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

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

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

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

http://rapidmicromethods.com/files/EUA.php

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

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

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

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

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

How the current SARS-CoV-2 assays work

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

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

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

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

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

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

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

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

Who does the testing

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

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

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

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

SARS-CoV-2 tests in development

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

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

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

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

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

Source: TheScientist

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Portable Nanohole Device Will Rapidly Diagnose Sepsis

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

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

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

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

Trapping biomarkers in nanoholes

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

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

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

Reference

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

Source: École polytechnique fédérale de Lausanne (EPFL)

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

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

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

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

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

Unique gene signatures

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

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

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

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

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

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

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

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

Gene library

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

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

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

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

New approach to diagnosis

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Source: Imperial College London

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