Wednesday, December 22, 2021

E-Beacon Method May Provide Faster, More Accurate Test for Coronavirus

New research from Binghamton University Associate Professor of Chemistry Brian Callahan could be a game-changer on the detection of Coronavirus. He uses a new methodology to detect SARS-CoV-2 that can produce reliable results more quickly than other methods.

His article, “Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid,” was accepted for publication by the journal ChemBioChem. Co-authors include graduate student Xiaoyu Zhang, postdoctoral researcher Venubabu Kotikam and Chemistry Professor Eriks Rozners. A two-year pilot grant for $150,000 from the National Institute of Allergy and Infectious Diseases helped fund the research.

Methods to detect SARS-CoV-2, the virus that causes COVID-19, come in two types. The first detects the virus protein or “antigen,” the basis of the rapid tests found at local stores, with results typically coming back in around 15 minutes. The second type are molecular tests designed to detect virus nucleic acid, which can take anywhere from one to three days to return results.

Why so long? In the very specific and sensitive molecular tests, specimens must be shipped to testing labs, where the samples are then processed and analyzed by technicians with specialized training. As a result, they’re considered by scientists as the gold standard for testing due to their reliability, although their long wait time makes them cumbersome for patients.

“We focused on cutting down the wait time for molecular testing. We developed a nucleic acid sensor — we call it an E-beacon — that has the potential to speed sample turn-around time while maintaining the sensitivity and specificity parameters that make molecular testing so powerful,” Callahan said.

Enzymatic beacons

Enzymatic beacons are engineered “bioconjugates” with two key components: a light-generating enzyme and a DNA probe, Callahan explained. The components are stitched together via a recently-patented method.

In the E-beacons prepared for SARS-CoV-2, the DNA probe recognizes a specific sequence in the virus’ spike gene; that recognition event in turn causes the light output from the attached enzyme to increase. The more virus nucleic acid in a sample, the brighter the light signal from the enzyme component of the E-beacon, Callahan explained.

E-beacons can provide positive or negative results more rapidly than molecular tests, and without the expensive instrumentation required by polymerase chain reaction (PCR) based testing.

“As of now, our E-beacons appear to be just as specific and even more sensitive than detection methods used in current SARS-CoV-2 molecular tests,” said Callahan.

He acknowledged that the E-beacon experiments haven’t yet been done outside the lab, which is the likely next step.

Where could this lead? Imagine a walk-up, automated testing device that somewhat resembles a vending machine. Users would deposit a testing swab into a collection port. The molecular tests would then run autonomously within the machine, sending out the results via cell phone in about two hours.

E-beacons represent an attractive alternative to the current testing methods, and not just for SARS-CoV-2. Because of their modular design, they can be reconfigured easily for detecting other viral or bacterial pathogens, Callahan said.

“I am an eternal pessimist, so anytime a project works as well as the E-beacons, I’m surprised,” Callahan said.

There were setbacks, of course, including delays for materials and supplies they needed. Those delays led to a collaboration with Rozners, whose lab began preparing a vital component for the E-beacons. The project began to progress more quickly as a result.

Another essential ingredient to the research project’s pace and success: Zhang, whose efforts proved critical.

“Early mornings, late nights, weekends in the lab — he really hustled,” Callahan said.

Source: Binghamton University 

Thursday, December 2, 2021

Rochester Students Develop Game Changing Technology that Instantly Detects Sepsis Via Sweat

Sepsis is the body’s extreme response to an infection. It is a life-threatening medical emergency.  Sepsis happens when an infection you already have triggers a chain reaction throughout your body.  Infections that lead to sepsis most often start in the lung, urinary tract, skin, or gastrointestinal tract. Without timely treatment, sepsis can rapidly lead to tissue damage, organ failure, and death.

Undergraduate students at the University of Rochester recently developed a game changing technology that can instantaneously detect sepsis biomarkers in sweat. 

The following overview is from U of Rochester's News Center.

Every year, approximately 1.7 million American adults develop sepsis, a life-threatening complication that arises when the body has an overwhelming immune response to an infection. According to the Centers for Disease Control and Prevention, sepsis causes more than 20 percent of all deaths worldwide and one in every three deaths in US hospitals.

A crucial aspect of treating sepsis is to catch it at an early stage when a patient’s infection is still curable. Current methods to diagnose sepsis, however, rely on tests that can take days to yield results, while early sepsis can turn into full-blown septic shock within only one hour after the first symptoms emerge.

In order to address this problem, a team of 12 undergraduate students at the University of Rochester developed a novel device that instantaneously diagnoses sepsis based on biomarkers in a person’s sweat. The device offers a noninvasive way to monitor sepsis in real-time and uses materials that are environmentally friendly and affordable, making the device easily deployable in low-income countries.

The team recently entered their device in the International Genetically Engineered Machine (iGEM) competition, where it was nominated for best diagnostics project, best hardware, and best education awards and won a gold medal, making the team the second-most-awarded iGEM team in North America.

“After researching statistics on sepsis and talking to a variety of medical experts, we got a sense of its immense medical and economic impacts and the need to develop better options for sepsis diagnosis,” says iGEM team member Amanda Adams ’22, a biomedical engineering major. “Our goal was to create a biosensor that could provide up-to-date information about a patient’s condition. Getting to work in a student-led team where we were directly responsible for the entire project from planning it to presenting it was very rewarding.”

Worldwide synthetic biology competition

In 2020, Rochester launched an undergraduate class composed of students who compete in a worldwide synthetic biology competition with the goal to solve a real-world problem using innovative biological ideas. (Synthetic biology involves creating new biological parts or systems using materials already found in nature.) During the iGEM competition, held in mid-November, the undergraduates present to a panel of judges the projects they have spent the year designing and implementing.

“This year’s iGEM team tackled a problem that has a huge impact on society,” says Anne S. Meyer, an associate professor of biology, and one of the advisors for Rochester’s iGEM team. “The students realized that a patient’s sweat contains specific biomarkers that can report on whether or not the patient has sepsis. So, monitoring the levels of these biomarkers in patient sweat would be an easy and noninvasive way to diagnose sepsis in real time to get instant information.”

Overcoming the limitations of current sepsis diagnostic tools

Doctors use many different tools to diagnose patients, one of which is the presence and concentration of certain biomarkers—molecules such as proteins or sugar that are associated with a particular disease, condition, or biological process. There are several ways to measure biomarker concentrations, including test strips and lab-on-a-chip devices, but many of these approaches only show biomarker concentrations at one specific point in time. These methods can also be expensive, and many take hours to perform.

“This means that doctors often need to wait for the results of a test, and the results may not even be accurate if the patient developed a condition after the sample was taken,” Adams says.

The Rochester students consulted with sepsis survivors, scientists, and clinicians at the University of Rochester Medical Center to design a sepsis-sensing device, which they named “Bio-Spire,” a combination of “biology” and “perspire.” Bio-Spire is a biosensor that continuously monitors the levels of biomarkers in sweat. Unlike blood, sweat is a noninvasive medium to collect, and unlike saliva or urine, biomarkers in sweat can be continuously analyzed. The levels of biomarkers in blood and in sweat are correlated, so changes in the amount of biomarkers in sweat are indicative of changes in the blood.

That is, a change in biomarker levels in a patient’s sweat can signify a deterioration of the patient’s condition—and may signify sepsis.

Designing a ‘game-changer’ diagnostic device

Bio-Spire is designed to collect a tiny amount of sweat from a patient’s skin and wick the sweat past an integrated set of electrodes covered in biomarker detectors. The biomarker detectors consist of short pieces of DNA receptors attached to a small sheet of graphene—an ultra-thin layer of material that is highly conductive. The students synthetically created their own graphene and DNA in an environmentally-friendly manner by using engineered biological components.

When the sleeve-like device is placed on a patient’s arm, biomarkers associated with sepsis bind to the DNA receptors, changing the conductivity of the graphene sheet and triggering an electrical resistance in the electrodes, which is then recorded on a computer. The students created software that displays the concentrations of sepsis biomarkers in real time, permitting health care workers to receive up-to-the-minute updates on a patient’s condition.

“The Rochester team’s real-time sepsis diagnosis device is a game-changer because all of its parts can be created in an accessible, inexpensive way,” Meyer says. “Plus, it is the fastest sepsis diagnostic device ever created.”

In addition to developing the device, the team worked to increase awareness of sepsis and synthetic biology in the local community and beyond through a variety of education and outreach programs, including interactive science lessons with children’s summer camps in Rochester. The team also collaborated with an iGEM team from the Ohio State University to virtually publish a children’s book called A Trip to the Hospital: Randall’s Lesson on Sepsis, which is available on Amazon and Apple Books.

“We are excited by the promising results of this project and honored to be recognized for our efforts in addressing such an important, interdisciplinary issue in the medical community,” Adams says.

Because iGEM is an open-source competition, the team’s work is documented and available on their Bio-Spire Wiki page. This format allows future students or developers to take up the design and build upon the ideas.

Source: University of Rochester News Center

Sunday, November 14, 2021

SMART Develops 10-minute Test for Detection of COVID Immunity

Recent advances in rapid COVID test methods have been realized via a research collaboration in Singapore, where collaborators have developed a rapid test for the detection of SARS-CoV-2 neutralising antibodies. 

Researchers from the Antimicrobial Resistance (AMR) Interdisciplinary Research Group (IRG) at Singapore-MIT Alliance for Research and Technology (SMART) and the Nanyang Technological University, Singapore (NTU Singapore), alongside collaborators at National University Hospital (NUH), Massachusetts Institute of Technology (MIT), and the Centre for Life Sciences (CeLS) and Yong Loo Lin School of Medicine at National University of Singapore (NUS), have successfully developed a rapid point-of-care test for the detection of SARS-CoV-2 neutralising antibodies (NAbs). This simple test, only requiring a drop of blood from a fingertip, can be performed within 10 minutes without the need for a laboratory or specially trained personnel. Currently, no similar NAb tests are commercially available within Singapore or elsewhere.

To curb the transmission of SARS-CoV-2, countries have imposed strict measures to minimise social interaction and cross-border movements. Despite being able to improve surveillance and prevent spread to some extent, these measures have severely impacted economies and livelihoods, and the path towards regaining normalcy involves achieving herd immunity against the virus either naturally or through mass vaccination. To evaluate herd immunity and the effectiveness of vaccine immunisation programmes, it is essential to screen populations for the presence of SARS-CoV-2 NAbs on a faster and larger scale.

As part of a body’s natural immune response, NAbs are generated by either exposure to the virus or a vaccine. For effective prevention of viral infections, NAbs must be generated in sufficient quantities. The number of NAbs present in individuals indicate if they possess protective immunity to the virus and their probability of experiencing severe outcomes should they be infected. NAb testing can determine whether vaccinated individuals should be considered for booster shots for additional protection against the virus.

Despite the availability of various COVID-19 diagnostic tests, the detection of SARs-CoV-2 NAbs is still generally conducted at hospitals and specialised diagnostic laboratories. Currently, NAbs are commonly detected using virus neutralisation tests (VNTs), which require handling of live virus, a facility with rigorous biosafety and containment precautions, skilled personnel and 2 to 4 days of processing time. Thus, these tests are not viable for large population testing and surveillance due to the lengthy process that may put a strain on existing laboratory capabilities. The development of a more efficient means of testing better allows for immediate point-of-care testing and mass monitoring for events or workplaces, specific localities, high traffic points, and critical points of entry such as immigration checkpoints.

“With the gradual opening up of borders, economies and society, having the right test, and information will be crucial to not only plan for this future but also ensure that it can be done safely without hampering current efforts to curb the spread of the virus,” said Dr Megan McBee, Scientific Director at SMART AMR. 

According to the research team’s data, which has been published in medical and public health journal Communications Medicine, the newly developed rapid cellulose pull-down viral neutralisation test (cpVNT) detects SARS-CoV-2 NAbs in plasma samples within 10 minutes, utilising a vertical flow paper-based assay format and protein engineering technology developed at SMART AMR and the Hadley D. Sikes lab at MIT. This same protein engineering technology has also been used to develop tests to detect other well-known viruses such as the Zika virus and Tuberculosis. Cellulose was adopted as a test material as it is cost-effective and easily manufactured, and to avoid reliance on nitrocellulose, which is in high demand due to its use in other rapid COVID-19 tests.

The developed test is simple to administer, non-invasive and offers quick results. To perform the test, a user mixes a drop of fingertip blood with the reaction solutions and places it on a paper strip, before inserting it into a portable reader device that will detect the NAb signals and reflect the results. This test offers up to 93% accuracy, higher than similar lab-based methods currently being used. 

“Schools and workplaces will also benefit greatly from the test. Whether a person should be considered for receiving a booster vaccine can also be evaluated with this quick test as the results are available within minutes from a fingertip blood sample. And, if we are able to quickly determine immunity on a larger scale, the review and relaxing of COVID-related measures can be done in a more controlled, data-driven manner,” said Professor Hadley Sikes, Principal Investigator at SMART AMR, Associate Professor at MIT and a co-corresponding author of the paper. 

Co-corresponding author Professor Peter Preiser, a Co-Lead Principal Investigator at SMART AMR and the Associate Vice President for Biomedical and Life Sciences at NTU Singapore, said: “Besides detecting immunity to the current vaccine version of SARS-CoV-2 virus, the NAb test can be modified to monitor immunity against the other variants of the virus. This can provide information on the potential efficacy of different vaccines against each variant, or whether one should travel to areas that may have a high incidence of a specific variant.”

Further development of the test is underway for its approval by regulatory authorities and manufacturing for public use. The team that has developed the tests at SMART has also spun off a biotech startup, Thrixen, that is developing the test into a commercially ready product.

Key development of the rapid test was done at SMART AMR and NTU’s School of Biological Sciences. The research carried out at SMART is supported by the National Research Foundation (NRF) Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) programme. The work was also supported by the National Medical Research Council (NMRC), under its COVID-19 Research Fund, and National Health Innovation Centre (NHIC), under its COVID-19 Gap funding grant.

Friday, April 3, 2020

2-Day Online Rapid Microbiological Methods Master Class - July 15-16, 2020

Last month we held a very exciting online training program for rapid methods. To accommodate additional requests to repeat the training, the next online 2-Day Rapid Microbiological Methods Master Class will be held on July 15-16, 2020, from 1000 - 1430 EDT. This will be a live event where you will learn about the current regulatory policies for validation and submissions, the scientific principles for commercially-available rapid technologies, a comprehensive,step-by-step guide for validation including the use of statistical models, case studies on rapid sterility testing for ATMPs (cell therapy) and real-time environmental monitoring, and how to develop a financial justification when purchasing a RMM system. For the complete agenda and information on how to register, please visit http://rapidmicromethods.com/events/masterclass-july2020.php.

Tuesday, March 24, 2020

Overview of Current COVID-19 Diagnostic Devices with FDA Emergency Use Authorization

Due to the size of this blog post, we have moved the information to a dedicated page on our website. You may access the page by clicking the following link:


This page will automatically be redirected to our FDA Emergency Use Authorization page in 15 seconds.

Friday, March 6, 2020

How SARS-CoV-2 Tests Work and Future Developments for Rapid Diagnostics

A recent overview from TheScientist explains that although current methods to detect infections of the novel coronavirus rely on identifying particular genetic sequences, new assays are being developed to meet the growing demand for rapid results.

The quick sequencing of the SARS-CoV-2 genome and distribution of the data early on in the COVID-19 outbreak has enabled the development of a variety of assays to diagnose patients based on snippets of the virus’s genetic code. But as the number of potential cases increases, and concerns rise about the possibility of a global pandemic, the pressure is on to enable even faster, more-accessible testing.

Current testing methods are considered accurate, but governments have restricted testing to central health agencies or a few accredited laboratories, limiting the ability to rapidly diagnose new cases, says epidemiologist and immunologist Michael Mina, the director of the pathology laboratory and molecular diagnostics at Brigham and Women’s Hospital in Boston. These circumstances are driving a commercial race to develop new COVID-19 tests that can be deployed within hospitals and clinics to provide diagnostic answers in short order.

Globally, over 100,000 cases have now been reported—more than 80,000 of these in China—along with more than 3,000 deaths. The virus has been found in 64 countries, six of those in just the past day.

How the current SARS-CoV-2 assays work

The full genome of the novel coronavirus was published on January 10 of this year, just weeks after the disease was first identified in Wuhan, China. A week later, a group of researchers led by German scientists released the first diagnostic protocol for COVID-19 using swabbed samples from a patient’s nose and throat; this PCR-based protocol has since been selected by the World Health Organization (WHO).

The assay was initially developed from genetic similarities between SARS-CoV-2 and its close relative SARS, and later refined using the SARS-CoV-2 genome data to target viral genes unique to the newly discovered virus. In particular, the test detects the presence of SARS-CoV-2’s E gene, which codes for the envelope that surrounds the viral shell, and the gene for the enzyme RNA-dependent RNA polymerase.

Yvonne Doyle, the medical director and the director of health protection for Public Health England, tells The Scientist in an email that once a sample is received by a laboratory, it takes 24–48 hours to get a result. Commenting on the test’s accuracy, she says all the positive results to date in the United Kingdom, a total of 36 so far, have been confirmed with whole genome sequencing of the virus isolated from patient samples, and “the analytical sensitivity of the tests in use is very high.”

This approach also underpins COVID-19 laboratory testing in Australia, where 27 cases have so far been diagnosed, says medical virologist Dominic Dwyer, the director of public health pathology for NSW Health Pathology at Westmead Hospital in Sydney. “We decided in the end to have a screening approach using the WHO primers that target the so-called E gene of the coronavirus,” he says. “If a screening test is positive, we then do some confirmatory testing which selects other targets of the virus genome.”

The laboratory at Westmead Hospital also does a complete sequencing of every virus sample to look for possible new strains of SARS-CoV-2 and has shared some of those sequences in the international Global Initiative on Sharing All Influenza Data (GISAID) database for other researchers to study. The staff also cultures the virus and images it using electron microscopy. “That’s not really a diagnostic test, but gives you some confirmation of what you’re seeing in the laboratory,” Dwyer says.

He adds that, so far, there’s no suggestion of false positive findings, because every positive test has been confirmed with whole genome sequencing, viral culture, or electron microscopy. As for false negatives, he adds, it would be hard to know if any infected patients were mistakenly given the all-clear.

Not all countries have adopted the WHO’s recommended diagnostic. The US Centers for Disease Control and Prevention (CDC), for instance, has developed its own assay that looks for three sequences in the N gene, which codes for the nucleocapsid phosphoprotein found in the virus’s shell, also known as the capsid. The assay also contains primers for the RNA-dependent RNA polymerase gene. Dwyer says that the principles of testing are the same; it’s just the genetic targets that vary.

Mina says it’s not clear why the CDC chose to develop a different assay to that selected by the WHO and taken up by other countries. “Was this actually based on superior knowledge that the CDC had, or was this more of an effort to just go our own route and have our own thing and feel good about developing our own test in the US versus the rest of the world?” says Mina, who is also assistant professor of epidemiology at the Harvard School of Public Health. The CDC declined to respond to questions from The Scientist.

Who does the testing

In the UK, testing for COVID-19 is being done by a range of accredited laboratories across the country. In the US, all laboratory testing for COVID-19 has until recently been done exclusively by the CDC. The turnaround time for a result has been 24–72 hours. Mina argues that enabling hospitals to conduct their own on-site diagnostics could speed up the process. For instance, hospitals can generate flu results within an hour, Mina says, most commonly using assays that detect viral antigens. “We spend a lot of money getting rapid turnaround tests in the hospital for flu, for example, because we have to know how to triage people.”

The day or two or three that it takes to get COVID-19 results has had logistical ramifications for hospitals, Mina says. “If we have a patient who we only suspect is positive, even if they are not positive, just the suspicion alone will lead us to have to find an isolation bed for them,” he says.

There has been a move by the CDC to send out RT-PCR test kits to state health laboratories, says Molly Fleece, an infectious diseases physician at the University of Alabama at Birmingham. “Hopefully, more laboratories around the country will be able to have access to these testing kits and be able to test specimens instead of having to send all the specimens to the CDC for testing,” she says.

However, that plan hit a snag recently when one of the CDC kits’ reagents was found to be faulty. The agency has announced that the reagent is now being remanufactured.

SARS-CoV-2 tests in development

There are now numerous companies working on commercial test kits in response to the rising diagnostic demands of the epidemic. Most are applying the same real-time PCR methods already in use, but others are taking a different approach. For instance, Mina and colleagues are trialling a diagnostic in partnership with Sherlock Biosciences, based in Cambridge, Massachusetts. The researchers are using CRISPR technology to tag the target SARS-CoV-2 sequences with a fluorescent probe.

“In many ways it’s similar to real-time PCR but it’s just more sensitive and much more rapid,” Mina says. Another CRISPR-based diagnostic protocol developed by researchers at the McGovern Institute at MIT uses paper strips to detect the presence of a target virus, and claims to take around one hour to deliver the result. It has not yet been tested on COVID-19 patient samples, and the institute has stressed the test still needs to be developed and validated for clinical use, for COVID-19 or any other viral disease. Meanwhile, Anglo-French biotech company Novacyte has announced the release of its real-time PCR diagnostic kit for COVID-19, which it says will deliver results in two hours.

A different diagnostics approach would be to devise blood tests for antibodies against the SARS-CoV-2 virus, a development that Mina says will be an important next step for monitoring the spread of the virus. “Could we just start taking blood samples from people around the world and see how many people who had no symptoms or very minimal symptoms may have actually been exposed to this?” Mina asks.

Dwyer says such approaches could help detect any false negatives that slip through the PCR-based protocols, but “we’re not at that stage yet of rolling out the serology or antibody tests.” Numerous groups are trying to isolate antibodies, some with more success than others. Researchers at Duke-NUS Medical School in Singapore have used antibody testing to demonstrate a link between two separate clusters of infections, and in patients who had cleared their symptoms at the time they were given the antibody test. Meanwhile, researchers in Taiwan are also working to identify a SARS-CoV-2 antibody that could be used for diagnostic testing, and they say such a test could deliver a result in a matter of minutes rather than hours.

Over the past few weeks, rapidmicromethods.com has reported numerous developments in the area of rapid diagnostics for the SARS-CoV-2 virus. Please visit the website's News Page for more information.

Source: TheScientist

Friday, January 31, 2020

Rapid Microbiological Methods Online Master Class - April 1-2, 2020

For the first time ever, I am offering my intensive two-day Rapid Microbiological Methods Master Class online! This will take place on Wednesday and Thursday, April 1st and 2nd, 2020, from 10:00 AM EDT to 2:30 PM EDT. This live, online class will discuss the same industry best practices I have taught in similar training programs around the world. Attendees will be immersed in discussions regarding current regulatory policies and expectations, guidance on rapid sterility testing for gene and cell therapies (ATMP), validation strategies, statistical analysis, technology reviews and return-on-investment considerations. For the complete agenda and information on how to register, please visit http://rapidmicromethods.com/events/masterclass-april2020.php.

Thursday, January 23, 2020

Portable Nanohole Device Will Rapidly Diagnose Sepsis

EPFL researchers have developed a highly sensitive and portable optical biosensor that stands to accelerate the diagnosis of fatal conditions like sepsis. It could be used by ambulances and hospitals to improve the triage process and save lives. Their press release and associated reference paper are provided below.

Sepsis claims one life every four seconds. It is the primary cause of death in hospitals, and one of the ten leading causes of death worldwide. Sepsis is associated with the body’s inflammatory response to a bacterial infection and progresses extremely rapidly: every hour that goes by before it is properly diagnosed and treated increases the mortality rate by nearly 8%. Time is critical with sepsis, but the tests currently used in hospitals can take up to 72 hours to provide a diagnosis.

Many scientists are working on this critical issue, including those at Abionic, an EPFL spin-off. Researchers at the Laboratory of Bionanophotonic Systems (BIOS) at EPFL’s School of Engineering have just unveiled a new technology. They have developed an optical biosensor that slashes the sepsis diagnosis time from several days to just a few minutes. Their novel approach draws on recent developments in nanotechnology and on light effects at a nano scale to create a highly portable, easy-to-use device that can rapidly detect sepsis biomarkers in a patient’s bloodstream. And their device takes just a few minutes to deliver a result, like a pregnancy test.

Because the biosensor uses a unique plasmonics technology, it can be built from small, inexpensive components, yet it can achieve an accuracy on par with gold-standard laboratory methods. The device can screen a large panel of biomarkers and be adapted for the rapid diagnosis of a number of diseases. It was installed at Vall d’Hebron University Hospital in Spain and used in blind tests to examine patient samples from the hospital’s sepsis bank. The researchers’ technology is patent-pending, and their findings were recently published in Small.

Trapping biomarkers in nanoholes

The device employs an optical metasurface – in this case a thin gold sheet containing arrays of billions of nanoholes. The metasurface concentrates light around the nanoholes so as to allow for exceptionally precise biomarker detection. With this type of metasurface, the researchers can detect sepsis biomarkers in a blood sample with nothing more than a simple LED and a standard CMOS camera.

L'appareil est compact et abordable© Alain Herzog / EPFL 2020

The researchers begin by adding a solution of special nanoparticles to the sample that are designed to capture the biomarkers. They then distribute this mixture on the metasurface. “Any nanoparticles that contain captured biomarkers are trapped quickly by antibodies on the nanoholes,” says Alexander Belushkin, the lead author of the study. When an LED is applied, those nanoparticles partially obstruct the light passing through the perforated metasurface. “These nano-scale interactions are imaged by the CMOS camera and digitally counted in real-time at high precision,” says Filiz Yesilkoy, the study’s co-author. The generated images are used to rapidly determine whether disease biomarkers are present in a sample and, if so, in what concentration. They used the new device to measure the blood serum levels of two important sepsis relevant biomarkers, procalcitonin and C-reactive protein. Doctors can use this information to accelerate the triage of sepsis patients, ultimately saving lives.

“We believe our low-cost, compact biosensor would be a valuable piece of equipment in ambulances and certain hospital wards,” says Hatice Altug, the head of BIOS. Scientists already have possible applications in mind. “There is an urgent need for such promising biosensors so that doctors can diagnosis sepsis accurately and quickly, thereby keeping patient mortality to a minimum,” say Anna Fàbrega and Juan José González, lead doctors at Vall d’Hebron University Hospital.

Reference

Alexander Belushkin, Filiz Yesilkoy, Juan Jose González‐López, Juan Carlos Ruiz‐Rodríguez, Ricard Ferrer, Anna Fàbrega, Hatice Altug, Rapid and Digital Detection of Inflammatory Biomarkers Enabled by a Novel Portable Nanoplasmonic Imager, Small

Source: École polytechnique fédérale de Lausanne (EPFL)

Monday, January 20, 2020

Imperial College Scientists Win €22.5m EU Funding to Develop Rapid Test Based on Gene Signatures

A rapid test to diagnose severe illnesses, using personalised gene signatures, is being developed by scientists at Imperial College London.

The new approach could speed up diagnosis times for many serious conditions including pneumonia, tuberculosis, sepsis, meningitis, and inflammatory and immune diseases, to under two hours.

The landmark project, involving an international consortium led by Imperial, has been awarded a major EU grant worth €22.5m over five years, to develop the test and bring it to hospitals across Europe. The current stepwise process of diagnosing infectious and inflammatory diseases involves doing many different blood tests and scans which can be slow and inefficient, meaning that there may be significant delays before the right treatment is given.

The researchers believe diagnosis can be made accurately and rapidly on the first blood sample taken when a patient attends a hospital or health centre, by identifying the pattern of genes switched on in each patient’s blood.

Unique gene signatures

The team of scientists, led by Imperial’s Professor Michael Levin from the Department of Infectious Disease, believe that the test could completely change the way patients are diagnosed.

The work will build on over a decade of research into the pattern of genes switched on in the blood in different conditions.

The team’s previous research discovered that each disease is associated with a unique pattern of genes that are switched on or off – which form a ‘molecular signature’ – which can be used to rapidly identify each disease.

Earlier studies using the technique found that it could predict a bacterial infection with 95-100 per cent accuracy.

The international group will build a ‘library of gene signatures’ where the signatures of all common infectious and inflammatory diseases will be stored and made publicly available.

By comparing the pattern of genes in each patient’s blood sample with the signature of all diseases in the ‘gene signature library’, the diagnosis in each individual can be made rapidly.

Currently if a patient enters hospital with symptoms such as a high fever and feeling unwell they could go through a whole series of investigations, such as blood tests, spinal fluid samples, MRI and CT scans, while medics try to identify the cause.

Patients can also be treated with antibiotics unnecessarily as a precaution in case they have a bacterial infection. Investigations can take days or weeks before an accurate diagnosis is made, delaying treatment, taking up resources and costing vast amounts of money.

Gene library

The team will spend the next two years building the library of gene signatures covering all common conditions.

In parallel to the search for diagnostic signatures, engineering and industry members of the team will develop novel device prototypes that can quickly and accurately determine gene expression in a blood sample – this is done by measuring the number of RNA molecules each gene is making.

They will turn this into a rapid test platform that can measure the small number of genes needed to diagnose most common infectious and inflammatory diseases. In the final stage they will conduct a trial of the new diagnostic approach compared to current diagnosis.

The team believe that measurement of 100-150 genes will enable identification of all common infectious and inflammatory diseases, and that this can be achieved within 1-2 hours, so a final diagnosis can be made rapidly and avoiding unnecessary investigations and treatment.

New approach to diagnosis

The scientists have called this new approach Personalised Molecular Signature Diagnosis (PMSD) and they aim to conduct the first pilot trials in UK and European hospitals in 2023 and 2024.

Project lead, Professor Michael Levin, from the Department of Infectious Disease at Imperial College London, said: “We’re very confident that identifying the pattern of genes switched on in each patient will enable us to make an accurate diagnosis rapidly, as every disease has its own unique signature.

“The ambition is to develop a rapid test that will make the correct diagnosis based on the gene signature on the first blood sample taken when a patient arrives in hospital, and with the result within 1-2 hours. In the future the whole basis of medical diagnosis could be based on molecular signatures.”

Dr Myrsini Kaforou, from the Department of Infectious Disease, said: “This award has resulted from several years collaborative and cross disciplinary work, linking the strength of Imperial in computational biology and big data analysis, genomics, and clinical medicine and engineering, with partner institutions across Europe.

"The DIAMONDS project has drawn from strengths of different departments at Imperial, and reflects what can be achieved in cross disciplinary research.”

The project, named DIAMONDS (Diagnosis and Management of Febrile Illness using RNA Personalised Molecular Signature Diagnosis), involves teams in Austria, France, Germany, Greece, Italy, Latvia, Slovenia, Netherlands, Spain, Switzerland, Taiwan, Gambia, Australia, Nepal and the UK.

The group will recruit thousands of patients from across Europe with conditions caused by infections, and inflammation. It is being funded by the EU’s Horizon 2020 Research and Innovation Actions.

The project is very multidisciplinary, also including the team of Dr. Pantelis Georgiou from the Department of Electrical and Electronic Engineering, who will be developing a rapid point of care test using microchip technology to detect the gene signatures, and Dr Jethro Herberg, Clinical Senior Lecturer in Paediatric Infectious Diseases, who was previously involved with the PERFORM study.

The team’s previous projects, ILULU, EUCLIDS and PERFORM have successfully identified gene patterns for several conditions such as tuberculosis, Kawasaki disease, bacterial and viral infections.

The EU has awarded Professor Michael Levin nearly 60 million euros since 2006. This vital funding paved the way for early studies and collaborations with partners across Europe.

In 2006, the EU awarded Professor Levin and his team 5 million euros to study tuberculosis. This initial grant enabled his team to begin using molecular signatures to diagnose TB.

Then in 2012, Professor Levin was awarded a 12 million euros grant to study the genetic factors that influence children’s susceptibility to bacterial infections. The EUCLIDS project, funded by the European Union’s Seventh Framework Programme for Research (FP7), involved 14 partner institutions in six countries.

In 2016, the EU awarded the team a further 18 million euros to develop a rapid test to allow medics to quickly identify bacterial infection in children. The PERFORM project built on their previous research that showed bacterial illnesses can be identified by a particular patterns of genes and proteins.

The new DIAMONDS project has been awarded 22.5 million to bring the revolutionary approach to diagnosis to hospitals across Europe.

Professor Levin said: “The EU has been our most valuable source of funding and has enabled us to establish a wonderful network of researchers in different countries working together, with exchange of ideas and movement of young scientists between countries.

“We were able to pull in expertise of the best laboratories from across Europe. It opened up a new way of doing research that wouldn’t have been possible without the EU funding.”

Source: Imperial College London