New Device Can Diagnose COVID-19 From Saliva Samples

Engineers at MIT and Harvard University have designed a small tabletop device that can detect SARS-CoV-2 from a saliva sample in about an hour. In a new study, they showed that the diagnostic is just as accurate as the PCR tests now used.

The device can also be used to detect specific viral mutations linked to some of the SARS-CoV-2 variants that are now circulating. This result can also be obtained within an hour, potentially making it much easier to track different variants of the virus, especially in regions that don’t have access to genetic sequencing facilities.

“We demonstrated that our platform can be programmed to detect new variants that emerge, and that we could repurpose it quite quickly,” says James Collins, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering. “In this study, we targeted the U.K., South African, and Brazilian variants, but you could readily adapt the diagnostic platform to address the Delta variant and other ones that are emerging.”

The new diagnostic, which relies on CRISPR technology, can be assembled for about $15, but those costs could come down significantly if the devices were produced at large scale, the researchers say.

Collins is the senior author of the new study, which appears in Science Advances. The paper’s lead authors are Helena de Puig, a postdoc at Harvard University’s Wyss Institute for Biologically Inspired Engineering; Rose Lee, an instructor in pediatrics at Boston Children’s Hospital and Beth Israel Deaconess Medical Center and a visiting fellow at the Wyss Institute; Devora Najjar, a graduate student in MIT’s Media Lab; and Xiao Tan, a clinical fellow at the Wyss Institute and an instructor in gastroenterology at Massachusetts General Hospital.

A self-contained diagnostic

The new diagnostic is based on SHERLOCK, a CRISPR-based tool that Collins and others first reported in 2017. Components of the system include an RNA guide strand that allows detection of specific target RNA sequences, and Cas enzymes that cleave those sequences and produce a fluorescent signal. All of these molecular components can be freeze-dried for long-term storage and reactivated upon exposure to water.

Last year, Collins’ lab began working on adapting this technology to detect the SARS-CoV-2 virus, hoping that they could design a diagnostic device that could yield rapid results and be operated with little or no expertise. They also wanted it to work with saliva samples, making it even easier for users.

To achieve that, the researchers had to incorporate a critical pre-processing step that disables enzymes called salivary nucleases, which destroy nucleic acids such as RNA. Once the sample goes into the device, the nucleases are inactivated by heat and two chemical reagents. Then, viral RNA is extracted and concentrated by passing the saliva through a membrane.

“That membrane was key to collecting the nucleic acids and concentrating them so that we can get the sensitivity that we are showing with this diagnostic,” Lee says.

This RNA sample is then exposed to freeze-dried CRISPR/Cas components, which are activated by automated puncturing of sealed water packets within the device. The one-pot reaction amplifies the RNA sample and then detects the target RNA sequence, if present.

“Our goal was to create an entirely self-contained diagnostic that requires no other equipment,” Tan says. “Essentially the patient spits into this device, and then you push down a plunger and you get an answer an hour later.”

The researchers designed the device, which they call minimally instrumented SHERLOCK (miSHERLOCK), so that it can have up to four modules that each look for a different target RNA sequence. The original module contains RNA guide strands that detect any strain of SARS-CoV-2. Other modules are specific to mutations associated with some of the variants that have arisen in the past year, including B.1.1.7, P.1, and B.1.351.

The Delta variant was not yet widespread when the researchers performed this study, but because the system is already built, they say it should be straightforward to design a new module to detect that variant. The system could also be easily programmed to monitor for new mutations that could make the virus more infectious.

“If you want to do more of a broad epidemiological survey, you can design assays before a mutation of concern appears in a population, to monitor for potentially dangerous mutations in the spike protein,” Najjar says.

Tracking variants

The researchers first tested their device with human saliva spiked with synthetic SARS-CoV-2 RNA sequences, and then with about 50 samples from patients who had tested positive for the virus. They found that the device was just as accurate as the gold standard PCR tests now used, which require nasal swabs and take more time and significantly more hardware and sample handling to yield results.

The device produces a fluorescent readout that can be seen with the naked eye, and the researchers also designed a smartphone app that can read the results and send them to public health departments for easier tracking.

The researchers believe their device could be produced at a cost as low as $2 to $3 per device. If approved by the FDA and manufactured at large scale, they envision that this kind of diagnostic could be useful either for people who want to be able to test at home, or in health care centers in areas without widespread access to PCR testing or genetic sequencing of SARS-CoV-2 variants.

“The ability to detect and track these variants is essential to effective public health, but unfortunately, variants are currently diagnosed only by nucleic acid sequencing at specialized epidemiological centers that are scarce even in resource-rich nations,” de Puig says.

Reference: de Puig H, Lee RA, Najjar D, et al. Minimally instrumented SHERLOCK (MiSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Sci Adv. 2021;7(32)

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Biosensors Transform the Diagnosis of Infections in Newborns

Sepsis refers to a systemic (body-wide) infection accompanied by inflammation. Newborn infants are particularly susceptible to developing sepsis, given their naïve and under-developed immune systems. The infant immune system reacts to the acquired pathogen by releasing inflammatory factors such as cytokines and free radicals. The heightened immune response mounted against the pathogen, if uncontrolled, can cause severe damage to other organs, which can be fatal for the newborn. The prevalence of neonatal sepsis and associated mortality rates are especially high in developing countries, owing to poor sanitation and the dearth of healthcare resources.

Early diagnosis is thus cardinal for effective management of the infection and decreasing neonatal mortality. Current point-of-care (POC) methods rely on conventional blood culture and molecular techniques that may be time-consuming and often detect a single parameter or biomarker. Hence, development of rapid, sensitive, and integrated diagnostic strategies is crucial to enhance detection and improve the standard of care.

In a new Clinica Chimica Acta article, researchers from Shoolini University, in collaboration with researchers from IIT Hyderabad and Amity University, Rajasthan, India, have reviewed the latest advancements in analytical devices that enable multi-analyte detection with high sensitivity and accuracy. They also describe the limitations of currently used methods and why a combinatorial approach may be better. Speaking of why this caught their attention, lead author of the study, Dr. Anupam Jyoti, says, "Developing countries like India report an increased incidence of neonatal sepsis (50–70/1000 live births) as compared to developed countries (1–5/1000 live births), with a substantial mortality rate of 11–19%. We were thus motivated to review the field of neonatal sepsis detection and propose new directions towards effective diagnosis."

Routinely used blood culture techniques often require two to five days to yield results. Meanwhile, the infection escalates, and the newborn is often pumped with unnecessary antibiotics that can lead to anti-microbial resistance. Techniques such as the polymerase chain reaction, which detects the genetic material of the pathogen, and mass spectrometry, which detects pathogen specific proteins, are more sensitive and require less time. However, they can yield false positive results and do not differentiate between viable and non-viable pathogens in the sample. While tests that detect serum biomarkers and immune factors, expressed in response to infection, may give a broad idea about the presence of sepsis, they cannot differentiate between specific pathogens. Together, the methods may however complement each other for robust diagnosis of sepsis.

Biosensing analytical technologies have emerged as a powerful tool in biomedical devices. Advanced biosensors that promise multi-analyte detection in a single platform are now being increasingly developed for rapid and sensitive diagnosis. Electrochemical sensors can detect various electrolytes and biomarkers based on their specific electrical properties. Given the minute size, stability and high binding affinity of aptamers, or single-stranded nucleic acid probes, are useful for detecting bacterial traces in the blood. Next, sensors based on the surface plasmon resonance technique can detect changes in the optical properties of the sample. They are highly sensitive with low limits of detection, thus enabling the detection of small concentrations of pathogens. Finally, microfluidic devices and chip-based sensors analyze samples based on their flow or size and can thus detect bacterial and blood cells in the samples of patients with sepsis.

In addition to these methods, integrated approaches that combine the principles of multiple techniques on a single platform are gaining popularity. Such hybrid biosensors will be capable of detecting multiple parameters in a short time from small samples at the bedside of the patient. Moreover, their wide applicability, cost-effectiveness, small size, and need for limited resources make them a practical and valuable tool for the diagnosis of neonatal sepsis.

Overall, the review sheds light on modern technologies that can help strengthen, and possibly replace conventional POC approaches in the future. "Integrated POC-based diagnosis will help reduce detection time considerably and thus translate diagnosis from bench to the bedside. An efficient POC sepsis diagnostic platform could expand health care access and impact populations worldwide," says Dr. Jyoti.

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Microwave Sensor for Rapid Antibiotic Sensitivity Testing

Researchers on the campus of the University of British Columbia Okanagan have developed a portable and economical microwave sensor that can quickly detect changes in bacterial growth to assess susceptibility to antibiotics. Using a split ring microwave resonator, the device can very significantly measure bacterial growth in the presence of different concentrations of antibiotic before there are visible changes in growth. The technology reduces the time and costs associated with these tests and could pave the way for personalized antibiotic therapy for regions with low or remote resources.

Antibiotics have revolutionized healthcare, allowing routine surgical procedures to continue without the excessive fear of devastating infections and ending a huge variety of nasty diseases that would previously have killed or disabled millions of people each year. . However, these advances are being eliminated slowly but surely by antibiotic resistance, which increases every year.

“Many types of bacteria are constantly evolving to develop antibiotic resistance. This is an urgent issue for hospitals around the world, while diagnostic and sensor technology has been slow to adapt, “Mohammad Zarifi, a researcher involved in the study, said in a press release.

The main problem is the inappropriate use of antibiotics and part of the solution is to choose the right antibiotic for each patient. After all, it is useless to prescribe an antibacterial agent for an infection caused by bacteria that are already resistant to that agent. This is where personalized antibiotic therapy comes in, which is to test a sample of disease-causing bacteria for a specific patient to determine their antibiotic susceptibility before prescribing a suitable antibiotic.

The problem is that this process is time consuming and expensive, often taking 48 hours, which is no joke if you have a serious infection. “Longer waiting times can significantly delay the treatments patients receive, which can lead to medical or even fatal complications. This method demonstrates the requirement for a reliable, fast and cost-effective screening tool,” he said. Zarifi.

This new technology is based on the detection of microwaves as a means to control the growth of the bacterial sample in the presence of different concentrations of antibiotic. The system is sensitive enough that it can detect differences in bacterial growth that are invisible to the human eye, and achieves this through a split-ring microwave resonator. The charged substances released by bacterial cells, when affected by antibiotics, can help with the measurement, but in essence, the resonant response of the split ring is affected by the growth of a bacterial sample on agar.

Ultimately, researchers hope to incorporate an element of artificial intelligence into the technology to help detect and predict personalized antibiotic treatment.

“Our ultimate goal is to reduce the inappropriate use of antibiotics and improve the quality of patient care,” Zarifi said. “The more quality tools health professionals have at their disposal, the greater their ability to fight bacteria and viruses.”

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Using Two CRISPR Enzymes, UC Berkeley Scientists Develop a 20-Minute COVID Diagnostic

While today’s gold standard COVID-19 diagnostic test, which uses qRT-PCR — quantitative reverse-transcriptase-polymerase chain reaction (PCR) — is extremely sensitive, detecting down to one copy of RNA per microliter, it requires specialized equipment, a runtime of several hours and a centralized laboratory facility. As a result, testing typically takes at least one to two days.

A research team led by scientists in the labs of Jennifer Doudna, David Savage and Patrick Hsu at the University of California, Berkeley, is aiming to develop a diagnostic test that is much faster and easier to deploy than qRT-PCR. It has now combined two different types of CRISPR enzymes to create an assay that can detect small amounts of viral RNA in less than an hour. Doudna shared the 2020 Nobel Prize in Chemistry for invention of CRISPR-Cas9 genome editing.

While the new technique is not yet at the stage where it rivals the sensitivity of qRT-PCR, which can detect just a few copies of the virus per microliter of liquid, it is already able to pick up levels of viral RNA — about 30 copies per microliter — sufficient to be used to surveil the population and limit the spread of infections.

“You don’t need the sensitivity of PCR to basically catch and diagnose COVID-19 in the community, if the test’s convenient enough and fast enough,” said co-author David Savage, professor of molecular and cell biology. “Our hope was to drive the biochemistry as far as possible to the point where you could imagine a very convenient format in a setting where you can get tested every day, say, at the entrance to work.”

The researchers will report their results online August 5 in the journal Nature Chemical Biology.

Several CRISPR-based assays have been authorized for emergency use by the Food and Drug Administration, but all require an initial step in which the viral RNA is amplified so that the detection signal — which involves release of a fluorescent molecule that glows under blue light — is bright enough to see. While this initial amplification increases the test’s sensitivity to a similar level as qRT-PCR, it also introduces steps that make the test more difficult to carry out outside of a laboratory.

The UC Berkeley-led team sought to reach a useful sensitivity and speed without sacrificing the simplicity of the assay.

“For point of care applications, you want to have a rapid response so that people can quickly know if they’re infected or not, before you get on a flight, for example, or go visit relatives,” said team leader Tina Liu, a research scientist in Doudna’s lab at the Innovative Genomics Institute (IGI), a CRISPR-focused center involving UC Berkeley and UC San Francisco scientists.

Aside from having an added step, another disadvantage of initial amplification is that, because it makes billions of copies of viral RNA, there is a greater chance of cross-contamination across patient samples. The new technique developed by the team flips this around and instead boosts the fluorescent signal, eliminating a major source of cross-contamination.

The amplification-free technique, which they term Fast Integrated Nuclease Detection In Tandem (FIND-IT), could enable quick and inexpensive diagnostic tests for many other infectious diseases.

“While we did start this project for the express purpose of impacting COVID-19, I think this particular technique could be applicable to more than just this pandemic because, ultimately, CRISPR is programable,” Liu said. “So, you could load the CRISPR enzyme with a sequence targeting flu virus or HIV virus or any type of RNA virus, and the system has the potential to work in the same way. This paper really establishes that this biochemistry is a simpler way to detect RNA and has the capability to detect that RNA in a sensitive and fast time frame that could be amenable for future applications in point of care diagnostics.”

The researchers are currently in the process of building such a diagnostic using FIND-IT, which would include steps to collect and process samples and to run the assay on a compact microfluidic device.

Employing tandem Cas proteins

To remove target amplification from the equation, the team employed a CRISPR enzyme — Cas13 — to first detect the viral RNA, and another type of Cas protein, called Csm6, to amplify the fluorescence signal.

Cas13 is a general purpose scissors for cutting RNA; once it binds to its target sequence, specified by a guide RNA, it is primed to cut a broad range of other RNA molecules. This target-triggered cutting activity can be harnessed to couple detection of a specific RNA sequence to release of a fluorescent reporter molecule. However, on its own, Cas13 can require hours to generate a detectable signal when very low amounts of target RNA are present.

Liu’s insight was to use Csm6 to amplify the effect of Cas13. Csm6 is a CRISPR enzyme that senses the presence of small rings of RNA and becomes activated to cut a broad range of RNA molecules in cells.

To boost Cas13 detection, she and her colleagues designed a specially engineered activator molecule that gets cut when Cas13 detects viral RNA. A fragment of this molecule can bind to and trigger Csm6 to cut and release a bright fluorescent molecule from a piece of RNA. Normally, the activator molecule is quickly broken down by Csm6, thus limiting the amount of fluorescent signal it can generate. Liu and her colleagues devised a way to chemically modify the activator so that it is protected from degradation and can supercharge Csm6 to repeatedly cut and release fluorescent molecules linked to RNA. This results in a sensitivity that is 100 times better than the original activator.

“When Cas13 gets activated, it cleaves this small activator, removing a segment that protects it,” Liu said. “Now that it’s liberated, it can activate lots of different molecules of that second enzyme, Csm6. And so, one target recognized by Cas13 doesn’t just lead to activation of its own RNA-cutting ability; it leads to the generation of many more active enzymes that can each then cleave even more fluorescent reporters.”

The team of researchers also incorporated an optimized combination of guide RNAs that enables more sensitive recognition of the viral RNA by Cas13. When this was combined with Csm6 and its activator, the team was able to detect down to 31 copies per microliter of SARS-CoV-2 RNA in as little as 20 minutes.

The researchers also added extracted RNA from patient samples to the FIND-IT assay in a microfluidic cartridge, to see if this assay could be adapted to run on a portable device. Using a small device with a camera, they could detect SARS-CoV-2 RNA extracted from patient samples at a sensitivity that would capture COVID-19 infections at their peak.

“This tandem nuclease approach — Cas13 plus Csm6 — combines everything into a single reaction at a single temperature, 37 degrees Celsius, so it does not require high temperature heating or multiple steps, as is necessary for other diagnostic techniques,” Liu said. “I think this opens up opportunities for faster, simpler tests that can reach a comparable sensitivity to other current techniques and could potentially reach even higher sensitivities in the future.”

The development of this amplification-free method for RNA detection resulted from a reorientation of research within IGI when the pandemic began toward problems of COVID-19 diagnosis and treatment. Ultimately, five labs at UC Berkeley and two labs at UCSF became involved in this research project, one of many within the IGI.

“When we started this, we had hopes of creating something that reached parity with PCR, but didn’t require amplification — that would be the dream,” said Savage, who was principal investigator for the project. “And from a sensitivity perspective, we had about a ten thousandfold gap to jump. We’ve made it about a thousandfold; we’ve driven it down about three orders of magnitude. So, we’re almost there. Last April, when we were really starting to map it out, that seemed almost impossible.”

The work was supported by the Defense Advanced Research Projects Agency (N66001-20-2-4033). Co-authors of the paper include members of the labs of Jennifer Doudna, David Savage, Patrick Hsu, Liana Lareau and Daniel Fletcher at UC Berkeley; Gavin Knott at Monash University in Australia; Melanie Ott and Katherine Pollard at Gladstone Institutes and UCSF; and Ming Tan at Wainamics, a research and development firm in Pleasanton, California, that produces microfluidic devices. Doudna, IGI’s founder and currently president and chair of the IGI governance board, is the Li Ka Shing Chancellor’s Chair at UC Berkeley and a professor of chemistry and of molecular and cell biology. Hsu, Lareau and Fletcher are faculty in the Department of Bioengineering.

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Immunexpress Announces SeptiCyte® RAPID Testing For Paediatric Sepsis

Immunexpress, Pty Ltd, a molecular diagnostic company founded in Brisbane, today announced that the SeptiCyte® RAPID test will be evaluated in the diagnosis of paediatric sepsis in Queensland children. 

The testing is in part funded through a Federal Government's Medical Research Future Fund Genomic Health Futures Mission grant for collaborative work between The University of Queensland and Immunexpress. One of the keys to the successful development of the SeptiCyte technology has been early investment funding through the foresight of Brian Flannery (Ilwella family office), and Australian Federal Government commercialization grants.

The work will be led by the paediatric sepsis research team working with Associate Professor Luregn Schlapbach (Child Health Research Centre - The University of Queensland) and Dr. Richard Brandon (co-founder and Chief Scientific Officer of Immunexpress) and will involve SeptiCyte® RAPID testing on a near-patient testing platform (Biocartis Idylla™).  From a small blood sample, and within approximately one hour, SeptiCyte® RAPID provides a probability of sepsis in children presenting with clinical signs of systemic inflammation, such as fever or rapid breathing. 

"Immunexpress was founded in Queensland and now SeptiCyte technology is coming home," said Dr. Brandon. "SeptiCyte LAB was FDA cleared for use in adults, while the fully automated 2nd generation product, SeptiCyte RAPID is CE marked and it is now important that we demonstrate clinical utility of SeptiCyte RAPID in children. Our collaboration with The University of Queensland is providing us with this opportunity."

Associate Professor Schlapbach said, "The results of the collaborative work will help save the lives of critically-ill children by improving diagnosis of sepsis using genomic technology. Early and accurate diagnosis of sepsis is crucial in successful management of these patients." Sepsis remains a leading cause of mortality in children worldwide. 

About SeptiCyte® RAPID

SeptiCyte® RAPID is a gene expression assay discovered and patented from Australia, which uses reverse transcription polymerase chain reaction (PCR) to quantify the relative expression levels of host response genes isolated from whole blood collected in the PAXgene® Blood RNA Tube. SeptiCyte® RAPID is used in conjunction with clinical assessments, vital signs and laboratory findings as an aid to differentiate infection-positive (sepsis) from infection-negative systemic inflammation in patients suspected of sepsis. SeptiCyte® RAPID generates a score (SeptiScore®) that falls within one of four discrete Interpretation Bands based on the increasing likelihood of infection-positive systemic inflammation. SeptiCyte® RAPID is intended for in-vitro diagnostic use and is used on the Biocartis Idylla™ System.

SeptiCyte® RAPID is CE Marked as a near-patient sample-to-answer test in European Union (EU) member countries and those harmonized with the EU IVD Directive (98/79/EC).  SeptiCyte® LAB was FDA cleared in 2019.  Australian TGA registration is expected later in 2021.

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Diagnostics Startup ID Genomics Receives NIH Grant to Develop Rapid Test for COVID-19 Variants

Diagnostics startup ID Genomics will accelerate its development of a quick test for variants of the COVID-19 virus with a new grant from the U.S. National Institutes of Health.

The Seattle-based company announced the $300,000 small business grant Tuesday for the dipstick-based test, currently dubbed CovNET. ID Genomics is also eligible for a follow-on grant of up to $3 million.

Most tests for the virus simply provide a ‘yes’ or ‘no’ answer to whether someone is infected. ID Genomics’ prototype test can also distinguish which variant an individual is infected with, and it can do so within two hours.

That’s faster than the gold-standard method, which involves sequencing the genome of the virus to detect variants. Some existing rapid tests can also pick up a single variant or a few, but CovNET stands out by distinguishing among dozens, according to ID Genomics’ co-founder Evgeni Sokurenko.

Sokurenko co-founded ID Genomics in 2014 with the goal of combining epidemiological surveillance, bioinformatics and molecular diagnostics. The 6-person company provides a variety of services to identify different microbes and their subtypes.

In addition to developing the CovNET rapid test, ID Genomics will launch a next-day sequencing service for variants within the next few weeks. The researchers showcased their sequencing approach in a recent study of a variant that emerged in California.

But the new two-hour test could ultimately be easier to deploy and potentially cheaper, aiding “real-time” monitoring of current and emerging variants, said Sokurenko, who is also a professor of microbiology at the University of Washington. The UW is the academic partner on the grant.

Sokurenko said that easy detection of variants could “help with close monitoring of pandemic dynamics, viral evolution and spread as well as timely detection and containment of local outbreaks.” In addition, better detection could support the development of treatments tailored to each version of the virus.

New variants are continually emerging, and the highly contagious delta variant is now dominant in the U.S. and many other countries. The World Health Organization has identified three other ‘Variants of Concern.’ These variants are known to be nastier than the original version of the virus, for instance transmitting more easily or making people sicker.

ID Genomics aims for an easy-to-use test that could be rapidly deployed across epidemiological surveillance labs globally. “With all stars aligned, we might start selling the test kit within months,” said Sokurenko of CovNET. “Affordability is the goal,” he added.

The prototype CovNET test uses a technique called PCR to identify variants, which show up as bands on a strip. The location and intensity of the bands can identify the predominant variant in a sample. Each double-sided strip can identify up to 24 variants and using more strips enables detection of more variants.

The company is also developing a smartphone app to rapidly decode the bands and identify which variant they correspond to.

CovNET adapts components of technology built by Bothell, Wash.-based IEH laboratories for other types of tests. IEH Laboratories is also collaborating with ID Genomics to a develop a pocket-size “nanocycler” to incubate the samples. The battery-powered device is capable of the rapid cycles of heating and cooling in the PCR portion of the test, which amplifies the genetic material of the virus.

The new grant will enable the startup to optimize the prototype test and validate it on a large number of clinical samples. ID Genomics is also working on agreements for manufacturing and distribution.

There is a growing pool of diagnostic tests for COVID-19, many tracked by Seattle-based PATH. New tests include a home-based PCR test to detect the virus from Amazon, and a test that can also tell if you’ve been infected with the virus in the past, developed by Seattle-based Adaptive Biotechnologies in partnership with Microsoft.

But there is a need for tests that can enable more efficient surveillance of variants. Washington state is currently sequencing close to 20% of virus samples for variants, but that is more than most states and many national labs.

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