Sunday, May 10, 2020

Three NSF RAPID Grants to Develop Quicker Test for COVID-19 for Holonyak Lab Faculty

Three Nick Holonyak Jr., Micro and Nanotechnology Lab (HMNTL) faculty members have received NSF Rapid Response Research (RAPID) program grants, all of which aim to shorten the amount of time it takes to process a COVID-19 test. Current tests can take as long as five days for results to be returned to the patient. Although more rapid nucleic acid tests that can give a result within an hour have become available, there are reports of a high rate of false negatives among these tests.

With the United States reaching the highest number of SARS-CoV-2 (this particular strain of coronavirus) cases out of any infected country, it is a national imperative to be able to test people before they show symptoms to reduce the spread of the deadly disease.

"As one of the only facilities in the country that incorporates both micro and nanofabrication cleanroom facilities and a BioNanotechnology Laboratory (BNL) under the same roof, HMNTL is proud to meet the moment and provide support to COVID-19 related essential research," said Xiuling Li, HMNTL interim director and Donald Biggar Willett Professor in Engineering.

Here is a more in-depth look at how HMNTL faculty are helping:

Rapid Electrical Detection of COVID-19 at Point-of-Care

A team led by Rashid Bashir, Dean of the Grainger College of Engineering, and Holonyak Lab faculty researcher, has proposed the development of a point-of-care device that uses nasal fluid samples to detect the presence of COVID-19 within 10 minutes.
Current tests are complex and labor-intensive, requiring each sample to be sent to a laboratory for confirmation. The test being developed by Bashir's group will simplify the process by eliminating the need to extract RNA from samples and simplify the test it as a whole. The new test will electrically detect specific nucleic acid molecules associated with the SARS-CoV2-2.

"Our approach can provide for a rapid electrical detection of the RNA amplification using graphene sensors and result in a miniaturized format for the test and also reduce the test's total processing time," said Bashir, Abel Bliss Professor of Engineering, professor of bioengineering, and member of the Center for Genomic Diagnostics.

The team hopes the proposed approach can be expanded beyond COVID-19 detection to become a global health technology that contributes to providing low-cost diagnostics of a number of viruses around the world in a portable and inexpensive way.

Rapid Single-Step Reagentless SARS-CoV-2 Viral Load Test by Detection of Intact Virus Particles

The next COVID-19 detection project combines capturing intact COVID-19 viruses with custom-designed DNA nanostructures so they can be immediately counted with a newly-invented type of biosensor imaging. This process could be completed and produce results in less than 15 minutes.

This new method would allow diagnostic facilities at the point of care to count each virus directly using a new form of ultrasensitive biosensor microscopy that amplifies the magnitude of light scattering produced by the virus when it is illuminated with a laser. To determine if the viewed virus is SARS-CoV-2, customized DNA nanostructure-based capture probes would be immobilized on a photonic crystal biosensor surface. When exposed to a sample, such as material eluted from a nasal swab, the DNA rhombus-shaped "virus net" would selectively attach the virus to the biosensor surface, while allowing all other materials to pass over the sensor without capture.

"Our approach would represent a new paradigm for virus diagnostics that does not require the chemical enzymatic amplification of nucleic acids, and so does not require temperature control, thermal cycles, viral lysis, nucleic acid purification, or fluorescent dyes," said Cunningham, Donald Biggar Willett Professor in Engineering and professor of electrical and computer engineering. "We just capture and count, so it is the simplest possible process, and our sensing method gives a result immediately as the viruses are captured."

The technology used in this method was recently demonstrated as a new form of biosensor microscopy called Photonic Resonator Interference Scattering Microscopy (PRISM), which allows researchers to detect and digitally count virus particles, protein molecules, and a variety of nanoparticles in real time without the use of additional labels or stains.

The team for this research also includes Xing Wang, associate professor of Chemistry, Taylor Canady, postdoc fellow at the Carl R. Woese Institute for Genomic Biology, and Nantao Li, Cunningham's ECE graduate student.

RAPID: Developing a Novel Biosensor for Rapid, Direct, and Selective Detection of COVID-19 using DNA Aptamer-Nanopore 

Holonyak Lab affiliate faculty member Yi Lu is working with Lijun Rong from the University of Illinois at Chicago to develop a biosensor that could detect and differentiate infectious SARS-CoV-2 from the SARS-CoV-2 that have been rendered noninfectious by patient's antibodies or disinfectants. This would allow patients to receive proper treatment in a timely manner, and would allow people who aren't infected or contagious to be released from quarantine.

The project aims to develop a modular and scalable sensor for direct detection of the intact coronavirus using DNA aptamers, short, single-stranded DNA molecules that can selectively bind infectious SARS-CoV-2. When coupled with nanopore, a pore of nanometer size, the result would be able to differentiate the infectious SARS-CoV-2 from the non-infectious forms or other viruses such as flu viruses with a high level of specificity.

"Achieving such a high level of specificity is very important for COVID-19 diagnostics," said Yi Lu, professor of chemistry and bioengineering. "This is because studies have shown that viral RNA levels that are being used in most COVID-19 diagnostic tests do not always correlate with viral transmissibility."

This technique is less resource-intensive than current methods due to not requiring pretreatment or RNA amplification. It also decreases the likelihood of cross contamination. It could also be used to test surface areas to ensure they have been properly sanitized after coming in contact with an infected patient.

COVID-19 Antigen Test Evaluated by European Scientists

Scientists in Europe recently evaluated the frontline capabilities of a commercially available, 15-minute disposable antigen test to detect COVID-19 infections.

Their findings, reported in Frontiers in Medicine, suggest the test could be useful as part of a broader triage strategy for slowing down the virus, which has infected more than seven million people and caused about 250,000 deaths as of May 4.

“The detection of viral infections in patients attending primary care centres would allow healthcare workers to rapidly identify new outbreak foci and define quarantine measures for high viral shedders and/or suspect patients to limit the spread of the epidemic,” the authors wrote.

The two-phase study examined the sensitivity and specificity of the new test during its development stage in the lab and later on using real-world biological samples from more than 300 previously infected patients.

Overall accuracy was 82 percent in the latter setting, with an overall sensitivity (how often a test correctly generates a positive result) of 57.6 percent and an overall specificity (how often a test correctly generates a negative result) of 99.5 percent.

In other words, the test was able to detect COVID-19 infections in about six out of 10 people, and it was nearly perfect in determining when an infection was not present. The test was more sensitive in patients with higher viral loads, positively identifying an infection in about seven out of 10 people.

The authors say the test — quicker, cheaper and less complicated but not as sensitive as reverse transcription-polymerase chain reaction (RT-PCR) assays, which ID the virus based on its genetic material — could be used to help screen patients during peak periods of the pandemic. Eventually, it could also be especially useful in screening higher-risk populations such as healthcare workers, they said.

The COVID-19 Ag Respi-Strip® test was developed by Belgian company Coris BioConcept, which specializes in rapid diagnostic kits for detecting respiratory and gastrointestinal pathogens like viruses and bacteria.

The test from Coris BioConcept is a type of immunochromatographic assay, or lateral flow test, which detects the presence or absence of a particular substance. Most people may be familiar with another type of lateral flow assay — a pregnancy test.

In the case of the COVID-19 Ag Respi-Strip, the antigen test uses a sample from a nasopharyngeal swab, which looks like a long, flexible Q-tip that enters through one nostril and extends down the nasal passage close to a person’s outer ear.

An antigen test works by looking for proteins on the surface of the virus. Coris BioConcept partly based the test on previous virology research on SARS-CoV-1, which caused the 2002-03 SARS epidemic. In fact, the two are so similar that the COVID-19 Ag Respi-Strip cannot differentiate between SARS-CoV-1 and -2.

The authors estimate the 15-minute antigen test, which can be conducted at point-of-care facilities following a few user-friendly protocols, could reduce the number of laboratory tests using RT-PCR by more than 13 percent.

Quidel Receives FDA Emergency Use Authorization for Rapid Antigen COVID-19 Diagnostic Assay

Quidel Corporation, a provider of rapid diagnostic testing solutions, cellular-based virology assays and molecular diagnostic systems, announced today that Quidel has received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) to market its Sofia® 2 SARS Antigen FIA, a rapid point-of-care test to be used with the Sofia 2 Fluorescent Immunoassay Analyzer for the rapid detection of SARS-CoV-2 in nasal or nasopharyngeal specimens from patients meeting the Centers for Disease Control and Prevention’s (CDC) criteria for suspected COVID-19 infection.

Sofia 2 is Quidel’s next-generation version of its best-selling Sofia instrumented system. Sofia 2 utilizes the original Sofia fluorescent chemistry design while improving upon the graphical user interface and optics system to provide an accurate, objective and automated result in 15 minutes. The next-generation Sofia 2 system also comes connected to Virena®, Quidel’s data management system, which provides aggregated, de-identified testing data in near real-time.

The Sofia 2 instrument also offers 2 distinct workflows: depending upon the user’s choice, the Sofia 2 SARS Antigen FIA cartridge is placed inside Sofia 2 for automatically timed development (WALK AWAY Mode); or test cartridges can be placed on the counter or bench top for a manually timed development and then placed into Sofia 2 to be scanned (READ NOW Mode), allowing the user to markedly increase testing throughput per hour.

“In the fight against COVID-19, our employees are truly making a difference, and I am tremendously proud of our organization’s ability to quickly develop and mobilize an accurate rapid antigen test,” said Douglas Bryant, president and chief executive officer of Quidel Corporation. “The EUA for our Sofia 2 SARS Antigen FIA allows us to arm our healthcare workers and first responders with a frontline solution for COVID-19 diagnosis, accelerating the time to diagnosis and potential treatment of COVID-19 for the patient.”

The assay is currently available for sale in the United States under EUA, and Quidel is now shipping the product to its customers. Quidel offers several other Sofia assays for sale, which are FDA cleared and CLIA waived, including tests for Influenza A and B, Respiratory Syncytial Virus (RSV), Group A Strep, and a 12-minute finger-stick whole blood test for Lyme Disease. In addition, Quidel also markets Sofia® tests for Lyme Disease, Legionella and S. pneumoniae in Europe.

Friday, May 01, 2020

CRISPR-based Technology Spots COVID-19

Researchers have developed a new technology that flexibly scales up CRISPR-based molecular diagnostics, using microfluidics chips that can run thousands of tests simultaneously. A single chip’s capacity ranges from detecting a single type of virus in more than 1,000 samples at a time to searching a small number of samples for more than 160 different viruses, including the COVID-19 virus.

Called Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), this technology — validated on patient samples — provides same-day results and could someday be harnessed for broad public-health efforts.

The work appears in Nature, led by co-first authors Cheri Ackerman and Cameron Myhrvold, both postdoctoral fellows at the Broad Institute of MIT and Harvard. Paul Blainey, core member of the Broad Institute and associate professor in the Department of Biological Engineering at MIT, and Pardis Sabeti, institute member at Broad, professor at Harvard University, and Howard Hughes Medical Institute Investigator, are co-senior authors.

“The current pandemic has only underscored that rapid and sensitive tools are critical for diagnosing, surveilling, and characterizing an infection within a population,” said Sabeti. “The need for innovative diagnostics that can be applied broadly in communities has never been more urgent.”

“CRISPR-based diagnostics are an attractive tool for their programmability, sensitivity, and ease of use,” said Myhrvold. “Now, with a way to scale up these diagnostics, we can explore their potential for comprehensive approaches — for example, enabling clinicians to see if patients are harboring multiple infections, to rule out a whole panel of diseases very quickly, or to test a large population of patients for a serious infection.”

Miniaturizing CRISPR diagnostics

To build a testing platform with this capacity, the team turned to microfluidics, adapting and improving on technology developed in 2018 by Blainey’s lab. The researchers created rubber chips, slightly larger than a smartphone, with tens of thousands of “microwells” — small compartments designed to each hold a pair of nanoliter-sized droplets. One droplet contains viral genetic material from a sample, and the other contains virus-detection reagents.

“The microwell chips are made like a stamp — it’s rubber poured over a mold,” explained Ackerman. “We’re easily able to replicate and share this technology with collaborators.”

The detection approach used on the chips is adapted from the CRISPR-based diagnostic SHERLOCK, first described in 2017 and developed by team of scientists from the Broad Institute, the McGovern Institute for Brain Research at MIT, the Institute for Medical Engineering & Science at MIT, and the Wyss Institute for Biologically Inspired Engineering at Harvard University.

To use the CARMEN platform, researchers first extract viral RNA from samples and make copies of this genetic material, similar to the preparation process for RT-qPCR diagnostics currently used for suspected COVID-19 cases. The researchers then add a unique fluorescent color dye to each prepared sample and divide the mixture into tiny droplets.

The detection mixtures, on the other hand, contain the CRISPR protein Cas13, a guide RNA that looks for a specific viral sequence, and molecules to report the results. These mixtures are also color-coded and separated into droplets.

Thousands of droplets from the samples and detection mixtures are then pooled together and loaded onto a chip in a single pipetting step. Each microwell in the chip catches two droplets. When a detection droplet finds its target — a specific viral genetic sequence — in a sample droplet in the same microwell, a signal is produced and detected by a fluorescence microscope. The entire protocol, from RNA extraction to results, takes under eight hours.

“Uniting these two technologies in a single platform gives us exciting new capabilities to investigate clinical and epidemiological questions,” said co-author Gowtham Thakku, an MIT graduate student in Broad’s Infectious Disease and Microbiome Program.

CARMEN enables more than 4,500 tests on a single microfluidics chip, which can apply to patient samples in a variety of ways using the available fluorescent codes. For example, a single chip could simultaneously test 1,048 samples for a single virus, or five samples for 169 viruses. The capacity can be easily scaled up further by adding more chips: “We normally run four or five chips in a single day,” noted Ackerman.

Multiplexing capabilities

To showcase the platform’s multidiagnostic capabilities, the team developed a strategy for rapidly testing dozens of samples for the 169 human-associated viruses that have more than 10 published genome sequences. The researchers tested this detection panel against 58 patient samples, using multiple chips. They additionally applied CARMEN on patient samples to differentiate between subtypes of influenza A strains and to detect drug-resistance mutations in HIV.

The team also incorporated detection mixtures for SARS-CoV-2 — the virus that causes COVID-19 — and other respiratory pathogens to demonstrate, using synthetic viral sequences, how the assay can be rapidly adapted to detect emerging viruses.

“CARMEN offers both impressive throughput and flexibility in diagnostic testing,” said co-author Catherine Freije, a Harvard graduate student in the Sabeti lab.

The researchers report that the platform’s sensitivity is comparable to previously published SHERLOCK assays, and they are continuing to improve and validate CARMEN using additional clinical samples. Coupled with the successful testing data from patient samples described in Nature today, this approach could be readily translatable in the clinic, according to the team.

“This miniaturized approach to diagnostics is resource-efficient and easy to implement,” said Blainey. “New tools require creativity and innovation, and with these advances in chemistry and microfluidics, we’re enthusiastic about the potential for CARMEN as the community works to beat back both COVID-19 and future infectious disease threats.”

Support for this study was provided in part by Howard Hughes Medical Institute, the Koch Institute for Integrative Cancer Research Bridge Project, an MIT Deshpande Center Innovation Award, the Merkin Institute for Transformative Technologies in Healthcare, a Burroughs Wellcome Fund CASI Award, the Defense Advanced Research Projects Agency (DARPA) grant D18AC00006, and the NIH (F32CA236425).

Source: The Havard Gazette

Mammoth Biosciences Announces Peer-Reviewed Validation Of Its Rapid, CRISPR-Based COVID-19 Diagnostic

Mammoth Biosciences announced the publication of a study demonstrating the power of its platform to detect SARS-CoV-2 from respiratory swab RNA extracts in under 45 minutes. The study, published in Nature Biotechnology, contains the first peer-reviewed data using CRISPR diagnostics for COVID-19, with the largest set of patient samples to-date.

There is an urgent need for rapid and accessible testing of the novel coronavirus for an effective public health response. The current and most common method for diagnosing SARS-CoV-2 is through quantitative polymerase chain reaction (qRT-PCR), which is restricted for use within specialized laboratories. As a result, the typical turnaround time for screening and diagnosing patients with suspected SARS-CoV-2 has been more than 24 hours, a pace that is far too slow to keep up with such a contagious disease.

Mammoth Biosciences has harnessed the power of CRISPR to offer a faster, lower-cost and visual alternative to traditional qRT-PCR assays. The company’s CRISPR-based diagnostic assay, DETECTR™, can deliver results in under 45 minutes as visualized on a lateral flow strip, similar to an at-home pregnancy test. DETECTR does not require a complex laboratory setting; it can be performed with portable heat blocks and readily available, “off-the-shelf” reagents and disposable lateral flow strips. The assay offers similar levels of sensitivity and specificity to qRT-PCR tests, with 95 percent positive predictive agreement and 100 percent negative predictive agreement.

The study was led by infectious disease expert Dr. Charles Chiu, researchers from the Department of Laboratory Medicine at the University of California, San Francisco (UCSF), along with Mammoth’s Chief Technology Officer Dr. Janice Chen and Research Lead Dr. James Broughton, and the California Department of Public Health. The researchers validated the method using contrived reference samples and clinical samples from US patients, including 36 patients with COVID-19 infection and 42 patients with other viral respiratory infections.

“We need faster, more accessible and scalable diagnostics. The point-of-care testing space is ripe for disruption and CRISPR diagnostics have the potential to bring reliable testing to the most vulnerable environments.,” says Mammoth’s Chief Technology Officer Janice Chen. “Because CRISPR can be programmed to detect any DNA or RNA sequence, we have been able to reconfigure our DETECTR platform within days to detect the SARS-CoV-2 virus from one of the first confirmed cases in the U.S., made possible by our collaboration with Dr. Charles Chiu at UCSF.”

From its inception, Mammoth Biosciences has focused on leveraging the diagnostic capabilities of CRISPR to develop decentralized, point-of-care tests for a variety of diseases. Shortly after the outbreak of SARS-CoV-2 in Wuhan, China, Mammoth began building its COVID-19 diagnostic and validated the efficacy of its CRISPR-based protocols on patient samples in less than two weeks. In mid-February, Mammoth published its white paper, open-sourcing its CRISPR-based detection protocols, and in early March, published the preprint containing initial patient sample validation.

Monday, April 27, 2020

Stream Bio and MIP Diagnostics Working on COVID-19 Rapid Diagnostic and Mass Screening Test

Stream Bio, a company that develops and manufactures a range of bioimaging molecular probes, has announced a new joint venture with MIP Diagnostics Ltd., a company that develops molecular imprinting for diagnostic and other applications. The collaborative project will focus on the development of a COVID-19 (or SARS-Cov-2) antigen reagent for assays, a lateral flow Rapid Diagnostic Test (RDT) and an “ELISA” type assay for high throughput screening (HTS) or mass testing.  

The unique properties of both Stream’s and MIP’s novel technologies are intended to allow for fast development of an extremely sensitive, and stable detection platform for the virus. The lateral flow project aims to reduce the diagnosis time to just 10 minutes, while the ELISA assay would enable a different detection system common in nearly all labs to be utilized alongside PCR, dramatically increasing capability.

With current PCR-based methods, it can take over a day to receive and act on lab results. The proposed point-of-care lateral flow technology (LFT) could reduce this by more than 140 times and once validated, be deployed anywhere for “on-the-spot” screening, for use by first responders on scene to transit hubs and airports.  The resulting LFT strip can easily be mass-produced.  

In this consortium, Stream Bio’s Conjugated Polymer Nanoparticles (CPNs) will combine their capabilities for temperature stability, intense fluorescence and magnetism, with the versatile, stable molecular imprinted polymers (nanoMIPs) or synthetic “plastic antibodies” from MIP Diagnostics Ltd.. The proprietary nanoMiPs work in the same way as conventional antibodies by targeting and latching onto a specific “binding site” of the virus, the “spike”, but without the significant development timeline or immunogenic requirement.  

Andy Chaloner, Founding Director and CEO of Stream Bio, commented “I am extremely excited by the possibilities of the combination of our two technologies, and the novel angle we can bring to the fight against the COVID-19 pandemic. CPNs have previously shown great capabilities in diagnostics, and implementing them in this collaboration is a huge milestone for Stream Bio.”  

“This is another great opportunity for nanoMIPs to make a significant impact on diagnostics development by leveraging the fast turnaround, high robustness and sensitivity benefits of MIPs with CPNs” said Stephane Argivier, Interim CEO, MIP Diagnostics Ltd., “and we are pleased to be working with another innovative platform on this collaboration to make a significant impact on the current worldwide need for rapid test development to COVID-19 diagnosis and monitoring.”

Portable Microfluidic Platform Developed for Detecting Coronavirus Using Smartphone

Researchers headed by a team at the University of Illinois, Urbana-Champaign, have developed what they claim is an inexpensive, sensitive smartphone-based device that can detect viral and bacterial pathogens in about 30 minutes, and could be adapted to test for SARS-CoV-2. The platform comprises a cartridge-housed microfluidic chip that carries out isothermal amplification of viral nucleic acids from nasal swab samples, which are then detected using the smartphone camera. The investigators report on their use of the system to detect equine viruses as a non-biohazard surrogate for SARS-CoV-2, but say that when adapted to test for coronavirus, the smartphone accessory, costing about $50, could be used to reduce the pressure on testing laboratories during pandemics such as COVID-19.

“This test can be performed rapidly on passengers before getting on a flight, on people going to a theme park, or before events like a conference or concert,” said University of Illinois, Urbana-Champaign electrical and computer engineering professor Brian Cunningham, PhD, who, together with bioengineering professor Rashid Bashir, PhD, led the development of the device. “Cloud computing via a smartphone application could allow a negative test result to be registered with event organizers or as part of a boarding pass for a flight. Or, a person in quarantine could give themselves daily tests, register the results with a doctor, and then know when it’s safe to come out and rejoin society.”

The multi-institutional researchers described their development and use of the device, in Lab on a Chip. The paper is titled, “Smartphone-Based Multiplex 30-minute Nucleic Acid Test of Live Virus from Nasal Swab Extract.”

As the COVID-19 pandemic has escalated, a “key failure” of health systems across every country has been the ability to rapidly and accurately diagnose disease, the authors stated. Contributing factors include “ … a limited number of available test kits, a limited number of certified testing facilities, combined with the length of time required to obtain a result and provide information to the patient.”

Most viral test kits rely on labor- and time-intensive laboratory preparation and analysis techniques, they continued. Testing for SARS-CoV-2 from nose swabs can take days. And “because available technologies remain expensive (in terms of capital equipment and reagents), technically challenging, and labor intensive, there is an urgent need for low-cost portable platforms that can provide fast, accurate, and multiplex diagnosis of infectious disease at the point of care,” the researchers pointed out. “The challenges associated with rapid pathogen testing contribute to a lot of uncertainty regarding which individuals are quarantined and a whole host of other health and economic issues,” Cunningham said.

Nucleic acid tests (NATs) represent an important class of point-of-care (POC) technologies for pathogen sensing that can achieve high specificity for the detection of pathogenic nucleic acid sequences, the authors noted. Such tests can also be designed to tag the amplified sequences using fluorometric or colorimetric markers. “Due to their success in laboratory settings, considerable efforts have been devoted to performing NATs in POC settings,” the investigators commented. While most NAT methods are based on polymerase chain reaction (PCR) amplification, which requires repeated heating and cooling cycles that are not ideal for POC applications, NATs that use isothermal nucleic acid amplification approaches, such as loop-mediated isothermal amplification (LAMP) are now being harnessed to develop simple, miniaturized POC devices. LAMP can rapidly amplify nucleic acids at a constant temperature, with just one type of enzyme and four to six primers.


The device developed by Cunningham and Bashir’s team started out as a project to detect a panel of equine viral and bacterial pathogens, including those that cause severe respiratory illnesses in horses, which are similar to those presented in COVID-19. “Utilizing the system in the context of equine respiratory diseases represents a model system for human pathogens such as SARS-CoV-2, which does not pose biosafety issues, but preserves the main features of a human COVID-19 testing protocol,” the researchers indicated. “Horse pathogens can lead to devastating diseases in animal populations, of course, but one reason we work with them has to do with safety,” Cunningham noted.

“The horse pathogens in our study are harmless to humans.” The researchers developed a device that could detect multiple horse viral pathogens quickly and cost-effectively, using LAMP technology. The device comprises a small cartridge containing the testing reagents and a port to insert a nasal extract or blood sample. The whole unit then clips to a smartphone. The test reagents break open the viral pathogens to gain access to the RNA. A primer molecule then amplifies the genetic material into many millions of copies in about 10 or 15 minutes. A fluorescent dye then stains the copies and glows green when illuminated by blue LED light, which is detected by the smartphone’s camera.

Recent research has consistently shown that image sensors integrated within today’s smartphones have enough sensitivity to detect fluorescence in the contexts of fluorescence microscopy of cells, viruses, and bacteria. Smartphone cameras can also sense fluorescence signals from a wide variety of biological assays, including LAMP, within microfluidic compartments, the authors noted. “The advantage of using a smartphone as the detection instrument for POC analysis is that it is possible to take advantage of the integrated optics, image sensor, computation power, user interface, and wireless communication capabilities of mobile devices, thus minimizing cost,” the team wrote.” With assistance from an inexpensive snap-in cradle or clip-on instrument, anyone that carries a smartphone would have the ability to perform testing.”

The investigators used their prototype device to detect nucleic acids from five different pathogens that cause equine respiratory infectious diseases. “Pathogen-spiked horse nasal swab samples were correctly diagnosed using our system, with a limit of detection comparable to that of the traditional lab-based test, polymerase chain reaction, with results achieved in ~30 minutes,” they wrote. And while the test system reported in the paper was used to detect pathogenic DNAs, the assay could be easily adapted for detecting RNA viruses, they suggested, by using a one-step RT-LAMP protocol that adds reverse transcriptase to the LAMP reaction mix without modifying the buffer or reaction conditions.

They suggest that using a smartphone in conjunction with a cradle that enables the phone’s camera to quickly gather a fluorescent endpoint image of the LAMP reaction, it will be possible to generate a positive/negative result, and incorporate integrated experimental controls and replicates to assure that the test has been carried out correctly. “ … we envision a detection instrument that clips onto a smartphone, with mechanical adapters that will align the rear-facing camera correctly with several popular phone models,” the scientists explained.

Using a mobile device as a detection instrument will also make it possible to report the data via integration with telemedicine platforms, both for epidemiology reporting and for sharing test results with doctors.

The researchers’ system does currently require a few preparatory steps to be performed outside of the device, but they are working on a cartridge that has all of the reagents needed to create a fully integrated system. “In future work, our plans include integrating the functions of viral lysis, LAMP buffer mixing, and LAMP reaction into a single cartridge with the reagents held within on-cartridge reservoirs,” they wrote.

Other researchers at the University of Illinois are using the novel coronavirus genome to create a mobile test for COVID-19, and making an easily manufactured cartridge that Cunningham said would improve testing efforts.

Source: Genetic Engineering & Biotechnology News

Monday, April 20, 2020

McKelvey Engineering Researchers Receives Funding for Rapid COVID-19 Test Based on Ultrabright Fluorescent Nanoprobe Technology

Engineers at the McKelvey School of Engineering at Washington University in St. Louis have received federal funding for a rapid COVID-19 test using a newly developed technology.

Srikanth Singamaneni, professor of mechanical engineering and materials science, and his team have developed a rapid, highly sensitive and accurate biosensor based on an ultrabright fluorescent nanoprobe, which has the potential to be broadly deployed.

Called plasmonic-fluor, the ultrabright fluorescent nanoprobe can also help in resource-limited conditions because it requires fewer complex instruments to read the results.

Singamaneni hypothesizes their plasmonic-fluor-based biosensor will be 100 times more sensitive compared with the conventional SARS-CoV-2 antibody detection method. Increased sensitivity would allow clinicians and researchers to more easily find positive cases and lessen the chance of false negatives.

Plasmonic-fluor works by increasing the fluorescence signal to background noise. Imagine trying to catch fireflies outside on a sunny day. You might net one or two, but against the glare of the sun, those little buggers are difficult to see. What if those fireflies had the similar brightness as a high-powered flashlight?

Plasmonic-fluor effectively turns up the brightness of fluorescent labels used in a variety of biosensing and bioimaging methods. In addition to COVID-19 testing, it could potentially be used to diagnose, for instance, that a person has had a heart attack by measuring the levels of relevant molecules in blood or urine samples.

Using plasmonic-fluor, which is composed of gold nanoparticles coated with conventional dyes, researchers have been able to achieve up to a 6,700-fold brighter fluorescent nanolabel compared with conventional dyes, which can potentially lead to early diagnosis. Using this nanolabel as an ultrabright flashlight, they have demonstrated the detection of extremely small amounts of target biomolecules in biofluids and even molecules present on the cells.

The study was published in the April 20 issue of Nature Biomedical Engineering.

Gold nanoparticles serve as beacons

In biomedical research and clinical labs, fluorescence is used as a beacon to see and follow target biomolecules with precision. It’s an extremely useful tool, but it’s not perfect.

“The problem in fluorescence is, in a lot of cases, it’s not sufficiently intense,” Singamaneni said. If the fluorescent signal isn’t strong enough to stand out against background signals, just like fireflies against the glare of the sun, researchers may miss seeing something less abundant but important.

“Increasing the brightness of a nanolabel is extremely challenging,” said Jingyi Luan, lead author of the paper. But here, it’s the gold nanoparticle sitting at the center of the plasmonic-fluor that really does the work of efficiently turning the fireflies into flashlights, so to speak. The gold nanoparticle acts as an antenna, strongly absorbing and scattering light. That highly concentrated light is funneled into the fluorophore placed around the nanoparticle. In addition to concentering the light, the nanoparticles speed up the emission rate of the fluorophores. Taken together, these two effects increase the fluorescence emission.

Essentially, each fluorophore becomes a more efficient beacon, and the 200 fluorophores sitting around the nanoparticle emit a signal that is equal to 6,700 fluorophores.

In addition to detecting low quantities of molecules, sensing time can be shortened using plasmonic-fluor as brighter beacons mean fewer captured proteins are needed to determine their presence.

The researchers have also shown that plasmonic-fluor allows the detection of multiple proteins simultaneously. And in flow cytometry, plasmonic-fluor’s brightening effect allows for a more precise and sensitive measurement of proteins on cell surface, whose signal may have been buried in the background noise using traditional fluorescent tagging.

There have been other efforts to enhance fluorescent tagging in imaging, but many require the use of an entirely new workflow and measurement platform. In addition to plasmonic-fluor’s ability to greatly increase the sensitivity and decrease the sensing time, it doesn’t require any changes to existing laboratory tools or techniques.

The technology has been licensed to Auragent Bioscience LLC by Washington University’s Office of Technology Management. Auragent is in the process of further development and scaling up the production of plasmonic-fluors for commercialization.

This work was supported by the National Science Foundation (CBET-1512043 and CBET 1254399); the National Institutes of Health (R01 DE02709802, R01 CA141521 and U54 CA199092); and a grant from the Barnes-Jewish Hospital Research Foundation (3706).

RIT Researchers Build Lab-on-a-Chip and Magnetic Nano-bead Device to Detect Bacteria and Viruses

Engineering researchers developed a next-generation miniature lab device that uses magnetic nano-beads to isolate minute bacterial particles that cause diseases. Using this new technology improves how clinicians isolate drug-resistant strains of bacterial infections and difficult-to-detect micro-particles such as those making up Ebola and coronaviruses.

Ke Du and Blanca Lapizco-Encinas, both faculty-researchers in Rochester Institute of Technology’s Kate Gleason College of Engineering, worked with an international team to collaborate on the design of the new system—a microfluidic device, essentially a lab-on-a-chip.

Drug-resistant bacterial infections are causing hundreds of thousands of deaths around the world every year, and this number is continuously increasing. Based on a report from the United Nations, the deaths caused by antibiotics resistance could reach to 10 million annually by 2050, Du explained.

“It is urgent for us to better detect, understand, and treat these diseases. To provide rapid and accurate detection, the sample purification and preparation is critical and essential, that is what we are trying to contribute. We are proposing to use this novel device for virus isolation and detection such as the coronavirus and Ebola,” said Du, an assistant professor of mechanical engineering whose background is in development of novel biosensors and gene editing technology.

The lab team is interested in the detection of bacterial infection, especially in bodily fluids. One of the major problems for detection is how to better isolate higher concentrations of pathogens.

The device is a sophisticated lab environment that can be used in field hospitals or clinics and should be much faster at collecting and analyzing specimens than the commercially available membrane filters. Its wide, shallow channels trap small bacteria molecules that are attracted to packed, magnetic microparticles.

This combination of the deeper channels on the nano-device, increased flow rate of fluids where bacteria are suspended, and the inclusion of magnetic beads along the device channels improves upon the process of capturing/isolating bacterial samples. Researchers were able to successfully isolate bacteria from various fluids with a microparticle-based matrix filter. The filter trapped particles in small voids in the device, providing a larger concentration of bacteria for analysis. An added advantage of a smaller device such as this allows for multiple samples to be tested at the same time.

“We can bring this portable device to a lake which has been contaminated by E. coli. We will be able to take a few milliliters of the water sample and run it through our device so the bacteria can be trapped and concentrated. We can either quickly detect these bacteria in the device or release them into certain chemicals to analyze them,” said Du, whose earlier work focused on devices that use the CRISPR gene-editing technology and the fundamental understanding of fluidic dynamics.

Teaming up with Lapizco-Encinas, a biomedical engineer with expertise in dielectrophoresis—a process that uses electrical current to separate biomolecules—their collaboration provided the increased capability toward better pathogen detection, specifically for bacteria and microalgae isolation and concentration.

“Our goal is not only isolating and detecting bacteria in water and human plasma, but also working with whole blood samples to understand and detect blood infection such as sepsis. We already have a concrete plan for that. The idea is to use a pair of the nano-sieve devices for sequential isolation,” said Lapizco-Encinas, an associate professor in RIT’s biomedical engineering department.

Du and Lapizco-Encinas were part of a team that consisted of mechanical and biomedical engineers from Rutgers, University of Alabama, SUNY Binghamton, and Tsinghua-Berkeley Shenzhen Institute in China to address the global challenges of disease pandemics. The new data is published in the article “Rapid Escherichia coli trapping and retrieval for bodily fluids via a three-dimensional bead-stacked nano-device,” in the journal ACS Applied Materials and Interfaces.

The research team is RIT engineering doctoral and graduate students Xinye Chen, Abbi Miller and Qian He; University of Alabama assistant professor of electrical and computer engineering Yu Gan and undergraduate student Shengting Cao; Ruo-Qian Wang, assistant professor of civil and environmental engineering from Rutgers University; Xin Yong, assistant professor of mechanical engineering from SUNY Binghamton; Peiwu Qin from the Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, China; and Jie Zhang, Carollo Engineers Inc. in Seattle.

Thursday, April 16, 2020

HeMemics Biotechnologies Receives HHS Support to Develop Rapid Antigen, Antibody Diagnostic to Identify COVID-19 Infected Individuals

HeMemics Biotechnologies Inc., announced that they are partnering with the Biomedical Advanced Research and Development Authority (BARDA), part of the office of the Assistant Secretary for Preparedness and Response at the U.S. Department of Health and Human Services, on the development of a rapid, Bluetooth®-connected, easy-to-use test to diagnose COVID-19 in 60 seconds or less. The test detects SARS-CoV-2 and associated antibodies from nasal swabs or whole blood, meeting a critical need to distinguish between individuals with active infections and those who have developed antibodies to the virus.

The device is about the size of a cell phone, allowing for ease of use in both the field and in traditional care settings. More importantly, the technology can link the test results with cloud- based data management networks, allowing for real-time geographical mapping of outbreaks, or for instantaneous pre-travel screening at airports or ship terminals.

The Hememics device utilizes a multiplex chip that could simultaneously test for up to 17 different pathogens using a single drop of blood or nasal swab. Thus, the technology can test for diseases of interest that may present along with COVID-19 or can be used to confirm known or suspected disease status in patient populations.

BARDA will contribute $638,000 of the total estimated development costs, with Hememics providing the remainder. These funds will be utilized to adapt and test this technology as a rapid diagnostic tool for identification of COVID-19 via detection of antibodies Immunoglobulin G(IgG), Immunoglobulin M (IgM) and viral particles in people. Under this contract, Hememics will work with BARDA to establish manufacturing reproducibility, scale up production, and generate clinical data for FDA review of the immuno-biosensor platform.

"The development of a diagnostic device and test that can screen patients almost instantly in the field or in a healthcare setting will help people determine whether they can return to work safely, provide timely information to inform decisions about treatment, and provide data health officials need in their continuous efforts to mitigate the spread of infection during this pandemic and potentially in future coronavirus outbreaks," said BARDA Director Rick Bright, Ph.D.

"This is a great opportunity for Hememics to serve the health concerns of so many Americans who need rapid answers to guide care and treatment for this viral epidemic," said John Warden, CEO and co-founder of the Company. "Our technology has the potential to detect SARS-CoV-2 in under a minute, which will allow physicians and providers the ability to address the virus at the point of diagnosis, to improve patient care and outcomes."

David Ho, PhD, CSO and co-founder of the Company added, "We have been working for years to develop a platform that could be adapted in days and scaled in a few weeks to counter emerging epidemics such as COVID-19. The BARDA support will help us demonstrate the rapid utility of our device, as well as the broader networking capability to inform healthcare agencies and providers about outbreaks."

This project has been funded in whole or in part with federal funds from the Department of Health and Human Services; Office of the Assistant Secretary for Preparedness and Response; Biomedical Advanced Research and Development Authority, Division of Research Innovation and Ventures under Contract No. 75A50120C00074.

One-Hour, Lab-Free COVID-19 Test Being Developed by Imperial College

Imperial College London’s Regius Professor of Engineering, Chris Toumazou FRS, is working with clinical researchers to test a rapid, lab-free PCR test that detects COVID-19 and delivers results in just over an hour.

The Lab-in-Cartridge rapid tests – based on Professor Toumazou’s DnaNudge consumer DNA testing innovation – have been clinically validated after a successful initial trial on COVID-19 patients and are continuing to validate on larger patient groups. The evaluation, which began in recent days, will now involve large-scale clinical testing with a view to extensive national roll-out, as part of the drive to meet the UK government’s testing targets.

The Department of Health and Social Care has procured 10,000 DnaNudge COVID-19 RNA testing cartridges to roll out to clinical sites. The Department of Health’s new COVID-19 Testing Strategy cited the work as among “Encouraging innovators that are producing promising new types of tests”.

Experts at Imperial College Healthcare NHS Trust are working with the Imperial College London and DnaNudge team to enable the new test to be applied to patients and staff if it continues to prove successful.

A key advantage of DnaNudge’s solution is that the RNA polymerase chain reaction (PCR) test requires no sample handling and is able to deliver processing outside of a laboratory environment – using DnaNudge’s patented and miniaturised “NudgeBox” analyser, which can be used anywhere. With results delivered in a little over an hour, the technology has the potential to offer a substantial improvement on current lab-based PCR testing times – which take at least 1-2 days before a patient can receive the results. The swab can be placed directly into the cartridge and then straight into the box for analysis.

Professor Christofer Toumazou, CEO and co-founder of DnaNudge and founder of the Institute of Biomedical Engineering at Imperial College London, said: “Early validation results for our technology in the COVID-19 patient study have been excellent. The DnaNudge test was developed as a lab-free, on-the-spot consumer service that can be delivered at scale, so we clearly believe it offers very significant potential in terms of mass population testing during the COVID-19 pandemic.”

Professor Graham Cooke, NIHR Research Professor of Infectious Diseases at Imperial College London, leading the clinical development said “This is one of the most exciting technologies I’ve seen in this area, particularly because it avoids the need for any sample handling. Our early results are very encouraging and now we need to see how the test performs in different clinical settings and understand where it might have the biggest impact on care at this critical time.”

The technology builds on a series of innovations developed by Professor Toumazou and his team at Imperial’s Institute of Biomedical Engineering, originally with other applications in mind. These advances include novel integration between biochemistry microfluidics, electronic circuits and miniaturisation based on smartphone technology.

Professor Nick Jennings, Vice Provost (Research and Enterprise) at Imperial College London, said: “We urgently need to increase coronavirus testing capacity, which is why Chris Toumazou’s innovations are so welcome. In normal times, Imperial researchers constantly seek to apply their discoveries for societal benefit. In this time of crisis, it is heartening to see so many colleagues think laterally and flexibly as they help improve NHS capacity and our understanding of COVID-19.”

Professor Toumazou, one of the world’s foremost biomedical engineers, is among the many Imperial researchers repurposing their expertise and resources to fight COVID-19. Among his colleagues are some of the world’s leading epidemiologists, virologists, diagnosticians, and frontline health workers redeploying labs, people and technologies as they work round-the-clock to help defeat coronavirus.

The DnaNudge in-store DNA testing service, which this coronavirus test is based on, was launched to consumers in November 2019.  The service currently focuses on nutrition, analysing and mapping users’ genetic profile to key nutrition-related health traits.  With the results of a quick, one-time test, customers can use a DnaNudge smartphone App or wrist-worn DnaBand to scan product barcodes in the majority of major UK supermarkets, and discover whether a food product is “red” or “green” for their unique genetic make-up. The test has been converted to detect the RNA of COVID-19.

DnaNudge is an Imperial College London spinout with labs at the College’s White City Campus.
The test was developed in collaboration with TTP in Cambridge, where the CEO and core development team are Imperial alumni.

BARDA to Work With Vela on Rapid Test for COVID-19

The Biomedical Advanced Research and Development Authority (BARDA) is working with Vela Diagnostics USA to develop a rapid diagnostic test for the COVID-19 pandemic.

The rapid diagnostic test would be for use on two instrument platforms, which is needed to test as many people as possible and identify those who are infected to slow the pandemic. Vela will develop two tests, both of which would allow rapid analysis and early detection of SARS-CoV-2 in upper respiratory tract specimens from symptomatic individuals.

The ViroKey SARS-CoV-2 RT-PCR Test can be applied using a manual workflow or by using an automated workflow. Using an automated workflow, 46 samples can be run in three hours. Manually, 16 samples can be run in approximately three hours. The company will develop the manual workflow test first and, shortly after that, will develop the automated workflow.

BARDA, which is part of the U.S. Department of Health and Human Services (HHS), will contribute approximately $224,000 to the project with Vela funding the rest. This award is part of BARDA’s Rapidly-Expanding COVID-19 Medical countermeasure portfolio.

After the tests are ready, Vela will seek Emergency Use Authorizations (EUAs) from the U.S. Food and Drug Administration for both the manual and automated tests.

Vela Diagnostics USA offers real-time PCR and Next-Generation sequencing on an integrated platform. The company has operations and distributions across North America, Europe, and Asia Pacific with R&D facilities in Singapore and the United States and manufacturing facilities in Singapore.

Tuesday, April 14, 2020

Amplidiag COVID-19 Molecular Diagnostic Test Granted Emergency Use Authorization in Finland

Mobidiag Ltd. today announces that it has received emergency use authorization in Finland for its Amplidiag ® COVID-19 molecular diagnostic test for the rapid detection of the SARS-CoV-2 virus, responsible for novel coronavirus infection (COVID-19). The Amplidiag ® COVID-19 is now available for use in Finland*. The test will be run for routine use at the main clinical laboratories in Finland (Helsinki University Hospital (Huslab), SYNLAB and Mehiläinen) doubling Finnish testing capacity and allowing testing coverage for most of the country. The process for obtaining emergency use authorization is now ongoing in Sweden, UK and France. Mobidiag will register this test for CE-IVD mark and it should be available for widespread use in Europe in the coming weeks through Mobidiag’s sales teams and local distributors.

The Amplidiag ® COVID-19 assay allows qualitative determination of SARS-CoV-2 (orf1ab and N genes) from nasopharyngeal swabs. The test runs on Mobidiag’s Amplidiag ® Easy platform, which enables to clinicians an optimized sample screening process with automated DNA extraction and PCR plate setup. Based on well-established high-throughput PCR technology, it can process 48 samples in less than three hours.

In addition, Mobidiag is developing Novodiag ® COVID-19, a molecular diagnostic test using its Novodiag ® system for the rapid and on-demand detection of SARS-CoV-2. This test will complement Amplidiag ® COVID-19 in enabling clinicians around the world to detect COVID-19 infections early, support decisions in managing efficiently epidemiological and infection control measures, isolate patients in a timely manner and improve patient care.

Tuomas Tenkanen, CEO of Mobidiag, said, “At Mobidiag, we recognize that we have a responsibility to support healthcare systems during this extraordinary situation and we are focusing our efforts in this endeavour. There is an urgent and growing need for reliable diagnostic solutions for the early detection of COVID-19, and Mobidiag has been able to leverage its capabilities and existing technologies to develop new diagnostic solutions quickly.

We are extremely pleased to bring our first diagnostic solution to the main clinical laboratories in Finland for large volume screening of COVID-19 and look forward to offering tests internationally in due course.”

* Amplidiag ® COVID-19 is now available in Finland as an emergency use test. Please note that Mobidiag tests are not home testing kits. They are only available for healthcare professionals, and not for patients directly. Please follow the recommended processes and guidance for your location if you believe you could be infected by SARS-CoV-2.

Monday, April 13, 2020

Avacta and Cytiva Collaborating on COVID-19 Rapid Test

Avacta Group plc, the developer of Affimer® biotherapeutics and reagents, is pleased to announce that it has entered into a collaboration with Cytiva, formerly known as GE Healthcare Life Sciences. The companies will develop and manufacture an Affimer-based point-of-care rapid test intended for screening of large populations to diagnose the COVID-19 coronavirus infection.

The World Health Organisation recently highlighted the need for the development of rapid tests to quickly diagnose COVID-19 at point-of-care to assist in limiting and tracking infections. Existing tests are not suitable for screening large numbers of people for the infection as they are laboratory based and it can take up to several days to get the results.

Avacta is already generating Affimer reagents that detect the COVID-19 virus and together with Cytiva will develop and manufacture a test capable of diagnosing the infection in minutes using a respiratory sample such as saliva. Cytiva will transfer this diagnostic assay onto its proprietary point-of-care test strip platform and both companies will work together to complete analytical and clinical validation of the test as quickly as possible.

Avacta will own the intellectual property relating to the COVID-19 Affimer-reagents and will retain all the commercial rights to future products. Further commercial details have not been disclosed.

Dr Alastair Smith, Chief Executive Officer of Avacta Group, commented: “I am delighted that we have established this collaboration with Cytiva to develop, manufacture and commercialise a rapid test for COVID-19 infection. Importantly the test will indicate if a person has the virus now, whether they are showing symptoms or not, and will do so in minutes, in-situ with no need for laboratory equipment.

Unfortunately, many millions of people around the world will ultimately become infected and it is likely to be an annual occurrence. There is a clear and urgent need for a test that can be carried out quickly in the community to limit the spread of the virus and track its progress.

We have demonstrated before in the case of the Zika virus that the Affimer platform can very quickly provide highly specific reagents in response to an outbreak of an infectious disease. Our partnership with Cytiva means that we now have a global technology partner for a COVID-19 diagnostic which is essential if a practical and commercial solution is to be provided to governments and healthcare providers around the world promptly.

Hundreds of millions of tests will be needed for population screening and we will be working hard to deliver an Affimer based solution on Cytiva’s platform, and potentially on the platforms of other partners with whom we are in active discussion, as soon as possible. We are aiming to have developed Affimer reagents for a COVID-19 test by the end of May that can be transferred to Cytiva and potentially to other global diagnostic manufacturers to implement in a test strip”.

Klaus Hochleitner, Global Lead, Technology Product Specialist at Cytiva, commented: “There is an urgent unmet need for rapid tests to screen large numbers of people for COVID-19. Affimers are tools that can be designed quickly and very specifically for specific epitopes. We will support Avacta with technology transfer and usability to ensure the test is ready at the earliest point for use in the field.”

Nanomix Awarded BARDA Contract for Development of Rapid, Mobile, Point-of-Care Assays to Detect COVID-19 Infection

Nanomix, a leader in the development of mobile, affordable, point-of-care diagnostics, today announced that the company has been awarded up to approximately $570,000 in funding from Biomedical Advanced Research and Development Authority (BARDA), part of the Office of the Assistant Secretary for Preparedness and Response at the U.S. Department of Health and Human Services. These funds support development and testing of COVID-19 point-of-care tests that will run on the Nanomix eLab analyzer, which provides results in less than 15 minutes.

The Nanomix COVID-19 assays detect either SARS-CoV-2 antigens or antibodies to SARS-CoV-2 to identify both active infections and previous exposure to the virus. The portable Nanomix eLab analyzer can be used in a wide range of settings, including hospitals, nursing homes, assisted living facilities, urgent care centers and emergency medical care.

“Accurate, rapid and mobile testing is critical to slow the spread of COVID-19 and reduce the devastating impact of this pandemic on the United States and the rest of the world,” said David Ludvigson, president and CEO of Nanomix. “We are thankful that the U.S. government is supporting our work to develop tests that are needed to battle SARS-CoV-2 in our communities and could help people safely and confidently return to work and other critical functions.”

The Nanomix approach can enhance current COVID-19 molecular-testing approaches and greatly increase the number of people who can be tested in any given period. The new assays will be able to distinguish SARS-CoV-2 from other coronaviruses, as well as a common flu strain, to aid in the diagnosis of patients with non-specific respiratory symptoms. The company expects to complete development in early June and file for Emergency Use Authorization shortly afterward.

“With a virus that may be spread by asymptomatic people, a rapid point-of-care platform that informs people if they have an active infection or had previously been infected is the key for many to returning to daily living,” said BARDA Director Rick Bright, Ph.D.

Nanomix conducted a similar project during the Ebola crisis, developing a test that simultaneously identified and differentiated Ebola, Dengue, and Lassa Fever. Nanomix developed that test in eight weeks and successfully completed field testing with the resulting assay.

The Nanomix eLab Analyzer has received CE Mark for a multiple marker test for screening serious infections including sepsis and is undergoing 510(k) review for clearance by the U.S. Food and Drug Administration (FDA).

This project has been funded in whole or in part with federal funds from the Department of Health and Human Services; Office of the Assistant Secretary for Preparedness and Response; Biomedical Advanced Research and Development Authority, Division of Research Innovation and Ventures under Contract No. 75A50120C00060.

InDevR Ships First Multiplexed COVID-19 Serology Test Kits for Clinical Validation

InDevR, Inc., a leader in progressive analytical technologies to support the development and production of vaccines and biotherapeutics, announced shipment of its first COVID-19 serology test kits this week for clinical validation. InDevR's VaxArray Coronavirus SeroAssay is a microscale multiplexed immunoassay that leverages the Company's established VaxArray platform to deliver a rapid, off-the-shelf test that can simultaneously screen for antibody responses to the spike protein of SARS-CoV-2, SARS-CoV-1, MERS, and other endemic coronaviruses. The serological test kit is designed to streamline development of SARS-CoV-2 vaccine candidates and to aid in seroprevalence studies for SARS-CoV-2. InDevR expects validation to take approximately 2-4 weeks and intends to have kits ready for commercial use by early May 2020.

Through an on-going collaboration with Kentucky BioProcessing ("KBP"), the first VaxArray CoV SeroAssay kits will be evaluated in pre-clinical studies for KBP's SARS-CoV-2 vaccine candidate, which is based on a proprietary fast-growing tobacco plant vaccine platform. KBP's platform was used to generate a SARS-CoV-2 vaccine candidate within four weeks of publication of the genetic sequence. "This is an ideal partnership," commented Kathy Rowlen, CEO of InDevR. "KBP's rapid vaccine manufacturing platform requires equally rapid and efficient analytical tools and we couldn't be more pleased that KBP has adopted the VaxArray technology."

"InDevR is at the forefront of streamlining serology testing that could directly impact the development of a COVID-19 vaccine as well as detection of antibodies to help determine whether an individual has previously been infected," noted KBP President, Hugh Haydon. "Their cutting-edge work makes it easier for developers to quantify antibodies of COVID-19 and thus speed development of a vaccine. We're proud of our productive relationship with InDevR. Whether it is our own or another vaccine, we hope that our role in this collaboration helps to speed up development of vaccines and other tools to fight this virus."

The VaxArray CoV SeroAssay is based on InDevR's VaxArray platform, a microscale multiplexed immunoassay that is already being used by several of the world's largest vaccine manufacturers to streamline development and characterization of seasonal influenza vaccines, with applications to a range of other vaccines currently under development in collaboration with the Bill & Melinda Gates Foundation. The portfolio of VaxArray products delivers highly-sensitive and quantitative measurements in a fraction of the time required for traditional characterization methods, thus reducing vaccine development timelines and manufacturing costs.

Kathy Rowlen, further noted that "In addition to the improvements in speed, usability, and information content relative to traditional ELISA immunoassays, we believe our VaxArray CoV SeroAssay kits can be used as a standardized benchmarking tool for the many organizations pursuing SARS-CoV-2 vaccine candidates, allowing apples-to-apples comparisons of baseline antibody levels and immune responses across the thousands of clinical study samples that will be collected in the coming months. Better comparability of serology data across vaccine candidates may help accelerate the identification of the most promising approaches."

Canon Medical Systems and Nagasaki University Develop Rapid LAMP COVID-19 Test

Canon Medical Systems Corporation working together with Nagasaki University, has completed development of Genelyzer KIT (1), a set of reagents for SARS-CoV-2 RNA testing based on a gene amplification technique known as the fluorescent LAMP method (2). The results of validation of the rapid genetic testing system employing this technique were released in a report titled "Validation of 2019-nCoV gene testing method in which clinical evaluation results were obtained using clinical specimens" (3) issued on March 26, 2020, by the Ministry of Health, Labour and Welfare and the National Institute of Infectious Diseases of Japan. This report showed a specificity of 100% and a sensitivity of 90% or more. Based on an administrative notification issued by the Ministry of Health, Labour and Welfare (4), the rapid genetic testing system has been granted approval for practical application in government-conducted testing.

In positive specimens, the testing system can detect 15 or more viral genome copies per reaction within approximately 10 minutes with 100% sensitivity. The entire test procedure, from preprocessing the sample to obtaining the test results, can be completed in as little as 40 minutes, which is much less than the time required for conventional genetic testing methods. In order to take full advantage of the testing system's rapid testing capabilities, Canon Medical Systems Corporation will continue evaluating its practical application in public health protection and border control measures at clinical sites, airports, and other locations where testing needs to be completed on the same day. This research project is part of a research program focusing on risk evaluation of emerging and re-emerging infectious diseases and the implementation of emergency management functions which is being conducted under Health and Labour Science Research Grants.

Together with Nagasaki University, Canon Medical Systems Corporation is participating in a research project on the practical application of rapid genetic testing systems led by the Japan Agency for Medical Research and Development (AMED) and has been working on the development of this testing system since receiving a request for cooperative development of a testing system from the National Institute of Infectious Diseases of Japan in February 2020. The testing system has now quickly entered the practical application phase under the framework of industry-academia-government collaboration with the support of the Ministry of Health, Labour and Welfare of Japan and other involved parties.
Canon Medical Systems Corporation hopes that the testing system will be used at a wide range of clinical sites in Japan to help control the spread of coronavirus disease 2019 (COVID-19). At the same time, our goal is to contribute to the development of effective measures against the spread of infectious diseases in all parts of the world using this rapid genetic testing system developed in Japan.

(1) This testing system makes it possible to quickly detect a novel coronavirus gene in patient specimens. The entire procedure, including extraction of the viral genome prior to testing, can be completed in a short time of 40 minutes or less. Due to the light weight, compact design, and ease of operation of the testing system, it is suitable for use at a wide range of clinical sites, including remote locations such as isolated islands.

(2) A nucleic acid amplification method known as LAMP (loop-mediated isothermal amplification) developed by Eiken Chemical Co., Ltd.

(3) https://www.niid.go.jp/niid/images/lab-manual/2019-nCoV-17-20200326.pdf

(4) Administrative notification issued on March 18, 2020, by the Tuberculosis and Infectious Diseases Control Division, Health Services Bureau, Ministry of Health, Labour and Welfare of Japan (Method for 2019-nCoV gene testing in government-conducted testing).

Tuesday, April 07, 2020

Genetron Health Announces Its Novel Coronavirus Nucleic Acid Detection Kit Is CE Marked and FDA-EUA Application Accepted

Genetron Holdings Limited (“Genetron Health”), a China-based precision oncology company that covers full-cycle cancer care, announces that its independently developed Detection Kit for Novel Coronavirus (SARS-CoV-2) RNA (PCR-Fluorescence Probing) has been issued CE marking and had its application accepted by FDA-EUA. Based on the test kit, three of Genetron Health’s clinical laboratories have passed the COVID-19 External Quality Assessment (EQA) by China’s National Center for Clinical Laboratories (NCCL).

In addition to CE marking and FDA-EUA application acceptance, Genetron Health’s nucleic acid detection kit has also performed excellently in a verification project held by the Beijing Center for Disease Prevention and Control. The kit enables comprehensive, accurate, efficient, and safe testing for larger-scale samples. Additionally, Genetron Health's new aerosol particle sampler for lower respiratory tracts has also applied for medical equipment approval and clinical verification, in hopes to help control the SARS-CoV-2 pandemic.

Moreover, the GENETRON S5 (China National Medical Device Registration 20193220820), semiconductor high-throughput sequencer, and supporting instruments have been donated to Wuhan Huoshenshan Hospital. As currently Huoshenshan Hospital’s only next-generation sequencing (NGS) platform, it can perform accurate molecular test of clinical samples to yield comprehensive genomic data. Such data is acutely instrumental in current and future clinical and epidemiology research in battling the disease, monitoring mutations of the coronavirus as well as in continuous management and prevention of the COVID-19 outbreak (including formulation of preventive measures, research and development of related diagnostic kits, vaccines and drug treatment).

GENETRON S5 sequencing platform also effectively and efficiently complements the current PCR test, thus enhances reliable testing for weak positive cases using a substantially shorter time. In addition, it can aid diagnosis of any co-infections and support follow-up precision treatment.

New Saliva Test to Instantly Detect Coronavirus with Lasers

European photonics scientists are developing an ultrasensitive laser sensor that detects coronavirus at the earliest point of infection from a saliva or nasal swab in minutes.

Responding to the European Commission's Express Calls to tackle the coronavirus pandemic, photonics scientists are developing a new rapid, non-invasive 'optical biosensor' demonstrator that will detect Covid-19 in humans as soon as it is present in the body.

Using photonics – technology that manipulates light – the ultrasensitive demonstrator could detect 'day 1' infections on patients who have a low viral load, representing a breakthrough in tackling the coronavirus pandemic.

With the ability to diagnose in real-time with high specificity from a low concentration sample, the sensor is much more reliable than the coronavirus rapid-test, 'finger-prick' kit which detects if a person has had the coronavirus before and has since recovered.

Looking at tiny molecules, the new point-of-care detector examines virus antigens using miniaturised chips – or 'nanophotonic biosensors' - from a simple nasal or saliva swab.

Once a sample is prepared and is in place, the device confirms a positive or negative for coronavirus instantaneously. However, allowing for preparation time and analysis, a result - from sample to diagnosis - may take up to 30 minutes.

Testing

Having already created six working laboratory demonstrators for other applications, the research team says the technology still needs further adaptation and testing but could be available in a year at the latest.

Calling themselves CONVAT and coordinated at 'ICN2' (the Catalan Institute of Nanoscience and Nanotechnology, Spain) the researchers have tested the demonstrators previously on patients' samples provided by Vall D´Hebrón Hospital in Barcelona and several other hospitals in Spain for other pathologies

Project coordinator, Professor Laura Lechuga said: "With thousands of deaths worldwide, we are in urgent need of a rapid new testing kit that is accurate, highly sensitive, non-invasive and cheap to produce".

"We are currently integrating all the instrumentation in a portable 25x15x25 cm box with a tablet control. At present, our detector is user-friendly, with the preparation being only technical expertise required, and could be widely deployed for GPs or nurses to test patients."

"Our nanosensor is capable of detecting RNA strands which will fully identify the new coronavirus.

Unique Interferometric Technology

The detector works by looking at the 'binding' of the coronavirus molecules to the sensor surface - producing a new signal when the virus is present.

The CONVAT team use a Nano-Interferometric Biosensor, the most sensitive, label-free detection technology available in the world today- identifying at the molecular level.

Since the bioreceptors on the sensor surface are specifically tuned to a particular antigen of the virus, only the coronavirus molecules are captured along the sensor.

Light travelling in the sensor generates an evanescent field of few nanometres over the sensor surface. Here, receptors (like antibodies or DNA strands) can recognise the antigens of the virus capsid, when a respiratory fluid sample passes through.

This recognition event produces a change in the refractive index, causing the light to slightly change its direction of travel.

This change can be measured and determined precisely against a set of existing values – and could give an instant diagnosis for coronavirus expected at the picomolar to attomolar (pM–aM) range without any need amplification.

Professor Lechuga said: "Our patented interferometric technology is unique for biosensing. We use our "Bimodal Waveguide interferometer" which uses two modes of a light beam (at visible wavelength) travelling in a single waveguide.

"The light interacts with analytes during their travel and at the end of the bimodal waveguide, we record the interference between both light modes. The signal is collected with a photodetector and processed by electronics, all instantly in real-time."

Clean Detection

"Photonics is renowned for its rapid, stand-off, and clean detection capabilities, so it made perfect sense to develop a device that exploited light amid this terrible pandemic," said Professor Lechuga.

With thousands of new cases reported each day, COVID-19 is a novel coronavirus that had not previously been present in humans. While it is not known exactly how the virus is spreading from person to person, it is thought the outbreak – similar to the 2002 SARS coronavirus – may have spread via cough and sneeze droplets.

"Our nanophotonic POC biosensor can examine respiratory body fluids for rapid diagnostics and screening. It looks directly at the human or animal reservoir samples without the need for PCR or other time-consuming treatments".

"In our previous work, we demonstrated sensitivities at the attomolar (aM) level for direct specific miRNA detection and 4 CFU/mL for whole pathogen detection.

"While our previous results are promising, our sensor will be further optimised and evaluated also for viral RNA analysis in a multiplexed format for more accurate diagnosis and identification of virus strains among different coronaviruses and other clinically relevant viruses," Professor Lechuga said.

Chair of the Photonics21 Healthcare Workgroup, Dr Jurgen Popp, said: "The CONVAT team are working round the clock to develop a rapid, non-invasive test for coronaviruses. The ability to spot this terrible virus quickly will contribute to the worldwide effort in fighting 2019-nCoV and highlights yet another success for photonics and light technologies.

Philippe Vannson, Head of the Photonics Unit, DG CONNECT, at the European Commission said: "Light-based technologies are providing tools and solutions to every industry in every region in the world. By creating Instant diagnosis of major diseases photonics is making healthcare fast, precise and cost-effective."

Existing Technology

The technology to be employed in the coronavirus detector was a pre-existing piece of apparatus developed by Dr Lechuga to examine different pathologies, like bacterial infections, or cancer biomarkers. However, in response to the 2019-nCoV pandemic, the researchers knew their technology could be modified to detect early, low viral load cases:

"My colleague, a researcher from the University of Barcelona, who has worked on the surveillance of Coronaviruses in animal reservoirs for many years, often suggested that we should work together on a project. So when we saw the Express Call for proposals, one of the specific Coronavirus fighting calls – with a deadline of 30 Jan 2020, I telephoned him and said, now is the time to work together.

"In just eight days we worked more than 12 hours per day to put together a consortium of four partners, writing a successful proposal to the EC. It was approved and now I've been contacted by the Spanish Minister for Science and Innovation an invited onto TV and radio talk shows."

Funded by Horizon 2020, the European Commission's scientific research initiative, the scientists only began work on their detector at the start of March, in response to the pandemic.

Source: Photonics 21

Friday, April 03, 2020

VTT Begins Development of Rapid Test for Coronavirus

VTT Technical Research Centre of Finland has started work on a new Covid-19 test based on the detection of viral antigens in nasopharyngeal samples.

The development of the test is being carried out in collaboration with the Meilahti Vaccine Research Center, a joint research facility run by the University of Helsinki and Helsinki University Hospital (HUS).

The test is designed to be performed by healthcare professionals, with results delivered in 15 minutes or less. VTT also hopes to make the new test considerably more cost-efficient than existing testing methods.

Antibody development has already commenced and the first versions of the new tests are expected by autumn.

VTT biosensors research team leader Dr Leena Hakalahti said: “As the situation with the epidemic began to worsen internationally, we started looking for solutions within our area of excellence. We have expertise in antibody development and production as well as previous experience in designing diagnostic tests. It was an easy decision for us to start working on the Covid-19 antibody.”

HUS is also playing an important role in the research. The samples used have been collected by HUS from patients who have had the coronavirus infection.

VTT began the project to develop new antibodies to the SARS-CoV-2 virus using internal funding, but is now urgently seeking additional funding and partners for the development of the rapid response test.

The tests and their analysis equipment could be carried out in Finland by VTT and other Finnish companies. In addition to responding to domestic needs, they could be sold internationally.

VTT research area vice president Dr Jussi Paakkari said: “Increasing the testing capacity plays a key role in monitoring the progress of the epidemic, but current testing methods require a lot of time and resources, which limits the capacity. The purpose of the rapid test is to enable growing the testing capacity and ensuring the availability of tests even as the epidemic continues.”

BD and BioMedomics Develop Blood Test to Detect Covid-19 Antibodies

Biotech company BD and BioMedomics have launched a new blood test to detect antibodies in blood to confirm current or past exposure to coronavirus (Covid-19) within 15 minutes.

Developed and manufactured by BioMedomics, the point-of-care rapid serology test identifies antibodies that are generated by the body as a result of Covid-19 infection.

The antibodies, which are normally present during the middle and final stages of infection, may remain in the body after the exposure.

It will help clinicians to determine past exposure to Covid-19 even if a patient no longer exhibits symptoms.

Data on past exposure is considered to be vital for researchers in understanding the possible occurrence of SARS-CoV-2 infection across a population. The information can aid future strategies for fighting the pandemic.

BD Integrated Diagnostic Solutions president Dave Hickey said: “Serology tests are important because they provide an additional piece of information to aid in characterising possible prior exposure to SARS-CoV-2, especially since many infections are mild or asymptomatic in severity.

“Initial evidence suggests that nearly all patients infected with SARS-CoV-2 will have developed a detectable antibody response within days of symptom onset, at which time a negative serologic test along with molecular diagnostics could be helpful in ruling out Covid-19.”

The test can analyse blood, serum or plasma samples for the presence of immunoglobulin M (IgM) and Immunoglobulin G (IgG) antibodies related to SARS-CoV-2.

IgM enables the first line of defence during viral infections, while high-affinity IgG is generated afterwards for long-term immunity and immunological memory.

The detection of Covid-19 IgM antibodies hints a recent exposure to the disease and the detection of Covid-19 IgG antibodies indicates a later stage of infection.

The combined antibody test could also help identify the stage of the disease in patients.

BioMedomics CEO Frank Wang said: “Our test has been clinically validated at several hospitals and clinical laboratories in both the US and China and our published clinical data in the Journal of Medical Virology was one of the world’s first for a Covid-19 serology test.

“It has been used widely in China during the Covid-19 outbreak and is now ready to help combat coronavirus in the US through our collaboration with BD.”

The companies also noted that additional testing may be required, depending on the clinical scenario, to further evaluate the possibility of SARS-CoV-2 infection.

Tuesday, March 31, 2020

Indiana University Develops Real-Time COVID-19 Diagnostic Tests


Indiana University researchers from the School of Informatics and Computing at IUPUI and the School of Medicine, in collaboration with Indiana University Health, are developing new diagnostic tests that combine speed and sensitivity for rapid detection of the viral strain.

These tests can eventually be employed for faster diagnosis of health care workers and others who are on the front lines and exposed to COVID-19 patients.

Benchtop and palm-held sequencing-based approaches being developed by IU principal investigator Sarath Janga and colleagues provide solutions for real-time detection of viral infections in clinical samples and further means to control the outbreaks.

"The issue with current accepted approaches for COVID-19 tests is that, while effective at detection, they are slow, with results taking up to a day or longer. We are testing our benchtop sequencing approach, which can potentially be done in two to three hours or even less," Janga said.

An additional advantage of this novel approach is that testing may be performed at point-of-care in the clinic, rather than transferring samples to the lab, further reducing time and the risk of more infections.

Given these challenges, the team hopes to leverage the findings from these new rapid tests to generate quantitative or semi-quantitative data that can be used to identify the COVID-19 strains prevalent in Indiana and reconstruct the development and evolution of the virus to inform surveillance, public health strategy and potential vaccine design going forward.

Janga's lab is also supporting current ongoing COVID-19 testing by providing personnel and necessary reagents to the clinical pathology lab at IU Health.

"Viral outbreaks such as COVID-19 need real-time detection of the status of infection in patients to control the spread," Janga said. "Since there are currently no specific treatments for coronavirus infections, and strains of these RNA viruses evolve rapidly, it is crucial to develop novel techniques that can provide rapid diagnostics and therapeutic intervention."

Like coronavirus, several viral strains are pathogenic in nature, difficult to detect and easy to transmit, leading to the emergence of pandemics. In the case of an outbreak, it is important to have a method to detect the virus as quickly and accurately as possible in order to prevent its transmission and efficiently treat infected patients.

Currently, most clinical diagnostic tests for viruses depend on either detecting viral antigens or on PCR amplification of viral nucleic acids. These two approaches offer trade-offs and benefits. Antigen tests are typically rapid but have low sensitivity, while PCR is more time-consuming and more sensitive.

Janga and his team are employing a commercially available Oxford Nanopore Technologies sequencing platform that generates full-length DNA or direct RNA virus sequences from clinical samples.

Janga, an associate professor in bioinformatics and data science in the School of Informatics and Computing at IUPUI, and visiting research associate Quoseena Mir, from the Department of Biohealth Informatics in the School of Informatics and Computing, are collaborating with Ryan Relich, head of the IU Health Clinical Pathology Laboratory and assistant professor of clinical pathology and laboratory medicine at IU School of Medicine, and Dr. Raj Vuppalanchi, director of the clinical hepatology division in the IU School of Medicine's Department of Medicine.

Source: Indiana University News