COVID-19 Tests | Wish List

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Researchers develop a novel method to test for COVID-19 antibodies

10/23/20


https://www.news-medical.net/news/20201 ... odies.aspx


When Dr. Stephen Smith of Seattle Children's Research Institute came down with muscle aches, gastrointestinal distress and a sudden loss of smell in late February, he suspected he had COVID-19.

The testing criteria had yet to be expanded to include individuals with Smith's symptoms and so he did what many scientists with his expertise would do: he developed a way to test himself.

The fruits of his curiosity, now published in The Journal of Infectious Diseases, offer a reliable way to quantify whether an individual has neutralizing antibodies that could prevent the novel coronavirus from infecting cells using a method that is more broadly applicable than those currently available.

" If you think you've had COVID-19 and go to the doctor, they can test your blood and tell you whether or not you have antibodies to COVID-19, but that doesn't tell you whether your antibodies are any good at functionally blocking the virus from binding to cells.

There are tests on the market now that can tell you that, but they are expensive and take a long time to get results. We wanted to develop a way to give you additional information about your immune status without all the barriers that make it difficult to use in a community setting."

- Dr. Stephen Smith, Seattle Children's Research Institute

The newly developed diagnostic could have a range of potential commercial applications from broad community testing to assessing vaccine responses and screening for convalescent plasmas that have particularly high levels of neutralizing antibodies as a potential treatment.
Cell-free test looks at protein interactions

The novel coronavirus enters cells when the viral spike protein binds to the ACE2 protein on the surface of human cells. Neutralizing antibodies that block this binding are thought to contribute to immunity to the virus in people who recover from COVID-19.

Smith applied a technique called immunoprecipitation detected by flow cytometry (IP-FCM) to study the interactions between the proteins and to look for evidence that antibodies were inhibiting the interaction and blocking the virus from binding to cells.

Instead of relying on live cells and viruses like other available blood tests, IP-FCM uses recombinant - or lab-made - proteins and instruments commonly available in commercial serological labs.

"Other tests that provide insight into immunity work by taking antibodies from your blood and mixing them together with a virus and then exposing that mixture to live cells.

Three days later they can determine immunity based on whether your blood prevented the viruses from infecting the cells or not," Smith said. "Our cell-free test can provide that same information overnight."

Collaborative science launches innovative study


Smith is among a small group of scientists in the U.S. who have pioneered IP-FCM to study the interactions between proteins.

His lab in Seattle Children's Center for Integrative Brain Research uses IP-FCM to uncover new treatments for autism by studying the more than 100 genetic variations known to contribute to the condition.

To apply his expertise to the current pandemic, Smith collaborated with Drs. Lisa Frenkel and Whitney Harrington from the research institute's Center for Global Infectious Global Disease Research who are following a community cohort of Seattle Children's employees who were never hospitalized and had recovered from mild to moderate COVID-19.

The researchers hope by tracking their recovery and taking blood samples over time as part of the Seattle Children's Recovered SARS2 Cohort study they can shed light on the immune responses to the novel coronavirus.

Funding in part by Seattle Children's COVID-19 Research Fund helped Smith design and launch the study.

Using IP-FCM, Smith tested the blood samples from 24 cohort participants. The test showed that 92% of the participants had antibodies to the novel coronavirus at an average of a little over a month post-infection. Results were validated with 30 control samples.

"Not only did the participants have antibodies, but our test also showed that their antibodies were pretty effective at neutralizing the binding between the spike protein and the cell's receptor," he said. "It's consistent with other studies from cell-based tests showing that people who get COVID do make neutralizing antibodies."

Interestingly, when researchers looked at the test results against other data gathered from the cohort, they found that those who mounted a fever had higher levels of antibodies. The research team also plans to retest the samples to see how antibody levels change over time.

"It's going to be very important to look at people over a longer time period to track their antibody levels and whether or not they get re-infected," Smith said. "Until we do those studies, we really don't know how these clinical measures of antibody neutralization relate to susceptibility in the real world."

Identifying new drug candidates for COVID-19

In addition to exploring opportunities to commercialize the diagnostic, Smith and his team are now using the test to rapidly screen thousands of approved drugs that could potentially interfere with the binding between ACE2 and the spike protein.

Lab manager, Edward Gniffke, and Stanford University undergraduate and summer intern, Kaleb Tsegay, helped run the initial screen that could potentially identify drugs capable of preventing or treating COVID-19.

"We already have some compounds that look like they are inhibiting, which is pretty exciting," Smith said. "This first line screen will help us pinpoint the most promising agents for further tests."

Source:

Seattle Children's

Journal reference:


Gniffke, E. P., et al. (2020) Plasma From Recovered COVID-19 Patients Inhibits Spike Protein Binding to ACE2 in a Microsphere-Based Inhibition Assay. The Journal of Infectious Diseases. doi.org/10.1093/infdis/jiaa508.
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New method can detect high levels of COVID-19 antibodies

10/23/20


https://www.news-medical.net/news/20201 ... odies.aspx


A more efficient and much faster method to assess high levels of neutralizing antibodies to COVID-19 could point the way to better understanding and treatment of the disease, according to new published findings by scientists from the Hackensack Meridian Center for Discovery and Innovation (CDI) and the University of Michigan (U-M).

A new portable "lab on a chip," developed by the U-M scientists and demonstrated with help of the CDI, can identify the presence of COVID-19 antibodies in blood donors with greater speed and efficiency than the current standard "enzyme-linked immunosorbent assay" or ELISA technology.

Together, the CDI and U-M researchers have shown the device can identify COVID-19 antibodies in human blood in 15 minutes – much shorter than the few days the process normally takes. The test can also be done with smaller amounts of blood.

The work could have particular value for the validation of convalescent plasma as a treatment for COVID-19. A paper on the findings is published in Biosensors and Bioelectronics.

"Convalescent plasma is a treatment that can be very effective – but for it to have the best chance to work, it needs to have rigorous standards, which include assessing the presence of high-titer neutralizing antibodies," said David Perlin, Ph.D., chief scientific officer and senior vice president of the Hackensack Meridian Center for Discovery and Innovation, and one of the new study's authors. "This paper shows how the antibody thresholds can mean a better potential COVID-19 treatment – and also better outcomes."

" This research shows what an important role microfluidics can play in both saving lives and costs during the COVID-19 pandemic."

- Xudong (Sherman) Fan, Biomedical Engineering Professor and Co-founder of Optofluidic Bioassay, University of Michigan

The U-M device detects the presence and amount of neutralizing immunoglobulin-;antibodies created by the immune system within seven to 10 days of a COVID-19 infection. Only donors with high levels are likely to provide samples that could be effective in treatment, such as convalescent plasma therapy.

The treatment involves taking plasma – the liquid portion of the blood that contains antibodies – from survivors and infusing it into sick patients to boost their immune response.

Thousands of patients nationally have been administered convalescent plasma through a program overseen by the Mayo Clinic. Hackensack University Medical Center also has its own clinical trial underway involving high-titer (levels) of antibodies.

The lab-on-a-chip approach developed by U-M analyzes on-site and requires just a finger prick's worth of blood-;8 microliters. The traditional ELISA methods require 100 microliters to do its work. The U-M system is contained in a device the size of a portable 3D printer.

Source:

Hackensack Meridian Health
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Covid-19: Experts question evidence behind prime minister’s promise of rapid tests

Published 02 November 2020


https://www.bmj.com/content/371/bmj.m4254


Concerns have been raised over the UK government’s claims that it will begin rolling out rapid covid-19 tests within days to whole cities to “help people discover whether or not they are infectious” and to allow them entry to certain places or events.

Announcing the second national lockdown in England on 31 October,1 Boris Johnson said that trials of rapid tests across the country in schools and hospitals had shown that they “drive down the disease.” As a result, millions of these self-administered tests, which provide results in 10-15 minutes, will now be rolled out “over the next few days and weeks.”

Johnson added that the tests would be used in an “ever growing number of situations,” including to allow partners of women giving birth to be in labour wards.

He did not name the test to be rolled out, and although three rapid antigen tests have passed Public Health England’s assessment there is little information on how they were tested or passed.2

One of these tests has since been purchased. The Telegraph reported that the government agreed a deal for 20 million of Innova’s SARS-CoV-2 antigen test kits on 19 October.3 The test involves a nose and throat swab and provides results similar to an at-home pregnancy test. However, the company’s instructions state that the test is intended only for use on people showing symptoms of covid-19 and should be used by “clinical laboratory personnel specifically instructed and trained in the techniques of in vitro diagnostic procedures.” As such, this test would not be suitable for testing asymptomatic people to allow access, as Johnson had claimed.

Jon Deeks, professor of biostatistics at the University of Birmingham and lead author of a recent Cochrane review of covid-19 antibody tests, has also raised concerns over Public Health England’s test assessments.4 He said, “These are initial validation studies and should not be the basis for national decision making . . . Boris [Johnson] described these as tests of whether you are infectious, but there is no mention of infectiousness in the protocol; they are assessed as tests of infection not infectiousness.”

Simon Clarke, associate professor of cellular microbiology at the University of Reading, said that Johnson’s testing announcement seemed hurried and may have been done “purely as a way to provide some sugar along with the bitter medicine of lockdown.” Nevertheless, he said that “mass rapid and effective testing and isolating of infected people really is the best way for the country to get out of this nightmare,” although the details on how this would be achieved were still “thin on the ground.”

He added, “We will need to see some serious concrete plans, and quickly, if we are not to suspect that the prime minister’s statement was purely about news management.”

Appointments challenged

The government is also facing criticism over how it appoints people to key public sector roles during the pandemic. In a legal challenge the Good Law Project and Runnymede Trust have joined forces to put forward the case that people who were personally or politically connected with senior members of the Conservative Party have been appointed without any open competition or proper process. This was indirect discrimination (contrary to the Equality Act 2010), they said, and a breach of the public sector equality duty.

Dido Harding, appointed head of the NHS Test and Trace service and then interim head of the National Institute for Health Protection, is named in the claim. She is married to the Conservative MP John Penrose.

Mike Coupe, Gareth Williams, Ben Stimson, and Paul de Laat, all appointed to senior positions at NHS Test and Trace, have also been named. Coupe is the former chief executive officer of Sainsbury’s and a former colleague and friend of Harding from their time at Sainsbury’s, said the Good Law Project and Runnymede Trust.

Halima Begum, the trust’s director, said, “When a recruitment process is not open and fair, it discriminates against those who are not already connected to the decision makers. This has a serious detrimental impact on equality and on the diversity of the people at the top of organisations who get to call the shots. This is always important, but even more so now so many lives depend on it, and particularly as we know black and Asian people continue to be disproportionately affected by the coronavirus.

“We are calling on the government to ensure a proper process is followed and for NHS bodies to be truly representative of the people they protect.”

References


Kmietowicz Z. Covid-19: “There is no alternative,” says Johnson, announcing new restrictions for England. BMJ2020;371:m4247.
FREE Full TextGoogle Scholar
↵Department of Health and Social Care. Protocol for evaluation of rapid diagnostic assays for specific SARS-CoV-2 antigens (lateral flow devices). 23 Oct 2020. https://www.gov.uk/government/publicati ... tigen-test.
↵Bodkin H, Mendick R. Government secures up to 20 million 15-minute covid test kits. Telegraph. 19 Oct 2020. https://www.telegraph.co.uk/news/2020/1 ... sting-kits.
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First EUA point-of-care (POC/Waived/Fingerstick) COVID-19 antibody test now available from Carolina Liquid Chemistries.

11/4/20

https://www.news-medical.net/news/20201 ... tries.aspx


The Fastep® COVID-19 IgG/IgM Rapid Test Device by Assure Tech., distributed in the USA by Carolina Liquid Chemistries, has received FDA Emergency Use Authorization for use with fingerstick whole blood specimens at the point-of-care, i.e. in patient care settings operating under CLIA Certificate of Waiver such as doctor's offices, hospitals, urgent care centers and emergency rooms rather than having to be sent to a central lab.

This COVID-19 IgG/IgM Rapid Test Device was first authorized in July to detect antibodies against the virus in venous whole blood, serum, and plasma to help identify individuals with antibodies SARS-CoV-2 indicating recent or prior COVID-19 infection. On September 23rd, this 15-minute lateral flow test received authorization for point-of-care use using finger-stick blood samples. External controls are also available for this product.

This test has been authorized only for the presence of IgM and IgG antibodies, against SARS-CoV-2, not for any other viruses or pathogens. This test has not been FDA cleared or approved and is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in-vitro diagnostics or if revoked sooner.

Instructions for Use and Fast Facts for Healthcare Providers and Patients available at https://www.carolinachemistries.com/poc-fastep/

Carolina Liquid Chemistries also supplies Real-Time PCR instruments, extraction systems, and Emergency Use Authorized test kits for SARS-CoV-2, the virus that causes COVID-19, as well as sample collection and transportation supplies. COVID-19 test kits offered by Carolina Liquid Chemistries are for use in authorized laboratories only.

Refer to carolinachemistries.com for instructions for use, fact sheets, FDA EUA letters, clinical performance studies, and material safety data sheets.

About Carolina Liquid Chemistries Corp.

Headquartered in Greensboro, NC, Carolina Liquid Chemistries is an ISO 13485:2016 certified manufacturer, repackager/relabeler, distributor, and technical service provider of chemistry systems and reagents for clinical and toxicology laboratories, along with a variety of rapid test kits.

The company offers chemistry analyzers that range in throughput from 300 to 6,400 tests per hour and markets a wide menu of general chemistry, special chemistry, and toxicology reagents, along with affordable service contracts.

The company has responded to the COVID-19 pandemic by bringing a number of PCR and antibody tests to market under the FDA’s Emergency Use Authorization. For more information, visit carolinachemistries.com or email contactsales@carolinachemistries.com.
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FDA warns of false positive results from rapid COVID-19 diagnostics after nursing homes found some antigen tests incorrectly say people have coronavirus up to 60% of the time

FDA regulators issued a warning that cheap antigen tests for coronavirus that return results in as little as 15 minutes may give false positive results
Antigen tests look for pieces of proteins on the virus's surface, unlike slower 'gold standard' lab tests that detect coronavirus genetic material
Rapid tests are known to have higher rates of false negatives, and regulators have long advised confirming negative results with PCR testing
Nevada officials ordered nursing homes here to stop using rapid tests made by Quidel after finding they had a false positive rate as high as 60%
The FDA's new warning echoes this, promises to investigate these tests, and pins the false-negatives largely on clinicians not following instructions properly


11/3/20

https://www.dailymail.co.uk/health/arti ... tests.html


The U.S. Food and Drug Administration (FDA) warned on Tuesday of the risk of false positive results from rapid COVID-19 tests.

It comes after a series of reports of high rates of false positives on quick antigen tests used in a number of nursing homes across the US.

FDA regulators said the risk of false positives is particularly high if they are used incorrectly.

Antigen tests look for specific proteins found on the surface of coronavirus. They can return results much faster than PCR tests, which detect the virus's genes, but they are not nearly as accurate.

The FDA underscored that reading the results of an antigen test too early or too late, or storing the diagnostics improperly, could result in false positive or negative results. The Tuesday update also advised giving a PCR test to back up results.

Seven antigen tests have been given emergency authorization by the FDA.

They are made by Celltrion, Access Bio, Quidel, Abbott, LumiraDx UK, Becton Dickinson and Quidel.

Antigen tests are helpful screeners because they can return results in a matter of minutes.

Quick results mean that contact tracing can start sooner and perhaps stop further transmissions.

Or, if a person gets a negative result, they might feel more comfortable returning to work soon, rather than waiting days or a week to get back a PCR result. Antigen tests can be run on-site, sidestepping the problem of backlogs that have plagued the U.S. since the pandemic kicked off in the nation.

But they're just not as accurate as the 'gold standard' PCR tests run in labs.

In previous guidance, the FDA warned that antigen tests are generally less sensitive than PCR tests, and are more likely to miss an infection if they are not used within five days of a person's first symptoms.

This is in part because antigen tests don't amplify viral particles the way that PCR tests do, boosting the concentration of the virus in a sample, while diluting everything else in it.

Abbott's rapid test came under scrutiny when it was being used in the White House despite high false-negative rates.

A study published this week by the University of Arizona found that Quidel's test performed particularly poorly in test when used to screen people with no symptoms.

It detected the virus in 80 percent of people who had symptoms and also tested positive using a slower PCR test.

But it missed Nearly 70 percent of asymptomatic cases caught by the PCR.

Its package insert claims that it can 96.7 percent of the infections detected by the slower gold standard test.

Even as drastic as those results were, the antigen test was expected to miss positive cases. The FDA had already advised these test are not made to rule out infection and a PCR should be used to confirm that someone does not have COVID-19.

False positive results were more unexpected.

Yet last month Nevada health officials ordered nursing homes there to stop using Quidel's test, which was being widely employed to detect outbreaks before they spread like wildfire among vulnerable elderly people.

Twelve facilities there sent out samples that had been tested using Quidel's Sofia or BD Veritor kit to labs.

About 60 percent of the samples that had tested negative were in fact positive.

Now, the FDA is warning of this possibility, which could lead to undue panic and isolation for nursing home residents - outcomes that are themselves dangerous to elderly people.

The U.S. agency said false positive results may occur when users do not follow the instructions for the use of antigen tests for rapid detection of SARS-CoV-2.
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Stanford researchers create a highly automated device that can detect COVID-19 in 30 minutes

11/5/20


https://www.news-medical.net/news/20201 ... nutes.aspx


Throughout the pandemic, infectious disease experts and frontline medical workers have asked for a faster, cheaper and more reliable COVID-19 test. Now, leveraging the so-called "lab on a chip" technology and the cutting-edge genetic editing technique known as CRISPR, researchers at Stanford have created a highly automated device that can identify the presence of the novel coronavirus in just a half-hour.

"The microlab is a microfluidic chip just half the size of a credit card containing a complex network of channels smaller than the width of a human hair," said the study's senior author, Juan G. Santiago, the Charles Lee Powell Foundation Professor of mechanical engineering at Stanford and an expert in microfluidics, a field devoted to controlling fluids and molecules at the microscale using chips.

The new COVID-19 test is detailed in a study published on Nov. 4 in the journal Proceedings of the National Academy of Sciences. "Our test can identify an active infection relatively quickly and cheaply. It's also not reliant on antibodies like many tests, which only indicates if someone has had the disease, and not whether they are currently infected and therefore contagious," explained Ashwin Ramachandran, a Stanford graduate student and the study's first author.

The microlab test takes advantage of the fact that coronaviruses like SARS-COV-2, the virus that causes COVID-19, leaves behind tiny genetic fingerprints wherever they go in the form of strands of RNA, the genetic precursor of DNA. If the coronavirus's RNA is present in a swab sample, the person from whom the sample was taken is infected.

To initiate a test, liquid from a nasal swab sample is dropped into the microlab, which uses electric fields to extract and purify any nucleic acids like RNA that it might contain. The purified RNA is then converted into DNA and then replicated many times over using a technique known as isothermal amplification.

Next, the team used an enzyme called CRISPR-Cas12 - a sibling of the CRISPR-Cas9 enzyme associated with this year's Nobel Prize in Chemistry - to determine if any of the amplified DNA came from the coronavirus.

If so, the activated enzyme triggers fluorescent probes that cause the sample to glow. Here also, electric fields play a crucial role by helping concentrate all of the important ingredients - the target DNA, the CRISPR enzyme and the fluorescent probes - together into a tiny space smaller than the width of a human hair, dramatically increasing the chances they will interact.


" Our chip is unique in that it uses electric fields to both purify nucleic acids from the sample and to speed up chemical reactions that let us know they are present."

- Juan G. Santiago, study's senior author

The team created its device on a shoestring budget of about $5,000. For now, the DNA amplification step must be performed outside of the chip, but Santiago expects that within months his lab will integrate all the steps into a single chip.

Several human-scale diagnostic tests use similar gene amplification and enzyme techniques, but they are slower and more expensive than the new test, which provides results in just 30 minutes. Other tests can require more manual steps and can take several hours.

The researchers say their approach is not specific to COVID-19 and could be adapted to detect the presence of other harmful microbes, such as E. coli in food or water samples, or tuberculosis and other diseases in the blood.

"If we want to look for a different disease, we simply design the appropriate nucleic acid sequence on a computer and send it over email to a commercial maker of synthetic RNA. They mail back a vial with the molecule that completely reconfigures our assay for a new disease," Ramachandran said.

The researchers are working with the Ford Motor Company to further integrate the steps and develop their prototype into a marketable product.

Source:


Stanford School of Engineering

Journal reference:


Ramachandran, A., et al. (2020) Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2. PNAS. doi.org/10.1073/pnas.2010254117.
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A digital CRISPR-based method for quick detection and absolute quantification of SARS-CoV-2

11/5/20


https://www.news-medical.net/news/20201 ... CoV-2.aspx


In a recent medRxiv* preprint manuscript, researchers from Singapore and the United States report the development of a digital CRISPR method for the sensitive, specific, and rapid detection of viral nucleic acids at a constant temperature, which could be exploited for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

To combat the global spread of coronavirus disease (COVID-19), improved methods for detecting SARS-CoV-2 and viral load quantification are urgently needed. Albeit the reverse transcription-polymerase chain reaction (RT-qPCR) is a current gold standard, quantification necessitates external standards or references with often variable results.

This is where digital PCR comes into play, with very sensitive detection and viral load analysis of SARS-CoV-2; nonetheless, the reaction time is protracted and takes approximately four hours compared to qPCR, which requires one hour.

Likewise, CRISPR-based methods can also detect SARS-CoV-2 within one hour but do not enable the absolute quantification of viral particles, which would reduce inter-laboratory variability and open the scientific field even more.

This research endeavor, led by Dr. Xiaolin Wu from the Singapore-MIT Alliance for Research and Technology, reveals an optimized RApid DIgital Crispr Approach (RADICA) that enables absolute quantification of viral nucleic acids at a constant temperature in one hour time.

Streamlined one-pot reaction on a commercial high-density chip

The method presented in this paper combines all the advantages of quantitative digital PCR, rapid isothermal amplification, as well as specific CRISPR detection into a one-pot reaction system that separates the individual reactions into ten thousand compartments on a commercial high-density chip.

Such a streamlined one-pot reaction combines CRISPR-based detection and nucleic acid amplification into a single step in a closed tube, significantly reducing the risk of sample cross-contamination during batch processing.

For validation purposes, DNA containing the nucleoprotein gene of SARS-CoV-2 was used, which showed linear signal-to-input response. Furthermore, RADICA was compared to digital PCR for quantifying synthetic SARS-CoV-2 DNA and Epstein-Barr (EBV) viral DNA.

The researchers have also tested for possible inhibitory effects of background DNA on reactions that were carried out in small partitions. The isothermal feature of RADICA-based detection assay utilizes a simple constant-temperature heat bath, which can enable rapid viral detection that can be utilized even in low-resource areas.

Compounding effect of precision and speed

In this study, the use of RADICA method resulted in sensitivity and detection limits comparable with those of real-time PCR and other isothermal methods, with the ability of absolute quantification. Furthermore, a significant advantage of RADICA observed in this study was its speed.

The aforementioned absolute quantification of DNA showed a dynamic range from 0.6 to 2027 copies per microliter, without any cross-reactivity on similar viruses or human background DNA. This study's findings also suggest that background DNA will not inhibit the RADICA sample reaction within the dynamic range that will be used for testing purposes.

Moreover, when speed is concerned, RADICA can precisely detect and quantify nucleic acid in one hour without thermal cycling, which is four times faster alternative when compared to digital PCR-based virus detection.

Potential uses of breakthrough technology

"We have established and characterized RADICA, which combines the speed and sensitivity of isothermal amplification, the specificity of CRISPR-based detection, and the ability to obtain absolute quantification by sample partitioning" study authors summarize their methodological breakthrough.

The absolute quantification approach for viral detection may not only support easier clinical processing but could also be exploited for research purposes. And since viral loads can be linked to transmission risk and disease severity (as is the case with SARS-CoV-2), this may prove pivotal in tackling this pandemic as well.

Future work will concentrate on expanding the applications of RADICA to scientific areas such as the analysis of gene expression, detection of rare mutants, sequencing library quantification and copy number variation – with significant benefits for clinical, pharmaceutical, ecological and public health fields.

*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.

Journal reference:

Wu, X. et al. (2020). A Digital CRISPR-based Method for the Rapid Detection and Absolute Quantification of Viral Nucleic Acids. medRxiv. https://doi.org/10.1101/2020.11.03.20223602, https://www.medrxiv.org/content/10.1101 ... 20223602v1
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Study shows iscan method could be effective for rapid COVID-19 testing

11/6/20


https://www.news-medical.net/news/20201 ... sting.aspx


A simple COVID-19 test kit combines virus amplification with a CRISPR-Cas system for effective SARS-CoV-2 detection. The kit, called iSCAN, uses reagents that can be locally manufactured.

" Our whole iSCAN procedure can be completed in less than an hour and can be easily adopted as a point-of-care detection system at airports and borders."

- Ahmed Mahas, PhD Student, King Abdullah University of Science & Technology

The current gold standard in SARS-CoV-2 testing is the PCR test, in which DNA primers recognize specific RNA sequences in the viral genome that are then copied using a specific enzyme.

This "amplification" process makes it easier to detect the originally small amounts of viral RNA present in the nasopharyngeal swabs taken from patients.

This test can reliably detect if a person really has the virus without providing too many false positive or negative results. But it needs highly skilled personnel to conduct the test, which is done in multiple steps in central laboratories with sophisticated equipment.

iSCAN, developed by a team led by KAUST bioengineer Magdy Mahfouz overcomes many of the disadvantages of the PCR test while providing relatively trustworthy results.

Significantly, the test's reagents were manufactured at KAUST. This includes the enzymes needed for amplification and another enzyme that specifically detects viral sequences within the copied material. The availability of reagents and equipment has been a huge obstacle since the start of the COVID-19 pandemic.

To use iSCAN, the contents from a patient's sample, collected with a nasopharyngeal swab, are placed in a small test tube containing the DNA primers and enzymes that can amplify SARS-CoV-2 genetic material. The contents are incubated at a temperature of 62 degrees Celsius for half an hour. This process is referred to as RT-LAMP.

Once enough viral RNA is amplified, a droplet containing the enzyme Cas12 is added to the mix and left for another 15 minutes. This enzyme only recognizes viral RNA belonging to SARS-CoV-2, overcoming an issue with RT-LAMP, where false amplification and cross-contamination can be a problem.

Finally, one of two methods can be used to visualize the result. One involves shining ultraviolet light on the sample, with a detector analyzing the light coming out from it to report the amount of viral RNA.

The other approach involves inserting specially designed strips into the tubes, similar to those used in pregnancy tests. Both approaches work well, although the ultraviolet light method provided more accurate results.

The scientists tested their kit on synthesized viral RNA and on real patient samples. "We are now improving and simplifying our system for users in order to commercialize our iSCAN detection kit," says KAUST research scientist Zahir Ali.

Source:

King Abdullah University of Science & Technology (KAUST)
Journal reference:

Ali, Z., et al. (2020) iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Research. doi.org/10.1016/j.virusres.2020.198129.
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Coronavirus: Quick turnaround Covid test could be 'major breakthrough' says Eustice

11/9/20


https://www.bbc.com/news/uk-54870145


New quick-turnaround Covid tests being trialled in Liverpool could be a "major breakthrough" in the battle against coronavirus, the environment secretary has said.

George Eustice said the new 'lateral flow' test is now available to everyone in Liverpool as part of the pilot.

Number 10 had been focusing on faster testing, which if successful, could be "a major breakthrough" he told the BBC.

Boris Johnson has said that NHS Test and Trace needs to give faster results.

A mass coronavirus testing programme is being carried out in Liverpool, with all residents being offered regular Covid-19 tests - whether or not they have symptoms.

It is the first trial of whole-city testing in England.

The pilot includes a mix of existing swab tests and the new lateral flow tests - which can provide a result within an hour without the need to use a lab.

Testing a whole city for Covid: How will it work?
Can mass testing save us from another lockdown?
City-wide Covid testing to be piloted in Liverpool

Mr Eustice told BBC Breakfast: "A test is only as good as the speed with which you can turn a result around.

"What we've really been focusing on more recently is a faster test, so that people can act more quickly to prevent the spread of the virus so this, if we can make it work, is a major breakthrough."

Rapid or "lateral flow" tests need there to be high levels of the virus in the body to work. They are similar to pregnancy tests and are easy, cheap and fast.

Fluid from a nasal swab or saliva goes on to one end of the test, then a marking appears if the person is positive.
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New three-step approach promises to improve COVID-19 testing accuracy

11/10/20


https://www.news-medical.net/news/20201 ... uracy.aspx


One critical barrier in efforts to control the COVID-19 pandemic has been the relatively high false-negative rate of the most commonly-used Reverse Transcription Polymerase Chain Reaction (RT-PCR) testing methods.

Often, these methods are not able to detect lower viral loads, which are typically present in asymptomatic individuals but below the limit of detection (LoD) of standard one- or two-step RT-PCR methods. Researchers from NYU Abu Dhabi's Biology Program and Center for Genomics and Systems Biology (CGSB) have implemented a new three-step testing approach that promises to significantly - and cost-effectively -- improve testing accuracy.

Rather than combining the RT and qPCR reactions, the NYUAD researchers, led by Professor of Biology at NYU and NYUAD Kris Gunsalus and Assistant Professor of Biology at NYUAD Youssef Idaghdour employed a technique involving sequential RT, cDNA preamplification, and qPCR, using a microfluidics platform.

The researchers demonstrated reliable ultra-sensitive and quantitative detection of low SARS-CoV-2 viral loads (less than one copy/microliter) using synthetic viral RNA, clinical nasopharyngeal swab samples and saliva samples, including samples previously diagnosed as negative by clinical diagnostic testing. Their findings, reported in the journal Processes are that this microfluidic RT-PCR assay is a sensitive, quantitative, and cost-effective detection strategy which could markedly reduce the false negative rate of clinical diagnostic tests - a potentially valuable tool in SARS-CoV-2 active screening and early detection programs.


" By adding a pre-amplification step and using microfluidic technology, we have demonstrated that this sensitive detection method can detect low viral loads, which is critical to enabling the most effective public health responses to the COVID-19 pandemic. Our three-step approach can significantly reduce the false negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV2 and other viral infections. This would allow public health officials to more readily identify and trace asymptomatic individuals, enhance the accuracy of air and environmental sampling for SARS-CoV-2, expand accurate detection to saliva testing and help curtail the spread of the virus."

- Youssef Idaghdour, Assistant Professor of Biology, NYUAD

Source:


New York University
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