COVID-19 Tests | Wish List

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Re: COVID-19 Tests | Wish List

Post by trader32176 »

Rapid, low-cost test for potential universal COVID-19 monitoring

10/7/20 ... oring.aspx

An international team of researchers has presented a convenient, low-cost serology test to detect antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that could potentially be made available universally.

SARS-CoV-2 is the agent responsible for the current coronavirus disease 2019 (COVID-19) pandemic that continues to threaten global public health and the economy.

Alain Townsend (University of Oxford) and colleagues report that the Hemagglutination Test (HAT) detects antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with a sensitivity of 90% and specificity of 99%.

The RBD is a subdomain found at the tip of the spike protein – the main structure the virus uses to bind to and enter human host cells.

The HAT can detect rising titers of RBD-specific antibodies within the first five days of infection, correlates well with an established commercial test, and can be applied in point-of-care (POC) testing.

This versatile, cost-effective test does not require specialist equipment or centralized laboratory facilities and could be made available to low- and middle-income countries.

Furthermore, the test can be lyophilized for ease of shipping, say Townsend and colleagues, who have now scaled-up production of this reagent to one gram – enough to provide ten million tests, at a cost of around 0.27 UK pence per test well.

“Aliquots of this reagent are ready to be supplied to qualified groups anywhere in the world that need to detect antibodies to SARS-CoV-2, but do not have the facilities for high-throughput commercial tests,” writes the team.

A pre-print version of the paper is available in the server medRxiv*, while the article undergoes peer review.

Affordable serology tests are urgently needed

Since the first cases of SARS-CoV-2 were identified in Wuhan, China, late last year, the virus has spread at an unprecedented rate and had a devastating effect on global public health and the worldwide economy.

“The appearance of such a new highly contagious virus will probably not be a unique occurrence in the decades ahead,” said Townsend and colleagues. “One of the lessons learned is the importance of developing affordable serological tests for the detection of immune responses to SARS-CoV-2.”

Such tests are crucial for determining seroconversion rates in populations, detecting seroconversion following vaccination, and for assessing whether antibody levels may be protective against COVID-19.

Several high-performance commercial antibody tests have been described, but they are not widely available to low- and middle-income countries, since they require costly centralized laboratory facilities.

Red cell agglutination tests, which involving linkage of a reporter molecule to the surface of red cells, have a long and distinguished history in blood typing and a wide variety of serology applications. They are inexpensive, and their application does not require specialist technology.

Furthermore, “in the recent era, the linkage of an antigen to the red cell surface has become easier with the possibility of fusing a protein antigen sequence with that of a single domain antibody or nanobody specific for a molecule on the red cell surface,” says the team.

What did the researchers do?

The researchers have applied this concept to provide a convenient HAT test for the detection of SARS-CoV-2 spike RBD-specific antibodies.

In order to link the spike RBD to red blood cells, the researchers used the nanobody IH4, which is specific for a conserved epitope on the transmembrane protein glycophorin A.

The team reports that in a formal assessment of sensitivity and specificity, HAT demonstrated a sensitivity of 90% and specificity of 99% for the detection of antibodies following a PCR-confirmed diagnosis of SARS-CoV-2 infection.

HAT correlated well with the commercially available Siemens Atellica Chemiluminescence test that detects spike RBD-specific antibodies.

Interestingly, says the team, the HAT titrations demonstrated slightly superior performance over the Siemens test when it was applied to stored plasma samples taken from donors within the first five days of their hospital admission.

In this scenario, HAT detected antibodies in 86% of samples from PCR-diagnosed donors, while the Siemens test detected 74%. HAT also demonstrated 100% specificity when applied to control plasma samples taken from healthy patients or those with sepsis.

“In situations of high clinical suspicion, the HAT could potentially have a place as a helpful test to support the diagnosis of COVID-19 by detecting a rising titer of antibodies to the RBD during hospital admission,” write the researchers.

The HAT might also be useful for detecting seroconversion following vaccination and for the identification of potential convalescent donors with high titer plasma that could potentially be used as a treatment.

Enough reagent for 10 million tests is available to the world

The team also says lyophilized IH4-RBF reagent that was sent to New Delhi performed well in POC testing of finger-prick samples. However, further evidence is needed to confirm that the sensitivity and specificity are comparable to those seen with tests of stored plasma samples.

“This will need to be done in field conditions, which is planned,” write Townsend and colleagues.

Finally, the team says: “We have produced one gram of the developing IH4-507 RBD reagent (enough for ten million test wells) and offer to ship lyophilized aliquots of this material (sufficient for 10,000 tests) anywhere in the world, free of charge, for use as a research reagent for serological studies of COVID-19.”

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
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Re: COVID-19 Tests | Wish List

Post by trader32176 »

Technological breakthrough may increase COVID-19 testing, reduce wait time and costs

10/8/20 ... costs.aspx

The U.S. Food and Drug Administration has granted emergency use authorization for scientists at UCLA Health to begin using a new method of COVID-19 detection using sequencing technology called SwabSeq. The method is capable of testing thousands of samples for coronavirus at the same time, producing accurate, individual results in 12 to 24 hours.

SwabSeq adds a unique molecular bar code to each sample in the first step of its processing. The samples are then combined in a sequencer and the bar codes allow for the identification of which specific sample has the virus. The underlying technology of SwabSeq can be applied to any type of sample collection, such as a nasopharyngeal, oropharyngeal or saliva test.

" This is a technological breakthrough that will dramatically increase the amount of COVID-19 testing while reducing the wait time for results and costs."

-Dr. John Mazziotta, Vice Chancellor for UCLA Health Sciences and CEO of UCLA Health

Dr. Eleazar Eskin, chair of the Department of Computational Medicine affiliated with both the David Geffen School of Medicine and the Samueli School of Engineering at UCLA, explains: "SwabSeq is highly scalable because it leverages two decades of advances in genomic sequencing technology. Using SwabSeq, a relatively small lab can process tens of thousands of samples per day."

Dr. Eskin's department collaborated on the groundbreaking technology with scientists at UCLA Health, the Department of Human Genetics, the Department of Pathology and Laboratory Medicine and Octant, a start-up company founded and incubated at UCLA. SwabSeq is a modification of Octant's technology that is being applied toward drug discovery and has been made available broadly to fight the pandemic. UCLA scientists have been leading a broader coalition of academic and industrial labs around the country and world developing the technology to scale testing.

Octant co-founder and CEO Dr. Sri Kosuri, says: "UCLA has been at the forefront of taking SwabSeq from an initial technology to validating its use in large-scale testing of real patients. We jump-started a whole community of researchers now using the technique to help bring people back to work and school."

"This is an innovative use of genomic sequencing for COVID-19 testing that is uniquely scalable to thousands of samples per day, sensitive and fast--a combination that is challenging to find in diagnostic testing," says Dr. Valerie Arboleda, an assistant professor in the Departments of Pathology & Laboratory Medicine and Human Genetics.

Dr. Jonathan Flint, professor in the Departments of Psychiatry and Biobehavioral Sciences at the David Geffen School of Medicine, says, "The sequencing technology is able to fill the gap in COVID-19 testing, particularly for the asymptomatic population, because it doesn't have the same supply chain bottlenecks that have limited further expansion of current clinical PCR testing."

"SwabSeq is simple, sensitive and flexible and can provide a turn-around time of less than a day," explains Dr. Leonid Kruglyak, chair of the department of Human Genetics at the David Geffen School of Medicine. "It has the potential to expand testing capacity to the scale required for pandemic suppression."
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Re: COVID-19 Tests | Wish List

Post by trader32176 »

Rapid and sensitive detection of SARS-CoV-2 with functionalized magnetic nanoparticles

10/11/20 ... icles.aspx

The current COVID-19 pandemic is caused by an RNA virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an enveloped virus with spikes composed of glycoproteins studding its bilayered lipid envelope. With its propensity for causing severe or critical pneumonic disease in a significant minority of patients, the virus has become a significant target of diagnostic and therapeutic research. A recent study published on the preprint server arXiv* in October 2020 shows the potential for using functionalized magnetic nanoparticles to detect the presence of the virus in a sample.

Importance of Testing

Testing is critical to containment efforts since not only symptomatic but asymptomatic patients, and contacts must be tested on a large scale in order to break the chain of transmission. As of now, the gold standard consists of polymerase chain reaction (PCR), which is complicated as well as time-consuming. Moreover, the procedures require sophisticated equipment, with a high cost, and requires operation by technically skilled staff. If carried out improperly, the odds of a false positive or negative result are high.

With an exponentially rising case count, it has become an overwhelming strain to test for COVID-19 in clinical situations. Moreover, in developing and underdeveloped countries, limited healthcare resources are likely to aggravate this difficulty. This lends urgency to the task of developing new methods or instruments to achieve a rapid diagnosis of this infection.

Magnetic Nanoparticles in Particle Detection

One of the upcoming techniques being explored is homogeneous biosensing based on magnetic nanoparticles (MNPs) in order to detect biomolecules of a specific kind. This could include nucleic acids or proteins. The principle of the test is the fluctuation in magnetization and the magnetic characteristics of the MNPs when exposed to magnetic fields varying in intensity over time.

The extent to which the biomolecules bind to functionalized MNPs is dictated by Brownian relaxation, which causes a change in their hydrodynamic size or induces cross-linking. This results in significant alterations in the Brownian relaxation time of the MNPs and the magnetization dynamics when exposed to time-varying magnetic fields.

The researchers quote the example of the observable decrease in harmonics in magnetic particle spectroscopy (MPS) due to the reduction in Brownian relaxation, when MNPs bound with biomolecules are exposed to an alternating current magnetic field of sufficient intensity. The higher harmonics are found to reduce more rapidly than the fundamental harmonic, causing a decrease in the harmonic ratio without relation to the MNP concentration.

This is, therefore a sound basis for the quantitative detection of specific biomolecules, using the measure of MNP magnetization and its susceptibility/spectra in ac magnetic fields. The use of MPS offers an inexpensive, flexible, and sensitive method of determining MNP magnetization and dynamics to detect biomolecules.

Experimental Evidence of Efficient Detection

The current study suggests the use of MPS to measure the binding of the spike protein to MNPs functionalized with antibody, and thus to detect the virus. This proof-of-concept experiment uses these MNPs as sensors to detect fake viral particles, comprising 100 nm polystyrene beads conjugated with the spike protein. They engineered an MPS apparatus for signal measurement, especially the ratio of the 3rd to 1st harmonics.

As well, they used a rotating magnetic field (RMF) system to assess the Brownian relaxation time using ac susceptibility (ACS) spectra. A range of particle concentrations was used to evaluate the sensitivity and the limit of detection (LOD) of this technique, which is found to be 0.084 nM (5.9 fmole).

This setup allows very sensitive detection of the mimic virus, with four repeated measurements being taken over a period of 36 seconds overall. If this is further customized, the LOD can be still further reduced to measure an average of 36 measurements within this period.

Using the ASSURED criteria of the World Health Organization (WHO), this method is found to be a good fit for disease control, being Affordable, Sensitive, Specific, User-friendly (requiring minimal training), Rapid and robust (results require below 30 minutes), and Deliverable to end-users, while using innocuous and cheap materials. The only non-applicable criterion is Equipment-free, but this test can be built as a point-of-care (POC) device at a low cost.


While current virus detection tests are binary, failing to yield information on the status of infection, this can help to quantitatively detect living virus particles, which will help to tailor treatment and containment measures to the tested individuals. In fact, the detection of the virus is more sensitive than of the spike protein on the functionalized MNPs, due to a much more significant change in hydrodynamic size with the former.

The researchers sum up: “The proposed approach is of great promise to highly sensitive and rapid detection with a low cost, easy handling of the sample to be detected (mix-and-measure).’

This approach can also be adjusted to produce a spatial map of virus distribution that will be useful not only in the containment of the current pandemic but in further fundamental research on the infection and proliferation of the virus.
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Re: COVID-19 Tests | Wish List

Post by Howzitgoing »

Voice recognition to diagnose COVID-19

Amazing. Alexa, do I have COVID-19? Download an app?

The science behind the idea: Covid-19 inflammation causes muscles across the tongue, lips, jaw, and more to become overly coupled, resulting in a less complex movement. "Picture these speech subsystems as if they are the wrist and fingers of a skilled pianist; normally, the movements are independent and highly complex," Quatieri says. Now, picture if the wrist and finger movements were to become stuck together, moving as one. This coupling would force the pianist to play a much simpler tune.

Preliminary results hint that biomarkers derived from vocal system coordination can indicate the presence of Covid-19. However, the researchers note that it's still early to draw conclusions, and more data are needed to validate their findings.

"A sensing system integrated into a mobile app could pick up on infections early, before people feel sick or, especially, for these subsets of people who don't ever feel sick or show symptoms," says Jeffrey Palmer, who leads the research group. "This is also something the U.S. Army is interested in as part of a holistic Covid-19 monitoring system." Even after a diagnosis, this sensing ability could help doctors remotely monitor their patients’ progress or monitor the effects of a vaccine or drug treatment.

"There are a lot of other interesting areas to look at. Here, we looked at the physiological impacts on the vocal tract. We're also looking to expand our biomarkers to consider neurophysiological impacts linked to Covid-19, like the loss of taste and smell," Quatieri says. "Those symptoms can affect speaking, too." ... gnals-0708
Signs of Covid-19 may be hidden in speech signals
> Processing vocal recordings of infected but asymptomatic people reveals potential indicators of Covid-19.
Alexa, do I have COVID-19?
> Researchers are exploring ways to use people’s voices to diagnose coronavirus infections, dementia, depression and much more.
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Joined: Fri Jun 26, 2020 5:22 am

Re: COVID-19 Tests | Wish List

Post by trader32176 »

New diagnostic test detects and identifies SARS-CoV-2 virus in less than five minutes

10/16/20 ... nutes.aspx

Scientists from Oxford University’s Department of Physics have developed an extremely rapid diagnostic test that detects and identifies viruses in less than five minutes.

The method, published on the preprint server MedRxiv, is able to differentiate with high accuracy SARS-CoV-2, the virus responsible for COVID-19, from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses.

Working directly on throat swabs from COVID-19 patients, without the need for genome extraction, purification or amplification of the viruses, the method starts with the rapid labeling of virus particles in the sample with short fluorescent DNA strands. A microscope is then used to collect images of the sample, with each image containing hundreds of fluorescently-labelled viruses.

Machine-learning software quickly and automatically identifies the virus present in the sample. This approach exploits the fact that distinct virus types have differences in their fluorescence labeling due to differences in their surface chemistry, size, and shape.

The scientists have worked with clinical collaborators at the John Radcliffe Hospital in Oxford to validate the assay on COVID-19 patient samples which were confirmed by conventional RT-PCR methods.

" Unlike other technologies that detect a delayed antibody response or that require expensive, tedious and time-consuming sample preparation, our method quickly detects intact virus particles; meaning the assay is simple, extremely rapid, and cost-effective."

- Professor Achilles Kapanidis, Department of Physics, University of Oxford

" Our test is much faster than other existing diagnostic technologies; viral diagnosis in less than 5 minutes can make mass testing a reality, providing a proactive means to control viral outbreaks."

- Nicolas Shiaelis, DPhil student, University of Oxford

Dr Nicole Robb, formally a Royal Society Fellow at the University of Oxford and now at Warwick Medical School, says: ‘A significant concern for the upcoming winter months is the unpredictable effects of co-circulation of SARS-CoV-2 with other seasonal respiratory viruses; we have shown that our assay can reliably distinguish between different viruses in clinical samples, a development that offers a crucial advantage in the next phase of the pandemic.’

The researchers aim to develop an integrated device that will eventually be used for testing in sites such as businesses, music venues, airports etc., to establish and safeguard COVID-19-free spaces.

They are currently working with Oxford University Innovation (OUI) and two external business/finance advisors to set up a spinout, and are seeking investment to accelerate the translation of the test into a fully integrated device to be deployed as a real-time diagnostic platform capable of detecting multiple virus threats.

They hope to incorporate the company by the end of the year, start product development in early 2021, and have an approved device available within 6 months of that time.


Oxford University

Journal reference:

Shiaelis, N., et al (2020) Virus detection and identification in minutes using single-particle imaging and deep learning. medRxiv.
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Re: COVID-19 Tests | Wish List

Post by Howzitgoing »
Breath test able to safely detect COVID-19, other signs of ill-health

Breathalyzer: Tohoku University and Shimadzu Corp., announcing the joint project Oct. 16, said the device not only can confirm infection within an hour but also determine if an individual is at risk of developing severe symptoms of COVID-19.

“We hope to commercialize it as soon as possible and sell it on a global scale.”

The device extracts elements derived from viruses found in a person’s breath and analyzes them using equipment developed by Shimadzu.

While it takes about five minutes to collect a breath sample, it is less intrusive than current test methods that involve swabbing a person’s nose or back of the throat.

At the same time, the method enables doctors to predict complications and detect a number of different viruses that are present.

They also plan to expand use of the system by applying the technology to diagnose other diseases, such as those linked to daily life as well as cancer.

Shimadzu has already developed a method for testing for COVID-19 using saliva rather than swabbing a patient.
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