sensitivity of 88.8 percent and specificity of 98.7 percent. Discrepant PCR analysis picked up HSV in only one of the samples that was missed, and the other was positive by AmpliVue but not culture. The test is rapid, taking only one hour, and is "easy to perform," but additional experiments are needed to determine whether this could ultimately reduce unnecessary antiviral use, Selvarangan said. Â