Sunday, August 29, 2021

New Device Can Diagnose COVID-19 From Saliva Samples

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

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

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

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

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

A self-contained diagnostic

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

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

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

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

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

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

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

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

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

Tracking variants

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

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

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

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

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

Biosensors Transform the Diagnosis of Infections in Newborns

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

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

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

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

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

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

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

Microwave Sensor for Rapid Antibiotic Sensitivity Testing

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Employing tandem Cas proteins

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

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

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

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

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

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

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

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

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

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

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

Immunexpress Announces SeptiCyte® RAPID Testing For Paediatric Sepsis

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

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

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

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

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

About SeptiCyte® RAPID

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Monday, April 26, 2021

Sense Biodetection Raises Funding Toward Developing a New COVID-19 Test

Sense Biodetection has completed a $50 million Series B financing, with the molecular diagnostics company saying it will use the proceeds to accelerate the launch of its Veros COVID-19 test, and further develop a portfolio of instrument-free, rapid molecular tests.

Those tests will be based on Sense’s Veros platform, which is designed to detect a variety of deadly and costly diseases by applying rapid molecular amplification technology.

The platform is intended to underpin a new class of rapid molecular diagnostic tests that emulate the performance of central laboratory PCR testing, but are disposable and easy-to-use since they do not need an accompanying instrument or reader.

As a result, Sense says, Veros diagnostics can be used beyond traditional healthcare settings–enabling better access, outcomes, and value for patients and providers.

Sense’s technology is based on isothermal amplification and non-fluorescent color detection of amplified analytes on an easy-to-use device.

“This Series B round is crucial in providing us with the resources to grow our Veros platform to revolutionize decentralized point-of-care testing, and it is particularly important as we commercialize our Veros COVID-19 test,” Sense CEO Harry Lamble said Tuesday in a statement.

Koch Disruptive Technologies (KDT), a subsidiary of Koch Industries, led the Series B financing, with participation from Sense’s existing investors Cambridge Innovation Capital, Earlybird Health, Jonathan Milner and Mercia Asset Management.

Based in Abingdon, U.K., Sense was founded in 2014. Five years later, it raised £12.3 million ($17.2 million) in Series A financing, with the proceeds intended toward test development.

Koch Industries operates in more than 70 countries and generates $115 billion in revenue, making it one of the largest privately-held companies in the world.

“KDT sees huge potential for Sense’s Veros platform to transform the way medical providers and patients approach healthcare, empowering more choice, increased access, and better quality of care,” stated KDT President Chase Koch. “Sense’s talented team and its innovative Veros platform are changing the way we manage healthcare and infectious diseases, and we expect even greater applications of their technology as they continue to grow.”

Thursday, April 08, 2021

Israeli Company Develops Faster, More Comprehensive Tuberculosis Test

Israeli tech company BATM Advanced Communications Ltd. announced on Monday that they have received full funding to develop a new rapid molecular diagnostics test for Tuberculosis (TB), which is expected to begin its testing and validation phases in the second half of 2021.

The testing and validation phases will be fully funded by Stop TB Partnership, an international alliance which is comprised of over governmental and non-governmental organisations in more than 100 countries, all dedicated to eliminating the disease.

While current gold standard tests take days to return results and have issues determining antibiotic resistance, BATM's new test returns results within approximately two hours, identifying the strain and its resistance to antibiotics. 

It does this using a combination of a one-step PCR test, developed by BATM subsidiary Adaltis, with a NATlab instrument, which uses a new isothermal RCA process developed by BATM's associate company, Ador Diagnostics. 

The testing and validation of the test will take place at the University of Heidelberg, with BATM anticipating it will officially begin selling them next year.

BATM CEO Dr. Zvi Marom said the company was delighted about the new testing method and the funding and research announcements, saying they believe it "will be particularly crucial in preventing the spread of drug-resistant TB strains." 

"We also expect our solution to be more affordable and accessible than those used today," he said.

Dr. Marom elaborated, saying that "The devastating health, social and economic consequences of TB have been with us for centuries and are still here today. It is vital that we develop innovative solutions and systems that will enable this disease, which is a leading cause of death but is both preventable and curable, to be eradicated." 

He said that advances in molecular diagnostics have caused science to enter "a new era in the fight against infectious diseases." 

"I believe that BATM has an important role to play in this as we focus on developing new, innovative technologies while continuing to provide critical solutions to combat COVID-19," he concluded.

TB is one of the top 10 causes of death worldwide and the leading (non-pandemic) cause from a single infectious agent The WHO estimates that around three million cases go undiagnosed each year.

Drug-resistance, which can emerge through the prescription of incorrect treatment, in TB is an increasing public health issue and a health security threat.  TB can also cause other severe illnesses, such as meningitis, and can be an early indicator for HIV infection.

However, "with rapid and accurate diagnosis," BATM says, "TB is preventable, treatable and curable in most cases."

MatMaCorp Launches MYRTA, a New Hand-Held Real-Time PCR Device for POC and OTC Molecular Diagnostics

MatMaCorp (Materials and Machines Corporation), a developer of comprehensive molecular diagnostic systems, today announced the launch of its new hand-held device capable of conducting polymerase chain reaction (PCR) amplification and real-time fluorescent detection, anytime, anywhere. The device, called MYRTA™ (MY Real-Time Analyzer) was developed to provide portable, PCR-based molecular diagnostic solutions for human and animal health.

“The COVID-19 pandemic has highlighted the substantial need for over-the-counter and point-of-care testing to detect viruses, like SARS-CoV-2, and other disease-causing agents, at any time and any location in the world,” said Dr. Abe Oommen, MatMaCorp founder and President. “Almost all of the current handheld molecular diagnostic solutions have focused on isothermal amplification methods, but real-time PCR is still the gold standard for diagnostics that require high sensitivity and specificity.”

Real-time PCR is the primary method to reliably detect active infection of SARS-CoV-2 (the coronavirus that causes COVID-19) in patient samples. Efforts at developing easy-to-use and affordable over-the-counter (OTC) and point-of-care (POC) devices have been constrained by the fact that RNA or DNA isolation from samples must be integrated into the PCR amplification and detection steps. This has resulted in PCR-based methods for OTC and POC devices being side-lined, regardless of the fact that real-time PCR is the benchmark by which other molecular tests are measured. MatMaCorp successfully overcame these issues in the development of MYRTA, which can simultaneously conduct PCR amplification and rapid, real-time fluorescence detection.

“The ability to detect nucleic acids in real-time while running PCR amplification directly from the sample is a game changer in molecular diagnostics,” said Dr. Oommen. “Our flexible, robust, and portable MYRTA device will enable the use of PCR in numerous situations, making point-of-care and over-the-counter PCR-based testing possible in any part of the globe. Remote hospitals and clinics, as well as the military, can use this device to monitor disease causing pathogens.”

MatMaCorp has demonstrated accurate detection of SARS-CoV-2 and influenza A and B viruses directly from samples. In addition to human health applications, the MYRTA system could also be used in animal health, as shown by its ability to detect porcine reproductive and respiratory syndrome virus (PRRSV), a virus that causes major respiratory disease in pigs.

MatMaCorp plans to submit the MYRTA system to the U.S. Food and Drug Administration’s (FDA) for consideration of Emergency Use Authorization (EUA) for COVID-19 in the coming months. The FDA previously granted EUA to MatMaCorp’s COVID-19 2SF RNA test for the detection of SARS-CoV-2 on the company’s Solas 8 portable detection system.

binx health Receives FDA CLIA Waiver for Chlamydia and Gonorrhea Test

binx health, a population health technology company that provides convenient healthcare solutions, announced today that the US Food and Drug Administration (FDA) has granted Clinical Laboratory Improvement Amendments (CLIA) waiver for the binx io system, a first-of-its kind molecular point-of-care testing platform capable of delivering central laboratory quality results in about 30 minutes, for the detection of chlamydia (CT) and gonorrhea (NG). The platform was previously 510(k) cleared by the FDA for testing male and female samples in moderate and high-complexity locations.

"With ever increasing sexually transmitted infection (STI) rates, point-of-care and CLIA-waived platforms like the binx io are essential additions to our STI control toolbox, which will increase accessibility and decrease the burden on traditional healthcare settings," said Barbara Van Der Pol, PhD, MPH, Professor of Medicine and Public Health at University of Alabama at Birmingham.

CLIA waiver clearance allows binx to facilitate single visit testing for CT/NG in any of the more than 220,000 locations across the Unites States holding a CLIA certificate of waiver, including convenient and accessible locations such as OBGYN and primary care offices, urgent care facilities, community health clinics, STD clinics and retail settings. Single-visit diagnosis and treatment have the potential to improve treatment compliance and reduce STI transmission across communities.

"Clinicians on the front lines of sexual health and wellness have long needed options for rapid diagnostic tools to address the epidemic growth in STIs. In a healthcare landscape where consumer convenience and rapid answers are an imperative, the binx io is the first chlamydia and gonorrhea test to be used in near patient settings combining the features essential to meet these needs in a critically important area of sexual health," said Jeffrey Luber, binx Chief Executive Officer. "The io Instrument's demonstrated clinical effectiveness, ease of operation, and patient convenience make it a much-needed tool with transformative implications for public health, especially now during the COVID-19 pandemic where STI prevention services nationwide have been dramatically reduced or cut altogether as resources have been allocated to focus on the COVID response. We are grateful to the countless scientists, physicians, and key opinion leaders who played an important role in today's watershed event."

The CDC estimates that 1 in 5 people in the U.S.1 have an STI; based on CDC and USPSTF guidelines There are an estimated 108M people in the United States, for whom regular STI testing is appropriate.2 3

Today, nearly all CT/NG tests are processed at central laboratories, with a delay between diagnoses and treatment in many cases of several days or more, which often results in infected patients not returning for treatment. Data show that treatment delays may lead to onward transmission and serious health consequences particularly in women, with 10-15% of un-treated women experiencing Pelvic Inflammatory Disease and nearly 30,000 cases of infertility annually in the US related to undetected chlamydia4. Due to these delays, and potentially detrimental follow-on health effects, published data5 also show that clinicians are more likely to presumptively treat symptomatic patients with antibiotics while the patient is in the clinic rather than wait for central laboratory test results. Inappropriate antibiotic treatment can promote antimicrobial resistance and can contribute to the onward transmission of the untreated infection.

The CLIA waived status allows for expansion by permitting the binx io, through its national commercial distribution partnership with McKesson, to be placed in the over 220,000 CLIA-waived locations nationwide.

IIT Delhi Develops Handheld Device For Early And Rapid Diagnosis Of Dengue

Dengue is a serious global health concern with a large population around the world facing the risk of getting infected. Early diagnosis of dengue is the key to prevent deterioration of a patient’s health. However, conventional diagnostic tools like nucleic acid detection using Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) is a time taking proess and it also requires expensive equipments and reagents for the diagnosis of dengue.

These types of common diseases require a rapid, scalable and point-of-care diagnosis to be implemented at the community level and to reduce the workload of healthcare professionals. Understanding this, the GLancing Angle Deposition (GLAD) research group at IIT Delhi’s Physics Department has developed a handheld Surface Enhanced Raman Spectroscopy (SERS) based platform for early diagnosis of dengue virus. It also gives dengue test results within one hour (rapid diagnosis).

The handheld device has been succsessfully tested on the clinical blood samples collected from hundreds of individuals in collaboration with ICMR-National Institute of Malaria Research (NIMR), New Delhi.

Principal Investigator of the project and Professor in the Department of Physics, IIT Delhi, Prof. J.P. Singh’s research group is known for the synthesis of nanoscultptured thin films using a specialized technique called GLAD. This technique was employed to fabricate silver nanorods array based SERS active biosensors in order to detect pathogens. Only 2 microlitres of a diluted serum was dropcasted on the SERS substartes and Raman spectra were collected by flashing 785 nm laser beam through the device. All the data were fed in a statistical tool principal component analyzer (PCA) software. The intergrated device was able to clearly differentiate the three sets of blood samples; dengue positive, negative and healthy. This method provides a sensitive, rapid, and field deployable diagnosis of dengue at the early stage.

The research work was funded by IMPRINT India program of the Ministry of Education with New Age Instruments and Materials Pvt Ltd as the industry partner. The research was published in the journal Analytical Chemistry 92, 2527-2534 (2020).

The detection and distinction of human immunodeficiency virus (HIV-1) was also carried out in collaboration with ICMR-National AIDS Research Institute (NARI), Pune through the handheld SERS based platform. Binding of viruses directly on Ag nanorods without using antibodies or intermediate reagents was successfully demonstrated. The SERS platform was capable of distinguishing different tropic strains of HIV-1 suggesting tropism-based detection. The SERS based platform gives HIV-1 test results within an hour.

Speaking of the hand-held device, the project’s PI, Prof. J.P. Singh, IIT Delhi said, “This ultrasensitive and handy device has wide range of applications in the early-stage on-site detection of viral diseases and can produce the final report of investigation within an hour.” The research work was published recently in journal Colloids and Surfaces B: Biointerfaces 198, 111477 (2021)

Ultra-sensitive and Rapid Diagnostic Developed to Detect Ebola

An interdisciplinary team of scientists at Duke University has developed a highly sensitive and rapid diagnostic test for Ebola virus (EBOV) infection. In monkeys infected with Ebola, this diagnostic, called the D4-assay, proved to be 1000 times more sensitive than the currently approved rapid diagnostic test and capable of detecting the virus a full day earlier than the gold standard polymerase chain reaction (PCR) test.

This work, which appears in Science Translational Medicine on April 7, was done by biomedical engineers, molecular biologists, and immunologists at Duke University, and the University of Texas Medical Branch in Galveston and the Galveston National Laboratory.

Ebola virus gained global notoriety in early 2014 after an outbreak began spreading across the populous capital cities in Guinea, Liberia and Sierra Leone in Western Africa. By the time the pandemic was officially declared ended in 2016, more than 28,000 people had been infected and more than 11,300 people had died of the virus.

As of March 2021, there are two ongoing Ebola outbreaks in the Democratic Republic of the Congo that have resulted in more than 2,200 deaths, and Guinea declared a new outbreak of Ebola virus disease (EVD) after a cluster of cases appeared in February.

Early treatment and contact tracing of Ebola virus disease is critical for two reasons: First, patients are highly contagious once they begin showing symptoms, and early diagnosis can help contain the spread of EVD by make contact tracing and patient isolation easier. Second, the fatality rate of EVD can be as high as 90 percent if left untreated or treated late, but can be reduced to roughly 10 percent with monoclonal antibodies if patients are treated early in the infection.

The current gold standard for detecting Ebola virus is the reverse transcriptase polymerase chain reaction (RT-PCR) test, which identifies and amplifies viral RNA. Although RT-PCR has proven to be sensitive and capable of diagnosing Ebola infection much earlier than current alternatives, it has been difficult to implement in the remote settings where EVD outbreaks frequently originate.

Recent advances in RT-PCR test design have made it easier for untrained technicians to use the platform and reduced the need for expensive equipment. However, at $22.50 per test, the platform is expensive and, because it is lab-based, can be slow. In some studies, the median time required to confirm a diagnosis in the field is 6 days, making it a suboptimal tool when dealing with a highly contagious virus.

The current alternate diagnostic option is lateral flow assays, which detect antibodies or antigens that appear during an infection. These tests are cheaper, easy to use, and typically yield results in less than 30 minutes, but the trade-off is a greatly diminished sensitivity, so there is a greater possibility of the test missing an early infection.

To help address the shortcomings of both tests, the Duke team adapted the D4 assay, an ultrasensitive, point-of-care diagnostic previously developed by the Ahsutosh Chilkoti lab, to quickly and accurately detect secreted glycoprotein (sGP), a biomarker produced by the Ebola virus during the early stages of infection.

Besides Chilkoti, the Alan L. Kaganov Distinguished Professor of Biomedical Engineering, the team included Cassio Fontes, a former graduate student and now a senior research scientist in the Chilkoti lab, Michael Gunn, MD, a professor of medicine and immunology, and Barbara Lipes, an assistant professor of medicine at the Duke University School of Medicine.

"Prior studies suggested that Ebola virus produces secreted glycoprotein at high levels early in infection to act as a decoy and distract the immune system while the virus replicates and binds to the host cells," Fontes said. "We thought that if we could detect that, we could help facilitate earlier diagnosis, containment, and treatment during Ebola outbreak."

However, antibodies against sGP were not available, so Lipes, an antibody engineering expert in the Gunn lab, created a large library of antibodies that bind to sGP and screened for the antibodies that bound most strongly.

The two labs then worked together to identify the capture-detection antibody pair that provided the greatest sensitivity on the D4 platform.

The D4 assay for Ebola is made by inkjet printing these two antibodies against secreted glycoprotein onto a glass slide: detection antibodies, which are tagged with a fluorescent marker, and capture antibodies, which are primed to bind the target antigen. When a drop of blood or a throat or nose swab is placed on the slide, the detection antibodies separate from the array and bind to the target in the sample. These antibody-biomarker complexes then attach to the capture antibodies on the slide, which glow to indicate a capture.

To further improve sensitivity, the D4 assay is printed on a stealth polymer brush coating developed by the Chilkoti lab, which prevents non-target proteins from attaching to the slide's surface. This removes any 'background noise' on the chip, making it easier to detect very low levels of the target proteins, which makes the D4 assay very sensitive.

In parallel, the Chilkoti lab also developed a cheap but highly sensitive hand-held detector -- the D4Scope -- to read the results of the D4 assay.

"Jason Liu, a graduate student in my lab, worked to develop the D4Scope, which is a low-cost, battery-powered, compact, wide-field fluorescence reader that can image microarray spots with high sensitivity," Chilkoti said. "It was specifically designed using off-the-shelf components, so that parts could easily be replaced if the reader was damaged in the field."

To test their platform, the team worked with collaborators at the University of Texas Medical Branch in Galveston, where they showed that the D4 assay could detect EBOV in non-human primates a full day earlier than the RT-PCR.

"We've put the lateral flow assay to shame, sensitivity wise," said Fontes. "This is exciting because by understanding the biology of this virus, we've shown that there may be a target to look for where immunoassays like the D4 can outperform the PCR. It's really breaking new ground."

As the team moves forward, they aim to continue to refine their platform with the goal of shortening the time to results from 60 minutes to 30 minutes. Experiments are underway using molecular evolution to increase the sensitivity of the capture and detection antibodies.

They are also improving the design of the platform to make it a fully self-contained test. This would mean that users would only need to add a drop of blood to one port of a flow cell and a buffer solution to a second port to run the test under gravity flow. These changes would also allow for improved biocontainment and biosafety when handling potentially dangerous fluids.

Once these changes are made, the team hopes to coordinate clinical experiments in the field.

"I think it's a tremendous opportunity to really change the way Ebola testing works," Gunn said.

"When controlling an outbreak, it's key to identify the infected and be able to trace their contacts very quickly, and our hope is that test would allow you to do that," Gunn said. "With such a simple and rapid assay, you can also quickly screen people who are at risk of having contracted Ebola. It seems simple, but in the grand scheme of things could represent the difference between an outbreak and a pandemic."

This research was funded by the National Institutes of Health (NIH, R01AI150888; U19AI142785; UC7AI094660), the US Special Operations Command (w81XWH- 16C-0219), the National Council for the Improvement of Higher Education and the Science Without Borders project. Partial support was provided by the Department of Health and Human Services. The team also received the support of the Biosafety Level 4 (BSL-4) lab at the Galveston National Laboratory.

Competing Interests: The underlying technology of the D4 was developed by Angus Hucknall and Ashutosh Chilkoti, and was acquired by Immucor Inc (Norcross, GA) in 2014. The other authors declare no competing financial interests.

REFERENCE

"Ultrasensitive Point-Of-Care Immunoassay for Secreted Glycoprotein Detects Ebola Infection Earlier Than PCR," Cassio Fontes, Barbara Lipes, Jason Liu, Krystle Agans, Aiwei Yan, Patricia Shi, Daniela Cruz, Garrett Kelly, Kelli Luginbuhl, Daniel Joh, Stephanie Foster, Jacob Heggestad, Angus Hucknall, Maiken Mikkelson, Carl Pieper, Roarke Horstmeyer, Thomas Geisbert, Michael Gunn, Ashutosh Chilkoti. Science Translational Medicine, April 7, 2021. DOI 10.1126/scitranslmed.abd9696

Friday, March 19, 2021

Microtox® BT Evaluation of SARS-CoV-2 from Breath Test with Clinical Samples

DeepVerge, the environmental and life science AI company, announces initial data for ongoing Phase III clinical studies on the detection of SARS-CoV-2 on breath samples and identification of confirmed COVID19 positive patients.

Since Q3 2020, DeepVerge scientists have been working under laboratory conditions with the Spike Protein (“S-Protein”) of SARS-CoV-2 on the SARS-CoV-2 virus inside the Containment Level 3 (“CL3”) laboratories at the University of Aberdeen. In these studies, they have detected and identified the virus S-Protein in quantities at 40 femtogrami per millilitre (“Fg/mL”) at close to 100% sensitivity and specificity on DeepVerge’s Microtox® BTii nano-optofluidic chip.

In addition, under the clinical trial supervision of the Royal College of Surgeons, Ireland, 40 subjects, 16 of which were independently confirmed as COVID19 positive with PCRiii tests, provided breath samples that were tested on the Microtox® BT nano-optofluidic chip surface with Affimer® reagents (“Avacta Group”)iv and Optimers (“Aptamer Group”)v together the (“Binding Agents”).

The breath samples detected binding on the nano-optofluidic chip with a secondary antibody to the Spike Protein which was initially selected for the isolated spike protein work. Detection of the live virus was confirmed indicating 9 times increase in the digital spectrum signal on the Microtox® BT when compared to controls of nano-optofluidic chips with binding agent; and 19 times increase in signal with nano-optofluidic chips without binding agents. Additional digital background noise was indicated due to the non-specific binding of the antibody. Further data is required to confirm the same high sensitivity and specificity is achieved on breath test clinical trials which are underway.

Gerard Brandon CEO of DeepVerge plc commented:

“DeepVerge scientists have transformed its AI based water contamination detection system, developed over five years for e.coli, into the breath condensate Microtox® BT unit. Having successfully completed Phase I testing on the Spike Protein and Phase II studies with SARS-CoV-2 virus in the safety of CL3 laboratories, the initial results of Phase III real-world clinical studies in COVID19 patients have reached a major milestone with the demonstration that our Microtox® BT can deliver results in under 60 seconds from breath samples.

“The requirement for the UK Target Product Profile (“TPP”) Rapid Breath Test requires 150 confirmed positive samples and 250 confirmed negative samples. Additional supervised breath test clinical trials from a larger group is expected to provide sufficient data to meet the desired and acceptable criteria in the TPP to roll out the COVID19 and other pathogen breath tests later this year.”

Tracking progress of the stages of the infection

The Company notes the publicationvi by UK Medicines & Healthcare products Regulatory Agency (“MHRA”) of the “Target Product Profile Rapid Breath Tests for the direct and indirect detection of SARS-CoV-2”. Microtox® BT satisfies many of the “Desired” and “Acceptable” criteria within the document.

Subject to the limitations of the Binding Agents’ ability to capture the virus, the Microtox® BT breath test does or does not see the virus, eliminating false positives and enabling each test the potential to predict the following conditions:

• Asymptomatic and non-infectious,

• Asymptomatic and infectious,

• Symptomatic and infectious, and

• Symptomatic and non-infectious

Point-of-Care makes it possible to track and trace the progress of the stages of any infection, including COVID19, subject to the type of pathogen (bacteria, virus, fungi or parasite) or biomarker of a disease being targeted by the Binding Agents.

AI algorithms are designed to assess the risk of steric hindrance, in the case of SARS-CoV-2, by the capture of one S-Protein and one viral particle, blocking the binding of other viral particles in the immediate vicinity.

With ability to detect and identify the binding of individual S-Proteins at Fg/mL, the viral particle can be calculated to generate a bigger shift in the laser signal. Using AI, this relates back in Fg/mL of S-Proteins which indicates a viral load for each test subject.

The joint development program of work on the PBM-HALETM breath condensate device from PulmoBioMed is ongoing using multiplex bio-marker binding agents to analyse breath for 40 other diseases which include cancer, neurodegenerative, respiratory and metabolic conditions.

Winers Selected in XPRIZE Rapid Covid testing Competition

XPRIZE, the world’s leader in designing and operating incentive competitions to solve humanity’s grand challenges, is pleased to announce today the five winning teams in the $6M XPRIZE Rapid Covid Testing competition, with each winner creating high-quality, affordable COVID-19 testing to help society safely reopen and return to everyday activities. 

Chosen by an independent panel of judges, the grand prize winning solutions are radically affordable compared to what is currently available on the market; and are comparable to commercial offerings at measuring sensitivity, specificity and limit of detection, with a maximum turnaround time of 12 hours from sample to result

The winning teams are: 

Reliable LFC, LLC, Antigen Testing, Carlsbad, United States

ChromaCode, RNA Testing, Carlsbad, United States

Mirimus, RNA Testing, Brooklyn, United States

La Jolla Institute for Immunology, RNA Testing, La Jolla, United States

Alveo Technologies, RNA Testing, Alameda, United States

“We are thrilled to announce the winners of the XPRIZE Rapid COVID Testing, which awarded multiple winners with unique testing solutions to help prevent future supply chain problems,” said Anousheh Ansari, CEO of XPRIZE. “We started this journey to ensure communities across the globe have access to fast, affordable, and easy-to-use COVID-19 tests. We are grateful to have the best entrepreneurial and scientific teams on board to help bring their solutions to scale so we can properly reopen schools, businesses, and other vital institutions around the world.”

Following the December finalist announcements, the 20 teams sent their testing kits and protocols to two separate laboratories, for clinical validation. The independent judges, composed of diverse experts in the healthcare and COVID-19 space, reviewed each team’s lab results, testing concepts, and proposals before deciding on the winners. 

“While vaccines are important, we cannot rely on them alone to prevent the spread of the coronavirus and future outbreaks, especially not until they are provided around the world, en masse and at-scale,” said Jeff Huber, President & Co-Founder of OpenCovidScreen. “These technological breakthroughs in rapid covid testing are providing a safety net to ensure the spread of the disease is contained and to enable a safe return to work and school, and to protect hotspots like nursing homes. These advancements are key to helping underserved, under-resourced communities get access to affordable, accurate tests and to ultimately save more lives now and in the future.”

Additionally, four other teams were selected as winners in the Open Innovation Track, whose approaches demonstrated high potential for impactful screening solutions, but could not be categorized as polymerase chain reaction (PCR), Isothermal Amplification, Next Generation Sequencing, or Antigen Detection and could not be tested through the competition rounds. 

The four winning teams in the Open Innovation Track are: 

Steradian Technologies, Inc., Houston, United States

U-smell-it, Guilford, United States

Ram Global, Zweibrücken, Germany

TeraGroup, Herzliya, Israel

The XPRIZE Rapid Covid Testing judges included:

Dr. Rick Bright, Ph.D, Immunology and Molecular Pathogenesis

Shawna Butler, R.N. M.D.A., Nurse Economist

Dr. Charity Dean, CEO and Co-Founder, The Public Health Company

Dr. Paul Drain, Associate Professor, Departments of Global Health, Medicine and Epidemiology at the University of Washington

Dr. Anita Goel, Physicist and Physician, Chairman and CEO, Nanobiosym

Dr. Michael Mina, Physician-Scientist and Assistant Professor, Epidemiology and Immunology and Infectious Diseases at the Harvard School of Public Health

Dr. Anne Wyllie, Associate Research Scientist, Yale School of Public Health

“The competition was open to all modalities of molecular testing, and the teams submitted an impressive range of ideas. The winners created innovative technologies in rapid PCR, novel antigens, and point-of-care LAMP as well as pioneering some of the first-ever olfaction and breathalyzer tests,” said Chris Mason, Leader of the Science Team and a Professor at Weill Cornell Medicine.

Launched this past July amid the COVID-19 pandemic, this prize comes out of the XPRIZE Pandemic Alliance to bring researchers, innovators, institutions, corporations, and governments together to share ideas and resources in the fight against the current and future pandemics. Since launch, 85 organizations have joined the Alliance, where they have been able to share ideas and research through its digital collaboration platform Exchange, as well as through the XPRIZE Data Collaborative, a unique platform for innovators to collaborate, share and learn from data in a broad spectrum of fields in their search for solutions. 

To amplify impact, a $50 million COVID Apollo Project led by experienced life sciences investors and company builders – including RA Capital, Bain Capital, Perceptive Advisors, Redmile Group, and Samsara Biocapital – will work with OpenCovidScreen, the XPRIZE community, and beyond to accelerate the best ideas, technologies, and innovations to market and scale them.

The Anthem Foundation and Anthem, Inc., serve as the Founding Anchor Partners of XPRIZE Rapid Covid Testing. Seven major national and regional health plans are collaborating as founding partners: Blue Shield of California, Cambia Health Solutions, Inc, Health Care Service Corporation, GuideWell Mutual Holding Corporation, Horizon Healthcare Services, Inc. (NJ), BlueCross BlueShield of South Carolina. Supporting partners include leading healthcare, laboratory and technology companies: Google, Amazon, Ilumina, Ancestry, Testing for America, Thermo Fisher Scientific, Exact Sciences, Centerview Partners, Twist Bioscience, Opentrons, HudsonAlpha Institute for Biotechnology, Weill Cornell Medicine , Biotia, Inc and Medical College of Wisconsin.

Teams will work the remainder of the year to accelerate the adoption of their solutions on a massive scale. XPRIZE will oversee the development of a multimedia playbook documenting the testing protocols,plans implemented and lessons learned at deployment sites where this incredible testing technology will be rolled out. XPRIZE is currently inviting communities like schools, offices, factories, nursing homes, homeless shelters, and other communities to apply to be part of this innovative roll-out. 

Scientists Evaluate Handheld DNA Sequencers for Microbial Monitoring of Food

Researchers have evaluated a handheld DNA sequencing device for use in environmental monitoring at food factories.

The study, by researchers from the Teagasc food research program and APC Microbiome Ireland’s Science Foundation Ireland Research Centre, tested portable DNA sequencers as a routine microbial monitoring tool in food production facilities. It was funded by the Department of Agriculture, Food and the Marine (DAFM).

Small, portable, DNA sequencers provide the first steps toward real-time industry paced microbial classification and analysis, said researchers in the journal npj Science of Food.

Microbes in food can cause spoilage and disease, so routine checks in production sites are necessary. Accurate identification of microorganisms in the food chain allows sources of contamination to be identified and control measures to be put in place. However, current techniques, while tried and tested, have some limitations, researchers reported.

Advancing microbiology

“Microbiology testing in the food chain has, and continues to, rely on older, classical microbiology testing such as the use of agar and petri dishes. This is a time-consuming approach and only microorganisms that are being specifically tested for are identified,” said professor Paul Cotter, the study’s senior author.

Instead of culturing bacterial samples in petri dishes, DNA sequencing can rapidly analyze bacterial DNA and identify the species in a sample. However, conventional sequencing involves expensive lab-based equipment and only highly trained technicians can do the procedure and analyze results. This means it isn’t a good fit for routine microbial surveillance in busy food production plants.

Professor Cotter and colleagues, led by Aoife McHugh, compared the performance of Oxford Nanopore Technologies and Illumina sequencing to culture-based methods for environmental monitoring of a dairy plant.

Oxford Nanopore’s MinION handheld device was similar to the larger lab-based sequencing system in terms of the number of bacterial species it could identify in samples, suggesting it has potential as a routine monitoring device in food production. However, the small device requires a minimum amount of DNA before it can function correctly.

A step toward non-experts using DNA sequencing tools

Eight locations in the facility were swabbed on three different days in October, November, and December 2018, after cleaning in place but before the next round of dairy processing.

In the cleaned dairy facility there weren’t enough bacteria in many of the samples, so researchers had to perform an extra step to amplify the bacterial DNA before there was enough to analyze. They said further development of the technology may help to overcome this issue.

Researchers previously determined the ability of MinION-based rapid sequencing to correctly classify a four-strain, mock community of related spore-forming microorganisms of relevance to the dairy processing chain including Bacillus cereus, which can cause infections in humans.

Cotter said the use of DNA sequencing technologies to enhance food quality and safety can have an impact on everyday life.

“This study represents a key step toward a day when non-experts can use DNA sequencing tools to carry out microbiology testing in the food chain.”

Reference:

McHugh, A.J., Yap, M., Crispie, F. et al. Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples. npj Sci Food 5, 4 (2021). https://doi.org/10.1038/s41538-021-00087-2

Source: Food Safety News

Tuesday, March 09, 2021

Rutgers Develops Rapid Test to Detect New Emerging Coronavirus Variants

Rutgers researchers have designed a new rapid test that can detect all three of the rapidly spreading variants of the coronavirus in a little over one hour – much shorter than the three to five days required by current tests, which can also be more technically difficult and expensive to perform.

Details and information on easily creating and running the rapid test – which is not being patented by Rutgers because researchers believe it should be widely available to the public -- are published on the pre-print online server, MedRxiv, and is available at no charge.

The Rutgers researchers designed and clinically validated the test, which is the first to use “sloppy molecular beacon probes,” which are highly sensitive and specific DNA sequences used to detect frequent mutations in organisms.

“This rapid test was developed and tested over a few weeks in a crash program to respond to a serious public health need,” said David Alland, director of the Rutgers New Jersey Medical School Public Health Research Institute and professor and chief of infectious disease at Rutgers NJMS. “Despite our hurry to get the test completed, it performed extremely well with clinical samples in our initial studies. We are very pleased with these results and we hope that this test will help in the control of the rapidly evolving COVID-19 pandemic.”

The new more contagious variants, isolated in the United Kingdom, South Africa and Brazil, appear to be more easily transmitted, cause more severe disease and may be more resistant to some of the approved COVID-19 vaccines.

The new rapid test is easy to set up and can be adapted for labs that use varying types of equipment and methods. The Rutgers researchers said users are free to use the test as described or modify it as needed, although they strongly suggest that additional validation be done for any test modifications.

Researchers are also working to expand their test to more precisely differentiate among the three main viral variants and they expect to release a new and larger test menu along with supporting evidence in the next several weeks. Additional test modifications will be released in the future as additional variants emerge.

David Alland, Padmapriya Banada, Soumitesh Chakravorty, Raquel Green and Sukalyani Banik were co-researchers at Rutgers who helped develop the test.

UGA Researchers Develop New Rapid Test for Fusarium Watermelon Disease

Fusarium wilt, caused by a soilborne fungus, is one of the most damaging diseases of watermelons worldwide. Since it was discovered in 1894, it’s been a battle for producers to manage through crop rotation and chemical fungicides.

The fungus is persistent in both seedless and seeded varieties, and its spores can last for many years in the soil. While there are some watermelon varieties with known resistance, they are not resistant to all strains of the pathogen.

University of Georgia researchers have now developed a faster way to detect the disease’s presence and determine the races, or groups of strains, of the pathogen Fusarium oxysporum f. sp. niveum (FON) that cause the disease.

“At the microscopic level, you can diagnose Fusarium, but you can’t differentiate the races,” Emran Ali in the Department of Plant Pathology at the College of Agricultural and Environmental Sciences said. “Traditional bioassay methods have been used for this, but it takes weeks to grow watermelon plants and evaluate the disease, and watermelon cultivars used for the bioassay can be difficult to source. This method is not only inefficient, it is also sometimes inaccurate.”

The new molecular detection method, published in the International Journal of Molecular Sciences, allows differentiation of the different races of the pathogen.

Ali, who is head of the Plant Molecular Diagnostic Laboratory at the UGA Tifton campus, worked with Pingsheng Ji, a professor of plant pathology, and Owen Hudson, a graduate student in the department, as well as faculty at the University of Florida and Clemson University to identify more than 160 Fusarium samples collected from Georgia, Florida and South Carolina. Most of the results matched those done with the traditional bioassay method for the same samples.

The new process should improve the speed and accuracy of current diagnostic ability for FON races and facilitate research in related areas — especially breeders who are developing new varieties — to develop options such as host resistance against the disease.

“The whole process takes about three hours to diagnose races; traditional bioassay takes more than a month, at least,” Ali said.

Determining the races can help farmers better mitigate the issue and make the right management decisions. So far, four races of FON have been identified. Some commercial watermelon varieties are resistant to races zero and one, but not races two and three.

“Resistant watermelon varieties are effective against some races but not others,” Ali said. “If you quickly diagnose, growers can have more time in advance to know what’s going on in their fields. It’s good to know what’s going on. Watermelon varieties resistant to races zero and one are available, so you may grow resistant varieties to control disease caused by these races; other races are more destructive and more difficult to control.”

Georgia is continually a national leader in watermelon production, ranking second or third each year. The crop’s farm gate value was $180 million in 2019 and, with already thin profit margins, finding more efficient ways to battle diseases like Fusarium wilt could make a big difference for farmers.

Ali and his team at the Plant Molecular Diagnostic Laboratory also have developed faster tools for tracking other pathogens, including cucurbit leaf crumple virus in vegetables, dollar spot in turfgrass, citrus greening disease, root-knot nematodes in pecans, and irrigation water molds that can cause root rot. They say they hope these new detection methods will not only save time but also reduce pathogen prevalence in the field.

Coronavirus-like Particles Could Ensure Reliability of Simpler, Faster COVID-19 Tests

Rapid COVID-19 tests are on the rise to deliver results faster to more people, and scientists need an easy, foolproof way to know that these tests work correctly and the results can be trusted. Nanoparticles that pass detection as the novel coronavirus could be just the ticket.

Such coronavirus-like nanoparticles, developed by nanoengineers at the University of California San Diego, would serve as something called a positive control for COVID-19 tests. Positive controls are samples that always test positive. They are run and analyzed right alongside patient samples to verify that COVID-19 tests are working consistently and as intended.

The positive controls developed at UC San Diego offer several advantages over the ones currently used in COVID-19 testing: they do not need to be kept cold; they are easy to manufacture; they can be included in the entire testing process from start to finish, just like a patient sample; and because they are not actual virus samples from COVID-19 patients, they do not pose a risk of infection to the people running the tests.

Researchers led by Nicole Steinmetz, a professor of nanoengineering at UC San Diego, published their work in the journal Biomacromolecules.

Journal Reference:

Soo Khim Chan, Pinyi Du, Caroline Ignacio, Sanjay Mehta, Isabel G. Newton, Nicole F. Steinmetz. Virus-Like Particles as Positive Controls for COVID-19 RT-LAMP Diagnostic Assays. Biomacromolecules, 2021.


This work builds on an earlier version of the positive controls that Steinmetz's lab developed for the RT-PCR test, which is the gold standard for COVID-19 testing. The positive controls in the new study can be used not only for the RT-PCR test, but also for a cheaper, simpler and faster test called the RT-LAMP test, which can be done on the spot and provide results in about an hour.

Having a hardy tool to ensure these tests are running accurately -- especially for low-tech diagnostic assays like the RT-LAMP -- is critical, Steinmetz said. It could help enable rapid, mass testing of COVID-19 in low-resource, underserved areas and other places that do not have access to sophisticated testing equipment, specialized reagents and trained professionals.

Upgraded positive controls

The new positive controls are essentially tiny virus shells -- made of either plant virus or bacteriophage -- that house segments of coronavirus RNA inside. The RNA segments include binding sites for both of the primers used in the PCR and LAMP tests.

"This design creates an all-in-one control that can be used for either one of these assays, making it very versatile," said first author Soo Khim Chan, who is a postdoctoral researcher in Steinmetz's lab.

The team developed two types of positive controls. One was made from plant virus nanoparticles. To make them, the researchers infected cowpea plants in the lab with cowpea chlorotic mottle virus and then extracted the viruses from the plants. Afterwards, the researchers removed the virus' RNA and replaced it with a custom-made RNA template containing specific yet non-infectious sequences from the SARS-CoV-2 virus. The resulting nanoparticles consist of coronavirus RNA sequences packaged inside plant virus shells.

The other positive control was made from bacteriophage nanoparticles. It involved a similar recipe. The researchers infected E. coli bacteria with custom-made plasmids -- rings of DNA -- that contain specific fragments of sequences (which are also non-infectious) from the SARS-CoV-2 virus, as well as genes coding for surface proteins of a bacteriophage called Qbeta. This process caused the bacteria to produce nanoparticles that consist of coronavirus RNA sequences packaged inside bacteriophage shells.

The plant virus and bacteriophage shells are key to making these positive controls so sturdy. They protect the coronavirus RNA segments from breaking down at warmer temperatures -- tests showed that they can be stored for a week at temperatures up to 40 C (104 F). The shells also protect the RNA during the first step of the PCR and LAMP tests, which involves breaking down cells in the sample -- via enzymes or heat -- to release their genetic material for testing.

These protections are not present in the positive controls currently used in COVID-19 testing (naked synthetic RNAs, plasmids or RNA samples from infected patients). That's why existing controls either require refrigeration (which makes them inconvenient to handle, costly to ship and store) or have to be added at a later stage of the test (which means that means scientists will not know if something went wrong in the first steps).

As a next step, the researchers are looking to partner up with industry to implement this technology. The positive controls can be adapted to any established RT-PCR or RT-LAMP assay, and using them would help negate false readouts, Steinmetz's team said. Plus, these positive controls can be easily produced in large quantities by molecular farming in plants or microbial culture fermentation, which is good news for translating them to large-scale manufacturing.

"With mutants and variants emerging, continued testing will be imperative to keep the population safe," Steinmetz said. "The new technology could find utility in particular for at-home tests, which may have a higher rate of false readouts due to the less controlled experimental conditions."

This work was funded in part by the National Science Foundation (RAPID CBET-2032196 and RAPID CMMI-2027668) and the University of California (UCOP-R00RG2471 and a Galvanizing Engineering in Medicine Award).

Liquid Crystal Sensor Offers Breakthrough for Rapid COVID-19 Diagnostic Test

The global outbreak of COVID-19 has prompted scientists to focus their research on rapid and robust diagnostic tests. Reverse-transcription polymerase chain reaction (RT-PCR) assays – the ‘gold-standard’ for molecular clinical diagnostics – became available quickly, however this provides relatively long characterisation times and the need for specialised equipment.

Researchers at OSU have subsequently designed a liquid crystal (LC) based diagnostic kit and a smartphone-based application to enable automatic detection of SARS-CoV-2 ssRNA, which could be used for reliable self-test of SARS-CoV-2 at home without the need for complex equipment or procedures.

Prof Xiaoguang (William) Wang, PhD led the research team at OSU, and commented on his decision to consider LCs as a prospective diagnostic technology to meet the need: “It is well known that thermotropic LCs are ultrasensitive to small chemical modulations, and we felt that we could use this property to develop a rapid LC-based detection method for SARS CoV-2 virus that could be contained in a portable and economical sensor.”

A series of experiments were required to prove this concept and develop a prototype sensor, which included three key steps. 

1. The characterisation of a substrate layer that had been ‘functionalised’ with a liquid crystal mixture.

2. Validation of the reliable binding of an ssDNA ‘probe’ to this layer.

3. The detection and quantitation of ssRNAcov extracted from the virus as it bound to the probe.

Important for this last step was holding the temperature of the system at precisely 48.7°C, the melting temperature of ssRNA. The Linkam PE120 stage was integral to this phase and gave the team at OSU the reproducible control of the temperature of the sensor they needed during the process.

The PE120 Peltier system is straightforward to integrate with microscopes and other equipment, and ensures precise control of the temperature of microscope slides to +/-0.1°C at temperatures between  25°C to 120°C. 

Prof Wang’s research has recently been published, and it has shown that LC-based sensors offer a highly sensitive, reproducible and robust method of detection of target ssRNAcov – with detection limits in the nanomolar to femtomolar range.

Commenting on the work, Robert Gurney PhD, Marketing and Applications Specialist at Linkam Scientific, said: “What Prof Wang and his colleagues have achieved is extremely exciting. It’s great that one of the Linkam temperature control stages has played a key part in the team’s proof-of-concept studies, and I’m looking forward to seeing the results of the next stage – trials of the sensor with patient samples.”

Mobidiag Receives CE-IVD Marking for Amplidiag® RESP-4 for Simultaneous Detection of COVID-19, Flu A, Flu B and RSV

Mobidiag Ltd. today announces that it has received CE-IVD marking for its Amplidiag® RESP-4 molecular diagnostic test for the rapid and simultaneous detection of some of the most prevalent respiratory viruses: SARS-CoV-2 (responsible for COVID-19 infection), Influenza A, Influenza B and RSV.

These viruses present similar symptoms, making it difficult for physicians to determine accurately which virus a patient has. The Amplidiag® RESP-4 assay can rapidly and simultaneously determine an accurate diagnosis from one patient sample using nasopharyngeal swabs, helping to guide clinicians to the relevant treatment decision for each patient. The test runs on the Mobidiag Amplidiag® Easy platform, which provides clinicians with an optimized sample screening process, with automated DNA/RNA extraction and PCR plate setup. Based on well-established high-throughput PCR technology, the platform can process 46 samples in approximately three hours.

This new test further broadens Mobidiag’s already available portfolio of diagnostics tests.

Tuomas Tenkanen, CEO of Mobidiag said, “We are very pleased to announce the CE-IVD marking for the Amplidiag® RESP-4 assay, which is highly relevant to both the traditional flu season and COVID-19. Symptoms caused by these viruses [SARS-CoV-2, Influenza A, Influenza B and RSV] can be very similar, and it is imperative that healthcare professionals are able to rapidly distinguish between them, in order to start the appropriate treatment for the benefit of patients.

In response to the growing need for fast and reliable diagnostics, at Mobidiag we are putting all our efforts into maintaining a high degree of autonomy in the production of our Amplidiag® tests by securing critical components to provide continuous support for our customers, as we all work together to control the spread of COVID-19.”

Mobidiag is currently developing Novodiag® RESP-4, a molecular diagnostic test using its Novodiag® platform for the rapid and on-demand detection of SARS-CoV-2, Influenza A, Influenza B and RSV. This test will complement Amplidiag® RESP-4 and enable clinicians to detect respiratory viruses to support early decisions in managing efficiently epidemiological and infection control measures, isolate patients in a timely manner, and ultimately improve patient care and outcomes.

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 have any symptoms of respiratory infections.

About Mobidiag

Mobidiag is a fast-growing molecular diagnostics company whose rapid, cost-effective, widely applicable and robust technology makes the power of molecular diagnostics available to address the spread of infectious diseases and antimicrobial resistance (AMR) by rapid detection of pathogens and their potential resistance to antibiotics. Through its Amplidiag® and Novodiag® solutions, Mobidiag offers a comprehensive range of molecular diagnostic solutions for the detection of infectious diseases to laboratories of all sizes.

Tuesday, February 23, 2021

U of Minnesota Researchers Develop Two New RZapid COVID-19 Diagnostic Tests

University of Minnesota Medical School researchers have developed two new rapid diagnostic tests for COVID-19 - one to detect COVID-19 variants and one to help differentiate with other illnesses that have COVID-19-like symptoms. The findings were recently published in the journal Bioengineering.

Although many people are hopeful about COVID-19 vaccines, widespread vaccine distribution isn't predicted to be available until several months from now. Until that happens, the ability to diagnose COVID-19 quickly and accurately is crucial to help minimize loss of life and continued spread of the virus.

The technology for both tests uses the cutting-edge CRISPR/Cas9 system. Using commercial reagents, they describe a Cas-9-based methodology for nucleic acid detection using lateral flow assays and fluorescence signal generation.

The first test is a rapid diagnostic test that can differentiate between COVID-19 variants. This test can be performed without specialized expertise or equipment. It uses technology similar to at-home pregnancy testing and produces results in about an hour.

The second, more sensitive test allows researchers to analyze the same sample simultaneously for COVID-19 (SARS-CoV-2), Influenza A and B and respiratory syncytial virus by measuring fluorescence. These viruses manifest with similar symptoms, so being able to detect and differentiate them adds a new diagnostic tool to slow the spread of COVID-19. This test also takes about an hour and could be easily scaled so many more tests can be performed. The necessary equipment is present in most diagnostics laboratories and many research laboratories.

"The approval of the SARS-CoV-2 vaccine is highly promising, but the time between first doses and population immunity may be months," said Mark J. Osborn, PhD, assistant professor of Pediatrics at the University of Minnesota Medical School and first author of this paper. "This testing platform can help bridge the gap between immunization and immunity."

In collaboration with the U of M's Institute of Engineering in Medicine and Jakub Tolar, MD, PhD, dean of the U of M Medical School, Osborn and his team are now seeking to enhance sensitivity and real-world application of this test in support of rapidly detecting and identifying COVID-19 variants. In order to provide access to their new testing technology for healthcare providers and the public, the researchers are currently exploring ways to scale up and license their new diagnostics.