SMART Develops 10-minute Test for Detection of COVID Immunity

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

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

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

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

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

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

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

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

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

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

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

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

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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

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

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

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

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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.

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

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

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

Reference

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

Source: École polytechnique fédérale de Lausanne (EPFL)

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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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Pocket-Sized DNA Sequencers Could Stop Food-Borne Pathogen Outbreaks as Soon as They Start

I recently reviewed an interesting story on food-borne pathogen outbreaks and the need to rapidly detect microorganisms to minimize the impact on people's lives. In a recent Massive Science article, microbiologist Bhavya Singh describes the use of a pocket-sized DNA sequencer that makes it easier to detect outbreaks before they cause significant harm. The article is reprinted below.

A few months ago, the Canadian Food Inspection Agency (CFA) recalled frozen chocolate eclairs due to a possible Salmonella infection.

That’s just one. In the past year alone, there have been enough food-related outbreaks that I have now made it a regular habit to check for food recalls on the CFA website. Unfortunately, the biannual recall of romaine lettuce is the least of our worries. From leafy greens to herbal tea, food recalls due to pathogenic outbreaks are on the rise. The U.S. Center for Disease Control and Prevention (CDC) reports that 1 in 6 Americans are affected by food-borne pathogens, with roughly 3,000 people dying due to these illnesses. These statistics make food-borne pathogens a public health concern that affects everyone.

To combat this problem, scientists are now using a portable device to sequence DNA from food and detect infection-causing organisms in just a few hours. Being able to identify an infected product before it causes a pathogenic outbreak can save lives, and current research will finally allow us to do that.

The Oxford Nanopore MinION is a pocket-sized DNA sequencer – it’s smaller than a typical smartphone, and significantly faster at producing data than most sequencers currently in use. Current full-genome sequencing technologies require over 24 hours to go from DNA extraction to analysis, without including the extra time to culture and grow pathogens. Overall, it can take days. Days. That is more than enough time for infected food to travel from grocery stores to homes.

Perhaps the most exciting feature of this technology is that sequences can be analyzed in real-time, making this process even faster by reducing the data processing time typically required for sequencing data.

A joint study from the University of Massachusetts and New England Biolabs recently put the MinION to the test for detecting viable food pathogens. The researchers chose to use RNA sequencing, as opposed to DNA sequencing, to address one of the major issues with DNA-based analyses: the inability to differentiate between DNA from viable and living pathogens, versus background DNA. Since RNA is less stable than DNA and has a shorter life once cells have died, it is relatively safer to assume that any detected RNA is from living pathogens. The MinION had a turnaround time of just 6.5 hours to sequence the transcriptomes of multiple bacteria, from the first step to the final analysis. Another recent study that instead employed DNA sequencing was able to sequence the entire genome of a Salmonella strain with a total turnaround time of 10 hours, without including the 24 hours it took to grow the bacterial cultures prior to DNA extraction.

Current standard procedures for identifying outbreaks can also be a huge financial barrier. Isolating, culturing (for identification, older techniques often need to create more pathogen than a sample provides), and sequencing microorganisms requires expensive laboratory equipment and facilities. Unfortunately, these facilities might not be accessible in places where outbreaks can cause the most damage. Even the size of most sequencers can be a barrier to fast detection – most instruments cannot be picked up and carried from site to site, making them very impractical for the food industry, particularly in situations where something needs to be analyzed on-site.

Another research group, known as the Tree Lab, has been conducting a study in East Africa to see if the MinION’s success could be replicated in the field. The lack of access to equipment can require agricultural scientists to transport samples to third-party services, which are often in different countries. Delays caused by transportation, data analysis, and communication can increase the timeline of pathogen detection to a staggering six months. Such a large turnaround time hinders the quick decision-making that is required to protect crops and manage disease outbreaks. The Tree Lab aimed use a MinION to cut this timeline down to just a few hours, compared to the grueling months when relying on conventional approaches.  Instead of sending samples away for analysis, the researchers wanted to carry out every step of the procedure on-site, with local scientists and farmers. This would circumvent a lot of the previous caveats, such as the exorbitant costs, the potential of sample degradation and contamination during travel, and the arduous and memory-intensive task of sharing extremely large amounts of sequencing data over the internet.

With farm conditions that included no access to laboratories, reliable electricity, or internet connection, the researchers collected samples from cassava plants. As the fourth largest source of food in the world, cassava is a staple for 800 million people in the world. Unfortunately, pathogens such as the cassava mosaic begomoviruses can cause devastating damage to crop yields.

In their Cassava Virus Action Project, members of the Tree Lab were able to sequence and detect the cassava mosaic begomovirus in under four hours. In addition to the speed of the portable DNA sequences, this was made possible by a rapid DNA extraction technique, which further cut down the time it would typically require to culture and grow pathogens before extracting DNA. Pre-installed and pre-curated databases also circumvented the need for high-powered computers for data analysis.

While these results are promising, there are a few things to consider before portable DNA sequencers can become standard procedure for pathogen surveillance.

First, the Tree Lab conducted an excellent proof-of-concept experiment to show that portable DNA sequencers can be used in the field, where laboratory equipment and scientific experts are not readily available. However, transitioning out of current procedures and using portable DNA sequencers in practice will take time and additional investments. Secondly, while Nanopore sequencing is incredibly fast, one major trade-off is the reduced sequencing quality, which can affect the ability of bioinformatics tools to detect the source of the DNA sequences. Lastly, phasing out current technologies and introducing pocket sequencers will require large amounts of training, changes in current rapid-response procedures, and advances in other bioinformatics tools to aid in accurate detection and analysis of pathogens.

Currently, most food-borne pathogens are only detected after people get ill. Surveillance patterns of these cases are then used to find the source of the outbreak and identify the contaminated food. This outbreak is controlled by removing the contaminated food from shelves and homes. While scientist are making strides in streamlining pathogen detection, we have a long way to go. Until then, it doesn’t hurt to periodically check for food recalls on your local government websites.

Source: Massive Science

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Early Detection of Viruses in Biopharma

Researchers in Carnegie Mellon University’s Department of Chemical Engineering (ChemE) are collaborating with leading biotechnology company Genentech, a member of the Roche Group, and LumaCyte, a biotechnology instrumentation company based in Charlottesville, VA, to develop an advanced biomanufacturing technology for adventitious agent testing, or testing for unexpected viral infections during the production of biopharmaceuticals.

The research recently received funding from the National Institute for Innovation in Manufacturing Biopharmaceuticals (NIIMBL) to develop and test technologies for improving the safety testing of biologic medicines during production and prior to release. This project, which aims to rapidly and accurately detect viral infectivity in biopharmaceuticals, was one of the first four proposals funded by NIIMBL. The team, which includes Carnegie Mellon, Genentech, and LumaCyte, will receive $1.5 million in funding from NIIMBL over 18 months.

When using biological materials such as mammalian cell lines to produce pharmaceuticals, manufacturers face the risk of viruses infecting the batch. Currently, testing for adventitious agents such as viruses happens late in the manufacturing process—but the research team, which includes ChemE Professor Jim Schneider and Adjunct Professor Todd Przybycien, are developing technologies to test biopharmaceutical batches while they are being produced.

“If you don’t find out about infection until very late in the process, you will have wasted a lot of time and money as more downstream equipment and product becomes infected,” says Schneider. “Current infection detection techniques, such as cell-based assays and polymerase chain reaction, can take days to complete. Our methods can provide readout in less than 15 minutes, which enables a routine, continuous type of testing that could detect infections almost as soon as they take hold.”

Rapid DNA analysis has been in development for a number of years by Schneider and Przybycien, who is also a professor of chemical and biological engineering at Rensselaer Polytechnic Institute. Using a rapid DNA analysis technique developed in Schneider’s lab, the team is detecting viruses and bacteria in process streams used to make biologic pharmaceutical projects. By performing rapid electrophoresis, the researchers can separate tagged and untagged DNA in a sample, indicating the presence of virus or bacteria in biologic process streams.

The researchers aim to combine their method with LumaCyte’s LFC and Radiance technology for a faster, more reliable, and more cost-effective solution. LumaCyte’s Radiance and Carnegie Mellon’s patented rapid DNA analysis platform will combine to rapidly detect the presence of virus and/or bacteria in bio process streams.

“The focus of NIIMBL is to translate existing technologies into biomanufacturing contexts,” said Schneider. “One of the top priorities that the industry has identified is rapid adventitious agent screening. As one of the first four projects funded by NIIMBL, this research with LumaCyte and Genentech shows our commitment to collaboration between academia and the pharmaceutical industry."

NIIMBL is an Innovation Institute designed to revolutionize domestic biopharmaceutical manufacturing. Funded through a $70 million cooperative agreement with the National Institute of Standards and Technology (NIST) in the U.S. Department of Commerce, NIIMBL funds and collaborates on innovative manufacturing technologies that bring life-saving and life-enhancing products to market faster and at reduced cost, while maintaining safety and efficacy.

LumaCyte is an analytical instrument development company headquartered in Charlottesville, VA. LumaCyte produces a label-free cell analysis and sorting instrument called Radiance that does not require the use of antibody or genetic labelling for analysis of cells. Applications of LumaCyte’s label-free platform technology include viral infectivity for vaccine manufacturing, cell and gene therapy, cancer biology, infectious disease, and pre-clinical drug discovery.

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