NEW YORK (GenomeWeb) – A research team from the UK has determined that a rapid molecular Ebola assay from BioMérieux subsidiary BioFire Defense is sufficiently sensitive and specific to be an attractive option for relatively low-throughput laboratories testing for the disease.
However, the assay and accompanying platform may not yet be suitable in outbreak situations or in labs with relatively high testing throughput, the researchers suggested.
Rapid and specific testing is critical for patient care in suspected cases of Ebola virus infection, but rigorous evaluation of the numerous molecular diagnostics that have received Emergency Use Authorization from the US Food and Drug Administration is ongoing.
Since August of 2014, eight molecular diagnostics for Ebola have been authorized. These include the FilmArray NGDS BT-E Assay and Biothreat-E test from BioFire Defense, which have been the subject of at least three peer-reviewed evaluations since mid-July of this year.
The most recent study of the BioThreat-E test, published online last week in the Journal of Clinical Microbiology, was a collaborative effort of the Defence Science Technology Laboratory, Public Health England, and the Centre of Defence Pathology in the UK.
The group tested samples as they became available during the Ebola crisis last year. These included 44 patients in Sierra Leone as well as 70 patients in the UK who had symptoms and had recently traveled to West Africa. During that period, the rare and imported pathogens lab at PHE saw a 10-fold increase in testing frequency, although the majority of patients were not infected with Ebola, the study noted.
Importantly, the evaluation deviated from the BioFire FilmArray protocol by adding a heating step prior to testing of 60 °C for 15 minutes. This was intended to inactivate the virus and enable the assays to be performed at lower biological safety levels.
According to Simon Weller, first author on the JCM study and a researcher at DSTL, the three agencies had different aims in conducting the evaluation.
"From a defense perspective, we have an interest in low operative and logistic burden diagnostic technologies — the FilmArray fits neatly into this area — and therefore the Ebola outbreak was an opportunity to test such a platform in a real-world setting," Weller told GenomeWeb in an email.
Meanwhile, from a public health perspective, there was a requirement to enhance the UK capability to rapidly test suspected patients closer to where they presented for diagnosis, Weller said, noting that most regional PHE labs didn’t operate an Ebola testing service prior to the outbreak.
"The FilmArray was a candidate for a means to rapidly put a safe and sensitive testing capability into these regional labs," he added.
The study compared the FilmArray Biothreat E-test to a published TaqMan-based real-time PCR assay. That assay had been optimized and validated previously by PHE for use in the UK and Sierra Leone, and included a bacteriophage internal control, Weller said.
The BioThreat-E test showed comparable performance to the validated PCR, with a sensitivity of 84 percent and specificity of 89 percent in the Sierra Leone samples, and a sensitivity of 75 percent and specificity of 100 percent in the samples from the UK.
This difference between the sites was likely a function of different prevalence of Ebola in the two countries and the relatively low sample numbers, rather than a performance or geographic characteristic, Weller said.
There were also nine discrepant results, potentially attributable to waning viral load and inhibitors present in whole blood.
Safely handling patient samples that could be infected with Ebola is always a concern. The comparator RT-PCR required a centrifugation step, which can potentially create aerosols.
"Within the small isolators in Sierra Leone — the only containment available there — there was a significant operative and temporal penalty in having to centrifuge," Weller explained.
"There was a lot of packaging in the isolators from unpacking samples; blood then had to be transferred to microtubes for centrifugation and then plasma had to be transferred to a fresh microtube for inactivation and RNA extraction — it took a while to do, even with practice."
The BioThreat-E test, on the other hand, used only 200 microliters of whole blood.
Disposal of waste and cleaning the platform is also important. In Sierra Leone, test pouches were double bagged and put into a clinical waste stream for immediate on-site incineration, Weller said, while in the UK they were autoclaved prior to incineration.
"How to disinfect a platform and then be able to subsequently use it is something we have an interest in," he said, adding, "We didn’t experience a pouch split in our testing and, in any case, put in an inactivation step prior to PCR."
And while the one-hour BioThreat-E test was found to be an "attractive option" for lower-throughput testing, it may not meet requirements for outbreak situations.
"When I was in Sierra Leone, we routinely had batches of 40 samples or more," Weller said. "These would be unsustainable to test on the FilmArray — it would be very costly and take too long."
He noted that in his experience of Ebola testing, there were bottlenecks in the unpacking of samples, generating plasma to test, and EBOV inactivation, all of which must be performed in a small isolator, as well as in the manual RNA extraction and PCR.
"An integrated platform [that performs] RNA extraction and PCR [and] which is able to test whole blood samples and run samples concurrently might be an interesting thing to evaluate," he said. A rapid diagnostic test that also included viral inactivation steps would be interesting as well, he suggested, although overall the researchers found the general microbiological screening capability of the FilmArray very useful in Sierra Leone.
In the future, the three labs will use whichever test or technology is best for the particular scenario they are faced with, as the FilmArray "is a very useful tool but only as part of a wider microbiological [and] virological testing capability," Weller said.
However, he said that he would hope the international community has now evaluated enough platforms and technologies for Ebola testing, and that it has enough experience to be able to rapidly deploy the best technologies and approaches in any future Ebola outbreak.
"Hopefully there will not be one on the same scale again," he said.