Technologies Driving Advances in Molecular Diagnostics

Even before the COVID-19 pandemic, infectious diseases were a major public health concern with potential to cause global suffering, both physiologically and socioeconomically. Though we learned much from the world’s initial responses to COVID, ongoing scientific advances offer new tools for reducing the global instability and human tragedy that may ensue from future threats. An important ingredient in this endeavor is molecular testing to identify infectious pathogens for diagnosis, variant identification and surveillance, and vaccine development. Here’s a look at technologies that are improving molecular diagnostics in infectious disease today.

Essential PCR tools

Accurate COVID diagnostic tests were some of the most important tools developed during the pandemic’s onset, with the gold standard being the PCR-based test. Though PCR was already an essential tool, its importance was highlighted by the threat of COVID.

Bio-Rad’s comprehensive PCR tools provide ongoing support for the development of molecular diagnostics with instrumentation and reagents for PCR, qPCR, and droplet digital PCR (ddPCR). “The breadth and quality of this portfolio of products has encouraged the launch of numerous molecular diagnostic kits for pathogen detection from companies such as Altona, Seegene, and others who have chosen Bio-Rad qPCR platforms and reagents to standardize their infectious disease products on,” says Angelica Olcott, Market Development Manager at Bio-Rad Laboratories. “This enables the rapid deployment of tests for emerging infectious diseases, offering timely responses to new threats if they occur.”

The variety of PCR technologies offered by Bio-Rad support pathogen detection and disease research in different ways. “During the onset of the pandemic, Bio-Rad’s Instagene and Chelex reagents enabled cost-effective laboratory-developed tests when commercial kits were scarce,” says Olcott. The sensitive detection of ddPCR supports the identification of mutations and early monitoring for resistance tracking. “Scientists can easily create assay panels for research use to screen disease targets or look at immunologic responses using PrimePCR Assays for either quantitative PCR or ddPCR,” she says, adding that ultimately, continuing innovations may aid in improving the understanding of diseases, more efficient pathogen detection, and development of targeted treatments or interventions.

Testing anywhere

For everyday use or in developing countries, a drawback of PCR-based tests is the requirement for lab equipment and trained personnel to conduct the test. Sherlock Biosciences addresses this with single-molecule detection technology to make instrument-free diagnostic testing possible without the use of lab instrumentation.

Sherlock uses special CRISPR-Cas enzymes to detect single nucleic acid targets. Upon detection, enzyme activation generates a signal on a paper test strip. “CRISPR-based approaches hold the potential for addressing the need for decentralized diagnostics and improving access to molecular diagnostics worldwide,” says Bryan Dechairo, CEO of Sherlock Biosciences. “In low-cost, easy-to-use devices, CRISPR can bring molecular lab level accuracy to the home and low-resource settings for common respiratory and sexually-transmitted infections like COVID/flu/RSV and chlamydia and gonorrhea, respectively.”

Dechairo hopes that Sherlock Biosciences’ technology will contribute to decentralizing diagnostics, thereby improving global health and reducing healthcare inequities. Sherlock is aiming to power their second-generation testing devices with their own proprietary chemistries, making them usable in field settings with no power source.

Recently they were awarded Gates Foundation funding to develop fast molecular diagnostics for human papillomavirus, a major cause of cervical cancer worldwide. “Unfortunately, 81% of individuals in low- and middle-income regions are without access to essential diagnostics [in general],” he says. “As such, there is a global opportunity to bring decentralized testing to these patient populations by engineering diagnostics through synthetic biology, so we can bridge the gap in delivering life-saving medicines.”

One blood test, many answers

Instead of one test for one pathogen, it’s now possible to test one person for over 1000 pathogens simultaneously with the Karius Test, a liquid biopsy in the form of a quick and noninvasive single blood draw. This saves time and toil with very sick patients and their clinicians who need diagnostic information fast. The test sequences and identifies microbial cell-free DNA (mcfDNA), each one a distinct signature circulating in our blood when we’re infected by a particular pathogen.

The Karius Test is driven by recent technological advances in chemistry, computational technology, and artificial intelligence (AI). “The involvement of advanced chemistry for harvesting mcfDNA and computational technology for mapping microbial reads has enabled Karius to automate much of the testing process, achieving a quick turnaround time of just over a day from collecting the sample, to the physician receiving the report,” says Tim Blauwkamp, Karius Co-founder and Chief Scientific Officer. For vulnerable patients who may be immunocompromised and/or hospitalized, a fast result is especially important for diagnosis and treatment.

Karius sequences mcfDNA using next-generation sequencing, and analyzes the genomic data in real-time with AI-enhanced machine learning algorithms. “This AI-driven approach allows for the quantitative identification of clinically relevant pathogens, potentially aiding clinicians in optimizing antimicrobial treatment,” says Blauwkamp. “[Taken together,] these advancements have enabled the test to provide rapid, non-invasive, and comprehensive pathogen detection, ultimately improving the diagnosis and management of infectious diseases.” A recent multi-center study called PICKUP found that the Karius Test increased the identification of pneumonia-causing pathogens by 40% when added to normal diagnostic routines, helping clinicians to optimize antimicrobial treatments and minimize unnecessary diagnostic procedures.

New next-gen sequencing tools

Technological advances in next-generation sequencing continue to strengthen our molecular diagnostics toolbox. Element Biosciences’ AVITI platform uses novel chemistry that allows for lower costs and greater flexibility, making its benchtop sequencer especially suitable for running diagnostic tests. “In all applications, we don't require large numbers of samples to be batched, so turnaround times can be faster because you can run a relatively small number of samples,” says Shawn Levy, Chief Technology Officer at Element Biosciences. “So, if the research is in critical applications, like it often is in infectious disease, such as sepsis or neonatal screening, you can return a sensitive and quicker result.” Element’s sequencing-by-avidity chemistry involves a multivalent interaction for improved kinetics, and their novel surface chemistry reduces noise.

Element’s AVITI system offers other features important for molecular diagnostics, such as the ability to index the % reads early on, to estimate the representation from each sample. “This is helpful for our customers who want to know that they’ll generate enough data on a precious, time-sensitive infectious disease sample,” says Levy. Element’s platform can also stream the data off the sequencer in real time, which allows users to begin an early analysis for time-sensitive assays. “From an infectious disease perspective, this allows customers to ask after the first 50 cycles whether there are any key sequences indicative of a particular organism,” says Levy. “If the data suggest a highly virulent or infectious organism present, they can initiate next steps at that earlier stage, while allowing the run to continue for final validation.”

Element can offer lower sequencing prices because their reactions use about 100-fold less reagents. In early 2024, they plan to introduce a new capability into the workflow: enriching for sequences important in infectious disease. “Element is at the beginning of its innovation curve,” says Levy. “We're excited about what this means to molecular diagnostics, basic research, and the future of increasing resolution at the molecular level in biology and related fields.” Such advances, as well as others discussed above, are just a few examples of current innovations in molecular diagnostics.