Polymerase Chain Reaction in Decentralized Diagnostics of Infectious Diseases

Polymerase Chain Reaction (PCR) is often considered the “Gold Standard” for molecular diagnostics. It is a specific, sensitive, powerful tool that amplifies a minute sample of genetic material, either in the form of DNA or RNA, in a short period of time. It mimics DNA synthesis in vitro. PCR’s sensitivity allows disease detection even in the smallest of signals. Its specificity narrows down the exact location of a change in DNA sequence. PCR can be used in laboratories for multiple applications. Some examples include DNA fingerprinting in forensics, genetic testing and diagnostics. In only a few hours, diseases can already be detected in the PCR product by physicians. Hence PCR is considered the Gold Standard for molecular diagnostics.

There are decentralized diagnostics strategies, like Point of Care (POC) tests, which accurately achieve real-time, lab-quality diagnostic results within minutes. POC are easy-to-use diagnostic tests that can be carried out in many places such as one’s own home, a physician’s office, ambulances and other various locations at or near a patient, and at the site where treatment is provided. The results are quick and allows the patient to receive treatment as rapidly as possible without delay. Some examples of POC tests include, but not limited to; home pregnancy testing, dipstick urinalysis and glucose meters for diabetes screening and monitoring. Decentralized diagnostics are much more preferable to central lab diagnostics because POC can produce rapid results and in turn, rapid treatment without causing potential damage to patient samples. Thus, decentralized diagnostics are sometimes preferable to central diagnostics.

The first example of a decentralized PCR diagnostic platform is the Roche cobas Liat PCR System. It is a small, fast, 3-step easy-to-use system that takes up to 20 minutes, depending on the assay used. It has an advanced PCR technology which was previously only available to complex molecular laboratories. It can provide accurate results in only 20 minutes and not much training is required to use it. The cobas Liat system can be used to detect and identify a few diseases which are; Influenza A, Influenza B, Respiratory Syncytial Virus (RSV), and Strep A. The highly specific and sensitive system, with above at least 94% sensitivity and specificity, also reduces the risk of false negatives & positives.

Secondly, there’s also the BioFire FilmArray Torch system. It is a multiplex PCR system which consists of multiple panels to simultaneously test for over 80 different sets of pathogens which are some of the most pressing healthcare challenges in today’s time and age. Panels include; a respiratory panel testing for 20 respiratory pathogens, which are mostly viruses and bacteria, a blood culture identification panel testing for 24 pathogens and 3 antibiotic resistant genes associated with bloodstream infections, a gastrointestinal panel testing for 22 most common gastrointestinal pathogens, including bacteria, viruses, parasites and even protozoa, and a meningitis/encephalitis panel testing the cerebrospinal fluid for the 14 most relevant ME-associated pathogens. It is fast and easy-to-use, requiring only 2 minutes of hands-on time and an hour to run. It also has a reduced footprint providing up to 6 times the throughput per square foot of laboratory bench space.

And lastly, there’s the Palm PCR System which is a battery-powered, palm-size portable PCR machine. It can deliver PCR amplification with high speed and sensitivity in a small, handheld format. It is automated, simple and convenient with high efficiency, which makes it ideal for diagnoses both indoors and outdoors. Its sensitivity is to the extent of down below 10 copies. It is also extremely fast, depending on the molecular weight of nearly all kinds of DNA, including human genomic DNA, it can be amplified in up to 40 minutes. The dynamic range can be extended for up to 2kbp using a slower protocol at 39 minutes for 30 PCR cycles.

In my opinion, I think the BioFire FilmArray Torch system is the most developed and ready-to-use platform. While it may not be portable like the Palm PCR System, or as fast as the cobas Liat System which takes 15-20 minutes to run PCR, it is the most well-developed, with the most comprehensive testing. It can test for over 80 pathogens in one system, while the other two has limited testing for only a few specific pathogens. It also has an easy-to-follow protocol and can efficiently diagnose a patient in a relatively short amount of time.

In rural communities, there is a constant need for decentralized diagnostic platforms for detection and routine surveillance of an infectious disease outbreak. There will be a high incidence rate for infectious diseases in rural communities thus increasing the importance of developing such platforms for detection of diseases. There are some challenges to this, however. One being the affordability of the decentralized diagnostic platforms. These platforms, even the smaller ones, cost at least $3000 and above. Rural communities may not have sufficient funds to afford such luxury systems.

Another challenge also includes the limited number of samples that can be tested on these platforms. Even on the BioFire FilmArray, which in my opinion, is the most developed platform yet, it can only fit up to 264 samples per day with 12 modules. In the case of an infectious disease outbreak, there will be many people infected, leading to a longer time needed to process the patients’ samples. Hence when developing a decentralized PCR platform for infectious disease outbreak in rural communities, there needs to be consideration put in for the cost of the platform and fitting a large number of samples in one platform.