Viral Detection and Spectroscopy

No matter the battle, one of the primary items to evaluate is the arsenal of tools at one’s disposal. Thanks to Covid-19, 2020 has placed us all in a unique fight, not against a physical army or intangible idea, but against a novel virus that attacks people of all nations, especially our most vulnerable citizens. But we have multiple avenues to fight back, including:

  • Distancing. By minimising person-to-person interaction, we also minimise potential transmissions.
  • Vaccines. With a well-designed vaccine, even if someone is exposed to the virus their chances of it turning into a notable infection can be greatly reduced.
  • Treatments. If someone is exposed to the virus and it does indeed turn into an infection, an effective menu of treatments can help minimise mortality rates and overall severity.
  • Detection and tracing. These are our eyes in the battle against an invisible foe, and the key tools we’ll examine here.

Virus Detection and Tracing

Detection and tracing are critical in understanding how virus spread occurs historically so that future spreading can be minimised. This allows us to consider what activities and scenarios carry the greatest risk, and who among us may be most vulnerable. We can calibrate our policies and actions when we know how and where transmission is occurring.

But while slow detection methods can serve this purpose to a reasonable extent, fast detection techniques bring us even closer to the return to normal routines. A rapid testing system deployed at the entrance of a stadium, school, airport, or nursing home could instantly prevent a super-spreader scenario that we hear about all too often.

Familiar and Newer Viral Detection Techniques

The tried-and-true method of viral detection leans on the revolutionary PCR, or polymerase chain reaction, technology. This approach uses polymerase enzymes to replicate or amplify a specific region of genetic material if it is present. Templates can be designed that specifically target parts of the Covid-19 genetic code; if those code segments are present, they will be amplified. This amplification requires thermal cycling for roughly 30-40 cycles, which is typically the most time-consuming part of the PCR technique.

Once thermal cycling is complete there are several methods to observe if the targeted genetic material is present. This is where the power of applied spectral knowledge first shows up as a hero in Covid-19 detection.

Common fluorophores such as fluorescein and its derivatives can be further complexed so they become fluorescent only when bound to the targeted Covid-19 genetic segment. With these unique fluorescent tools in hand, the next hurdle we face in decreasing test time and increasing test sensitivity is optimising that fluorescence detection.

The most common approach for this type of trace-level fluorescence is steady-state broadband spectroscopy, which is well-served by the Ocean HDX spectrometer and LSM LED kits. The Ocean HDX sets a new bar for low-light performance in an amazingly compact spectrometer form factor. Proprietary internal baffling and other optical design triumphs allow fluorescence detection at levels previously only attainable on much larger and more costly systems. Driving that trace fluorescence is one of Ocean Insight’s LSM LED options, providing high-power and stable excitations for clean and coherent emission signals.

The traditional broadband approach brings with it a range of advantages, including the ability to observe multiple fluorescent species at the same time with one device, and the ability to develop intricate numerical methods to deconvolute desired signals from the broadband trends.

But there is another way to observe this fluorescence signal, by using an approach that exploits the fast decay properties of fluorescent dyes in a time-resolved manner. Ocean Insight typically provides the NeoFox phase fluorimetry system as an optical oxygen sensor platform, since we also develop the oxygen-responsive sensor chemistries and supporting probe and patch components that comprise the sensor platform.

But the NeoFox is also popular for embedding into other devices, with modifications possible to LEDs, filters, and internal settings to optimise the system into a customised detection platform. By strobing the LED as a square wave at kHz speeds, the NeoFox ultra-sensitive avalanche photodiode detector sees the fluorescence signal grow during LED on-time but also decay during LED off-time. This decay time is observed on the microsecond-to-nanosecond scale and can be tightly correlated to the concentration of fluorophore in the test fluid, such as a small PCR sample. Benefits of this approach include simplified hardware, since the NeoFox contains all its optics and processing electronics in a single casing, and provides good interference immunity to variables like sample colour and ambient light.

Raman and Trace Level Detection

While PCR has done wonders in the world of genetic advancement, there are still time constraints related to the necessary thermal cycling. Ocean Insight provides yet another approach with the potential to offer immediate viral detection — with answers in just seconds — without any complex sample pre-processing. This approach exploits the Raman technique, which uses a laser to drive observable Raman scattering phenomena.

Raman is a fast, powerful identification technique based on the rare interaction of photons with the molecular structure of the sample, specifically looking at the increase or decrease in photon energy level at quantised amounts. These sharp emission signals are inherent ‘fingerprints’ for an analyte and can quickly tell you when a certain species is present. Ocean Insight has offered high-performance Raman systems for over a decade at multiple wavelength options, such as the highly popular QE-Pro Raman+ platform offered in 785 nm, 638 nm and 532 nm configurations. Adding the wavelength-appropriate laser and probe is all you need for basic Raman measurements.

For trace level detection, Raman emissions can be further amplified by utilising certain metals that are ‘in-tune’ with the laser frequency being used, leaning on an effect called SPR, or Surface Plasmon Resonance. By using nanoparticles or nanostructures of a metal such as gold or silver, analytes may come in proper proximity to this SPR effect and lead to a dramatic amplification of Raman emission photons, which is a technique called SERS, or Surface Enhanced Raman Spectroscopy. Ocean Insight has been a leading commercial SERS provider since 2014 and offers low-cost, consumable substrates in an easy-to-use form factor. These convenient 5-packs have a proprietary nanoparticle formulation embedded into a quartz matrix and mounted onto a standard glass microscope slide. The user can simply add a few microliters of sample to the nanoparticle-doped region and place it under the Raman probe for rapid detection of trace-level analytes.

Ocean Insight has worked with several developers including Botanisol Analytics using Raman for rapid Covid-19 detection, and even the preliminary scans with off-the-shelf components have shown repeatable Raman activities for both direct viral fragments and the respective antibodies. While these measurements were done in rather clean sample fluids versus patient-obtained clinical samples, the research establishes the regions of Raman activity to look for when checking a “dirtier” real-world fluid. When analyzed using Ocean Intelligence, the advanced spectral machine learning platform from Ocean Insight, scans of complex bio-fluids can be thoroughly and rapidly deconvoluted to provide a positive/negative result with high statistical confidence.

As with any development, your progress is only as good as the partners you find and the resources you make available. Ocean Insight brings a unique level of expertise in spectral hardware, the proper techniques to use with that hardware, and the insight to achieve what has not been done before. If you’re in the fight to dramatically advance viral detection to help the world subdue the Covid-19 pandemic, we are eager to learn about your vision and how our applied spectral knowledge can help you unlock the possible.

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