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Infectious Disease MDx 2014: qPCR for Ebola; Disease Panels; Isothermal Amplification

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NEW YORK (GenomeWeb) – Using PCR to diagnose infectious disease penetrated public awareness in an unprecedented new way last year when, during the height of public focus on Ebola, the technique began popping up even in general stories about the disease in popular media outlets.

Indeed, PCR remains the molecular analysis technology of choice for detecting and diagnosing infectious diseases, especially considering the single-target nature of many of these assays and the fact that PCR has traditionally excelled at quickly and accurately detecting one or a few targets, but has been difficult to multiplex on a larger scale.

However, many in the industry continue to refine pathogen detection by multiplexing nucleic acid amplification tests to get the most out of each sample, or by developing faster automated platforms that require less technical expertise to run. Still others are building point-of-care tests for low-resource settings, with paper-based nucleic acid amplification detection seemingly within reach.

Below are some notable trends over the past year in the use of PCR, isothermal amplification, and other nucleic acid amplification methodologies for molecular diagnosis of infectious diseases.

Low-hanging fruit

Although it is unclear how FDA Emergency Use Authorization of a diagnostic ultimately impacts commercialization, the number of companies developing Ebola tests since the FDA declared an Ebola emergency in August continues to grow.

Recent authorization of Roche's LightMix Ebola Zaire brought the total number of Ebola EUA recipients to seven, with firms such as Becton Dickinson, BioInnovation Solutions, STMicroelectronics, and Ubiquitome also recently announcing intent to seek it.

Uptake of FDA cleared molecular diagnostics can depend on many factors. A competitive edge in time to result, or resoundingly supportive scientific studies might influence diagnostics labs' purchasing choices.

With numerous economic factors in play, some firms seem to have focused portions of their testing portfolios on "low-hanging fruit" – diagnostics for common ailments with predictable cycles of contagion, ones with a plethora of research funding, or ones for which research strongly supports the link between a nucleic acid detection and illness.

Because of this, the number of available molecular assays for things like influenza or human papillomavirus seems to be burgeoning. When a recent study validated Cepheid's Xpert Flu in an ER setting, it may have gained some traction among the nearly two-dozen nucleic acid-based tests of influenza cleared or approved by the FDA. As covered recently in GenomeWeb, influenza is currently a target in many firms' diagnostics portfolio pipelines. Interestingly, a few of the approved tests were EUA recipients during the H1N1 influenza emergency.

Likewise, HPV detection has driven growth for many firms, but the landscape seems to be shifting with new assay platforms and changing cervical cancer screening guidelines. In this case, the relative importance of false positive versus false negative HPV test results and genotyping has now become part of the debate.

New guidelines unequivocally endorsing nucleic acid testing may also be fundamentally changing the way clinicians test for chlamydia and gonorrhea. There are currently 28 different FDA cleared or approved assays for Chlamydia trachomatis, Neisseria gonorrhoeae, or the two combined.

Tipping point for point of care?

Nucleic acid amplification tests are almost always more specific and sensitive than antibody-based testing. But wheeling a thermocycler into a clinical encounter and asking a patient to wait three hours for PCR-based test results is out of the question. As such, smaller, faster molecular diagnostics have increasingly been a goal in the industry.

Alere, a company traditionally dealing in immunoassays, now seems poised to become the first firm to claim true bedside diagnosis with its Alere i platform.

The platform uses isothermal nucleic acid amplification to run molecular diagnostic tests in about 15 minutes. The company obtained FDA clearance of an influenza A and B assay for the Alere i this past year, and intends to get this platform CLIA waived so that it can be run by clinicians, a spokesperson told GenomeWeb.

Also aiming for isothermal point-of-care, tests, Lucigen is capitalizing on a unique polymerase with reverse-transcription properties. The company has been building an assay of three viral hemorrhagic fevers, and has also announced plans to pursue EUA for an Ebola test. It is using the same technology to pursue a parallel path of buliding "penside" assays for animal health, with hopes of impacting the current epidemic viral disease affecting pigs in theUS.

Meanwhile, a number of other platforms nearing the end stages of development are designed to bring the lab to the clinic and can be run by people less skilled in lab protocols. Quidel's Savanna and Solana test platforms, for example, can run isothermal assays and debuted on the conference circuit this past summer. The firm expects to start trials of HIV testing in Africa and intends to leverage these to develop tests on the platforms for aUS market.

On a more grassroots level, isothermal recombinase polymerase amplification, or RPA, the technology developed by Alere subsidiary TwistDx, is being rapidly taken up by researchers to build point-of-care diagnostics for an assortment of pathogens. Researchers have also used RPA and other isothermal techniques to create electricity-free diagnostics, including ones that can be run using body heat.

And, although it is not isothermal in nature, Cepheid's GeneXpert platform remains one of the nearest-to-patient products currently commercially available, and the company continues to add to the test menu for that platform.

Panels and test menus

Panelization of lab-based molecular tests is a growing trend, and firms such as BioFire, Becton Dickinson, and Luminex have attained, or are pursuing, FDA clearance of molecular diagnostics panels. Companies with innovative amplification technologies are also embarking on the panel path. SpeeDx, for example, is developing a meningitis panel in Australia, and Seegene is looking to use its "multiplex quantification" chemistry to create panels for HPV detection.

Hospital clinical labs are major markets for molecular diagnostics, and demand from these customers has been a major factor in increasing panelization of tests. Assessing the preferences of laboratorians in high- and low-volume labs may be a way to spot future trends.

Points of consensus among end users currently seem to be an emphasis on ease of use and getting the most out of each patient sample. Lab directors GenomeWeb has spoken to, such as Nathan Ledeboer at Wisconsin Medical College or Romney Humphries at the University of California, Los Angeles, are also mindful of space, and seem to appreciate having more menu options on a single platform.

In fact, Qiagen has been rapidly expanding its molecular test menu to replace lost HPV business, while Cepheid has laid out an ambitious menu expansion plan through 2017, and menu expansion on the BioFire FilmArray will likely drive growth for new owners BioMérieux.

Smaller, multi-purpose platforms with bigger menus seem to have appeal, yet platforms that tend toward the larger end of the footprint spectrum but that can accomplish surprisingly accurate or sensitive diagnosis are not going unnoticed. These include Abbott's Iridica platform, which has impressed some users with the ability to detect rare and difficult to culture pathogens. The appeal of the wow factor could also encompass the developing diagnostic capabilities of digital droplet PCR, such as detecting ongoing beta-cell loss in people at risk of developing diabetes or measuring circulating miRNA biomarkers.

In the coming year it will be interesting to note how these trends impact the growing debate around lab-developed test regulation. The US Food and Drug Administration proposal to regulate LDTs — many of which utilize PCR or other nucleic acid amplification technologies — will likely continue to be a contentious topic, and could ultimately change established pathways of diagnostics development and commercialization.

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