CRISPR diagnostics identify specific genetic material, changing how diseases are detected. This technology uses components of a natural bacterial defense system to precisely locate and signal the presence of target DNA or RNA sequences. It holds promise for advancing diagnostic capabilities across medical fields.
What is CRISPR and How It Detects
CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, is a bacterial adaptive immune system against invading viruses. This system stores small pieces of viral genetic material, called spacers, within its own genome, allowing it to “remember” past infections. When a familiar invader reappears, the CRISPR system uses these stored memories to quickly identify and neutralize the threat.
For diagnostics, this bacterial defense mechanism is adapted. The core components are CRISPR-associated (Cas) enzymes, such as Cas9, Cas12, or Cas13, and a guide RNA (gRNA). The gRNA is designed to be complementary to a specific DNA or RNA sequence of interest, such as a pathogen’s genetic signature or a disease biomarker.
When the gRNA guides the Cas enzyme to its target sequence, the Cas enzyme becomes activated. This activation triggers “collateral cleavage” activity, where the enzyme cuts any surrounding single-stranded DNA or RNA molecules indiscriminately. Reporter molecules, labeled with a tag, are introduced. When cleaved by the activated Cas enzyme, these reporters release their signal, indicating the target’s presence.
Different Cas enzymes offer advantages for detection. Cas13 specifically targets RNA, suitable for direct detection of RNA viruses like SARS-CoV-2 without converting RNA to DNA. Cas12 targets DNA. This targeting and cleavage mechanism, often coupled with amplification techniques to increase target material, allows for sensitive detection of minute quantities of DNA or RNA.
Diverse Applications of CRISPR Diagnostics
CRISPR diagnostics are applied across various medical fields, identifying diverse disease markers. They detect infectious diseases, including viral infections such as COVID-19, influenza A and B viruses, Zika virus, and human papillomavirus (HPV). The technology also identifies bacterial infections, including Mycobacterium tuberculosis, Salmonella enteritidis, and Listeria monocytogenes, and genes associated with antibiotic resistance.
Beyond infectious agents, CRISPR diagnostics show promise in cancer detection by identifying specific cancer biomarkers. This includes detecting circulating tumor DNA (ctDNA) and genetic mutations associated with cancers. For example, CRISPR-based tools are being developed for early detection and monitoring of colorectal and breast cancer, and for identifying drug-resistant mutations in cancer cells.
The technology is also expanding into diagnosing genetic disorders. CRISPR’s ability to identify single nucleotide polymorphisms (SNPs) and other genetic markers allows for detecting conditions like sickle cell disease. This broad applicability suggests CRISPR diagnostics could become a comprehensive tool for molecular testing across many health conditions.
Advantages and Impact
CRISPR-based diagnostic tools offer advantages over traditional methods like polymerase chain reaction (PCR) or enzyme-linked immunosorbent assays (ELISA). One benefit is their speed, often providing results within 15 to 30 minutes, compared to hours or days for conventional laboratory tests. This rapid turnaround enables quicker patient management and disease containment, particularly for infectious outbreaks.
Another advantage is the high specificity and sensitivity of these tools. CRISPR systems can identify target nucleic acid sequences, minimizing false positives and negatives and ensuring reliable results. Some platforms can detect target DNA or RNA at attomolar to femtomolar concentrations, making them comparable to or more sensitive than traditional PCR in certain applications.
CRISPR diagnostics also show potential for cost-effectiveness due to simpler reagent requirements and the ability to operate without expensive laboratory equipment. This fosters accessibility, especially for point-of-care (POC) testing in resource-limited settings or remote areas where complex laboratory infrastructure is unavailable. These advantages enhance disease surveillance, particularly during epidemics, and support personalized medicine by enabling identification of genetic predispositions and guiding tailored treatment strategies.
Current Accessibility and Future Outlook
CRISPR diagnostics are currently in various stages of development, from research and clinical trials to emergency use authorizations for specific applications. During the COVID-19 pandemic, platforms like SHERLOCK and DETECTR rapidly received emergency use authorizations for SARS-CoV-2 detection, showing their potential for quick deployment in public health crises. Despite their promise, widespread clinical adoption faces hurdles, including the need for ultralow temperature storage for some CRISPR proteins and the requirement for sample processing steps like lysis or pretreatment.
Factors influencing broader adoption include navigating regulatory pathways and scaling up manufacturing. However, the market for CRISPR-based diagnostics is projected to grow, indicating increasing investment and development. For instance, in January 2025, CrisprBits Private Limited opened a new laboratory to advance CRISPR-based diagnostic solutions, particularly for hospital-acquired infections and antimicrobial resistance.
The future outlook for CRISPR diagnostics includes developing new diagnostic platforms and integrating them into routine healthcare. Efforts are underway to create more user-friendly, portable solutions for at-home and field use, improving access to testing. Companies are conducting clinical trials for rapid, over-the-counter diagnostic tests for sexually transmitted infections, aiming for results in under 30 minutes with self-collected samples. Further advancements may involve integrating CRISPR diagnostics with artificial intelligence and machine learning to enhance accuracy and automate analysis, expanding capabilities beyond nucleic acid detection to include proteins and small molecules.