Date of Release: Dec. 4, 2020 

SAN FRANCISCO /PRNewswire/ — Imagine swabbing your nostrils, putting the swab in a device, and getting a read-out on your phone in 15 to 30 minutes that tells you if you are infected with the COVID-19 virus. This has been the vision for a team of scientists at Gladstone Institutes, University of California, Berkeley (UC Berkeley), and University of California, San Francisco (UCSF). And now, they report a scientific breakthrough that brings them closer to making this vision a reality.

One of the major hurdles to combating the COVID-19 pandemic and fully reopening communities across the country is the availability of mass rapid testing. Knowing who is infected would provide valuable insights about the potential spread and threat of the virus for policymakers and citizens alike.

Yet, people must often wait several days for their results, or even longer when there is a backlog in processing lab tests. And, the situation is worsened by the fact that most infected people have mild or no symptoms, yet still carry and spread the virus.

In a new study published in the scientific journal Cell, the team from Gladstone, UC Berkeley, and UCSF has outlined the technology for a CRISPR-based test for COVID-19 that uses a smartphone camera to provide accurate results in under 30 minutes.

“It has been an urgent task for the scientific community to not only increase testing, but also to provide new testing options,” says Melanie Ott, MD, PhD, director of the Gladstone Institute of Virology and one of the leaders of the study. “The assay we developed could provide rapid, low-cost testing to help control the spread of COVID-19.”

The technique was designed in collaboration with UC Berkeley bioengineer Daniel Fletcher, PhD, as well as Jennifer Doudna, PhD, who is a senior investigator at Gladstone, a professor at UC Berkeley, president of the Innovative Genomics Institute, and an investigator of the Howard Hughes Medical Institute. Doudna recently won the 2020 Nobel Prize in Chemistry for co-discovering CRISPR-Cas genome editing, the technology that underlies this work.

Not only can their new diagnostic test generate a positive or negative result, it also measures the viral load (or the concentration of SARS-CoV-2, the virus that causes COVID-19) in a given sample.

“When coupled with repeated testing, measuring viral load could help determine whether an infection is increasing or decreasing,” says Fletcher, who is also a Chan Zuckerberg Biohub Investigator. “Monitoring the course of a patient’s infection could help health care professionals estimate the stage of infection and predict, in real time, how long is likely needed for recovery.”

A Simpler Test through Direct Detection

Current COVID-19 tests use a method called quantitative PCR—the gold standard of testing. However, one of the issues with using this technique to test for SARS-CoV-2 is that it requires DNA. Coronavirus is an RNA virus, which means that to use the PCR approach, the viral RNA must first be converted to DNA. In addition, this technique relies on a two-step chemical reaction, including an amplification step to provide enough of the DNA to make it detectable. So, current tests typically need trained users, specialized reagents, and cumbersome lab equipment, which severely limits where testing can occur and causes delays in receiving results.

As an alternative to PCR, scientists are developing testing strategies based on the gene-editing technology CRISPR, which excels at specifically identifying genetic material.

All CRISPR diagnostics to date have required that the viral RNA be converted to DNA and amplified before it can be detected, adding time and complexity. In contrast, the novel approach described in this recent study skips all the conversion and amplification steps, using CRISPR to directly detect the viral RNA.

“One reason we’re excited about CRISPR-based diagnostics is the potential for quick, accurate results at the point of need,” says Doudna. “This is especially helpful in places with limited access to testing, or when frequent, rapid testing is needed. It could eliminate a lot of the bottlenecks we’ve seen with COVID-19.”

Parinaz Fozouni, a UCSF graduate student working in Ott’s lab at Gladstone, had been working on an RNA detection system for HIV for the past few years. But in January 2020, when it became clear that the coronavirus was becoming a bigger issue globally and that testing was a potential pitfall, she and her colleagues decided to shift their focus to COVID-19.

“We knew the assay we were developing would be a logical fit to help the crisis by allowing rapid testing with minimal resources,” says Fozouni, who is co-first author of the paper, along with Sungmin Son and María Díaz de León Derby from Fletcher’s team at UC Berkeley. “Instead of the well-known CRISPR protein called Cas9, which recognizes and cleaves DNA, we used Cas13, which cleaves RNA.”

In the new test, the Cas13 protein is combined with a reporter molecule that becomes fluorescent when cut, and then mixed with a patient sample from a nasal swab. The sample is placed in a device that attaches to a smartphone. If the sample contains RNA from SARS-CoV-2, Cas13 will be activated and will cut the reporter molecule, causing the emission of a fluorescent signal. Then, the smartphone camera, essentially converted into a microscope, can detect the fluorescence and report that a swab tested positive for the virus.

“What really makes this test unique is that it uses a one-step reaction to directly test the viral RNA, as opposed to the two-step process in traditional PCR tests,” says Ott, who is also a professor in the Department of Medicine at UCSF. “The simpler chemistry, paired with the smartphone camera, cuts down detection time and doesn’t require complex lab equipment. It also allows the test to yield quantitative measurements rather than simply a positive or negative result.”

The researchers also say that their assay could be adapted to a variety of mobile phones, making the technology easily accessible.

“We chose to use mobile phones as the basis for our detection device since they have intuitive user interfaces and highly sensitive cameras that we can use to detect fluorescence,” explains Fletcher. “Mobile phones are also mass-produced and cost-effective, demonstrating that specialized lab instruments aren’t necessary for this assay.”

Accurate and Quick Results to Limit the Pandemic

When the scientists tested their device using patient samples, they confirmed that it could provide a very fast turnaround time of results for samples with clinically relevant viral loads. In fact, the device accurately detected a set of positive samples in under 5 minutes. For samples with a low viral load, the device required up to 30 minutes to distinguish it from a negative test.

“Recent models of SARS-CoV-2 suggest that frequent testing with a fast turnaround time is what we need to overcome the current pandemic,” says Ott. “We hope that with increased testing, we can avoid lockdowns and protect the most vulnerable populations.”

Not only does the new CRISPR-based test offer a promising option for rapid testing, but by using a smartphone and avoiding the need for bulky lab equipment, it has the potential to become portable and eventually be made available for point-of-care or even at-home use. And, it could also be expanded to diagnose other respiratory viruses beyond SARS-CoV-2.

In addition, the high sensitivity of smartphone cameras, together with their connectivity, GPS, and data-processing capabilities, have made them attractive tools for diagnosing disease in low-resource regions.

“We hope to develop our test into a device that could instantly upload results into cloud-based systems while maintaining patient privacy, which would be important for contact tracing and epidemiologic studies,” Ott says. “This type of smartphone-based diagnostic test could play a crucial role in controlling the current and future pandemics.”

About the Research Project

The study entitled “Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy,” was published online by Cell on December 4, 2020.

Other authors of the study include Gavin J. Knott, Michael V. D’Ambrosio, Abdul Bhuiya, Max Armstrong, and Andrew Harris from UC Berkeley; Carley N. Gray, G. Renuka Kumar, Stephanie I. Stephens, Daniela Boehm, Chia-Lin Tsou, Jeffrey Shu, Jeannette M. Osterloh, Anke Meyer-Franke, and Katherine S. Pollard from Gladstone Institutes; Chunyu Zhao, Emily D. Crawford, Andreas S. Puschnick, Maira Phelps, and Amy Kistler from the Chan Zuckerberg Biohub; Neil A. Switz from San Jose State University; and Charles Langelier and Joseph L. DeRisi from UCSF.

The research was supported by the National Institutes of Health (NIAID grant 5R61AI140465-03 and NIDA grant 1R61DA048444-01); the NIH Rapid Acceleration of Diagnostics (RADx) program; the National Heart, Lung, and Blood Institute; the National Institute of Biomedical Imaging and Bioengineering; the Department of Health and Human Services (Grant No. 3U54HL143541-02S1); as well as through philanthropic support from Fast Grants, the James B. Pendleton Charitable Trust, The Roddenberry Foundation, and multiple individual donors. This work was also made possible by a generous gift from an anonymous private donor in support of the ANCeR diagnostics consortium.

About Gladstone Institutes

To ensure our work does the greatest good, Gladstone Institutes focuses on conditions with profound medical, economic, and social impact—unsolved diseases. Gladstone is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease. It has an academic affiliation with UC San Francisco.

Sources

Gladstone Institutes: Julie Langelier | julie.langelier@gladstone.org | 415.734.5000

UC Berkeley: Kara Manke | kjmanke@berkeley.edu | 415.502.4608

SOURCE Gladstone Institutes; University of California, Berkeley

Related Links

https://gladstone.org

The post New CRISPR-Based Test for COVID-19 Uses a Smartphone Camera appeared first on Medika Life.

There is a sufficiency in the world for man’s need but not for man’s greed. — Mahatma Gandhi

The COVID-19 virus is overtaking the world (a third surge is evident in the US now) and causing death and economic ruin wherever it is found, but not for all. Whenever there’s a disaster, therein lies the seeds for greed for those who see incredible opportunity in the wake of helplessness.

Who among us doesn’t feel helpless in the face of this virus that can kill so quickly despite the age or the social position of the patient?

Yes, we should be following the guidelines offered by medical experts who have advised us what to do to slow down or stop the pandemic. But here is where helplessness meets greed in a most secretive manner. And it’s not the first time this has happened, and it won’t be the last unless we have legislative protection.

Legislative protection, you say? How could this be a legal matter? Do I mean we should mandate masks and throw people in jail? Or fine people for not maintaining social distance? No, that is far too obvious. I’m referring to something that is being done right under your nose, and you’ve given tacit approval to it without even knowing you are.

The Theft Begins Here

Medical experts are frantically calling for ever more testing for the coronavirus in symptomatic and asymptomatic people. In fact, it seems that the ones who don’t show symptoms are more problematic than those who are obviously ill. Taking temperatures?

Asymptomatic individuals have no heightened temperature readings. Therefore, it may seem like they’re screening, but it isn’t beneficial. The asymptomatic are shedding virus everywhere they go.

Several tests have been designed to collect specimens to check for the presence of the virus. Primarily, however, the result is that they collect your DNA with every swab, and it’s sent to a laboratory for analysis. Then where does that sample go, and who has access to the data extracted? Not you.

The UCDavis medical facility does a fine job of reassuring patients about the nasal swab, but where is the part about what happens to the material later? I couldn’t find that in their Q&A portion of their website.

Why Should You Be Sceptical

Clinical trials will be conducted with the specimens collected; of that, I have no doubt. They want to know if the virus is mutating and work on preventing it from replicating itself. This stands to reason. But what are your rights here?

A portion of a sample consent form from a protocol for MERS at Johns Hopkins reads this way:

Request to collect and store biospecimens for future research
As part of this research study, we would like to ask you to let us store your biospecimens, the MRSA bacteria, if found, and health information for future
MRSA research. This may include, comparing the bacteria on your swab to bacteria from sexual partners or in patients from other local hospitals. The
same rules and procedures to protect your privacy discussed here will be taken for all future research.

But you have to read on into the lengthy consent form to find:

If you join this study:  You will not own the data, or the tissue, blood, or other specimens given by you to the investigators for this research.  Both Johns Hopkins and any sponsor of this research may study your data and the tissue, blood or other specimens collected from you. 

What about future monetary benefits from your sample? This is how that portion is handled:

If data, tissue, blood or other specimens are in a form that we believe does not identify you, they may be shared with other academic medical centers,
non-profit organizations, corporate sponsors and other commercial companies without your consent or IRB approval.
 You will not own any product or idea created by the researchers working on this study.
 You will not receive any financial benefit from the creation, use or sale of such a product or idea.

You will not have any say in the matter regarding how your sample is used, who uses it (as long as you’re not identified), nor will you have “any financial benefit from the creation, use, or sale of such a product or idea.” You’ve just given someone a potential financial windfall, and you will not get a penny or any input.

Legal Cases in the Past

The Supreme Court of the US has ruled on cases of patent law dealing with biological samples. Their ruling states:

The long-awaited ruling by the US Supreme Court that human genes are products of nature and cannot be patented may effectively end the monopoly that companies such as Myriad Genetics and others have on genetic testing involving patented genes.

The missing piece is that while they cannot receive patents for your genetic material, it doesn’t rule out their using it once you’ve signed that consent form. And consent forms have not always been used in the past.

Henrietta Lacks is a prime case of nefarious research depriving a poor woman and her family of their rightful financial gain after her death. Tissue had been removed from her cancerous growth both before and after her death, cultured, and turned into a highly profitable, licensed product. No research with the HeLa immortalized cell line could go forward without paying a fee.

Since the 1950s, scientists have grown as much as 50 million metric tons of her cells, and there are almost 11,000 patents involving HeLa cells.

As was then the practice, no consent was obtained to culture her cells. Consistent with modern standards, neither she nor her family were compensated for their extraction or use.

Once the family became suspicious when they were asked for blood samples, the secretive culturing and licensing story came to light.

No one is saying you should not agree to a swab to curb the current virus. But no one should be benefitting without your agreement, either.

The post Unscrupulous Corporations Are Stealing Your DNA appeared first on Medika Life.

Have you just unwittingly provided one of the billions of DNA samples currently being collected across the globe? If you’ve been tested for Covid then the answer is a definitive yes. The Covid-19 test allows laboratories the opportunity to extract your DNA from the sample you’ve provided. The purpose of this article is not to prove that this is being done, but rather to question why no one has sounded the alarm bells. They should be ringing themselves off the wall and yet, the silence is deafening.

The premise is simple. The opportunity has presented itself. Two of the largest groups intimately involved with fighting the pandemic are government and large pharmaceutical conglomerates. If we have learned anything in the last few months it is that neither are to be trusted and both lack the ethical backbone to resist the temptation.

Why would they want your DNA? The list is as endless and the motivations as diverse as the samples themselves. DNA data is arguably one of the primary currencies of our brave new world. Corporations and governments that control this data can control you and I and quite literally, the world.

The purpose of this article is not spread wholesale panic but to raise awareness. The media and the scientific community have been completely remiss in highlighting this issue.

The value of your DNA

The US government holds a database of unsolved crimes with DNA samples as their only evidence. Somewhere out there, in cities across America, wanted felons are wandering into clinics to get tested for Covid. Do you think this once in a lifetime opportunity is going to pass by unnoticed? Can you imagine the potential savings months down the line to law enforcement? Future criminals have just left their name, address, and DNA at a testing center near you. Homeland Security must be rubbing their hands in glee.

Recently, in 2019, a US state judge forced a public genealogy site, GEDmatch, to allow police to search its entire database of DNA profiles. A detective wanted to find distant relatives of a serial rapist in hopes that their family trees could help him home in on a suspect — even though most of the 1.3 million people who shared their DNA data with the site had not agreed to such a search.

From a monetary viewpoint, access to a collection of DNA on a global or country wide scale would fundamentally shift power bases. It’s not a statement made lightly. Data – and your DNA is essentially data waiting to be interpreted – is our new currency and we now possess the computational power to make sense of it. We can now abuse it as never before.

Mortgages, college applications, work, access to healthcare and more will be determined by the content of your chromosomes. It is already happening across the US and other countries.

Companies can, for instance, refuse you insurance or load your premiums based on genetic markers in your DNA. It’s a simple but very clear example of how your DNA can be used against you. This already happens, as referenced further below in this article.

Your life will almost undoubtedly be dictated by your DNA in the not too distant future as more and more genetic markers are identified. Mortgages, college applications, work, and access to healthcare will be determined by the content of your chromosomes. Get tagged with a gene that indicates alcoholism and good luck getting that mortgage. Your risk profile just went north.

Test positive at birth for a genetic marker that indicates an increased risk of psychotic behavior and your future in politics is almost certainly guaranteed. A joke of sorts but you understand the real-world implications. They are terrifying and they aren’t the subject of science fiction. They are now a scientific fact and the subject of very concerned discussion in the halls of legal academia.

These concerns have led to the creation of LawSeq. A website has been set up with a searchable database of US laws that govern your genetic data. Just to be clear, currently, in the US, your genetic anonymity is almost never guaranteed.

Until recently, the issues we’d faced interpreting or identifying shared traits or markers from DNA samples was an insufficient data set and the means with which to analyze said data. Covid has just solved the first issue and quantum computing and vastly improved computational power are rapidly overcoming the second.

The pandemic has given governments across the globe the opportunity to harvest our DNA on a scale hitherto unimaginable. Never before have so many people handed over their DNA so willingly, apparently blissfully unaware of the potential for abuse. Not a single question has been raised about it. Not by the press and not by the public. Why? The paranoia and panic surrounding the pandemic may be partly to blame. It’s the perfect cover at a pivotal moment in the world.

The Covid-19 test is the ultimate DNA harvesting tool. It comes with a name, an address and is given without the need for coercion. In fact, people have been lining up for it, with hundreds of thousands being tested daily across the US.

Whilst the purpose behind getting the test isn’t primarily about your DNA, but trying rather to identify traces of the Coronavirus in your system, this opportunity will not be lost on those who make their living from our DNA or those who stand to profit from it. The temptation to peek into how DNA is impacting positive and negative tests will be overwhelming.

Legally, where do you stand?

Great question and not an easy one to answer. It depends, to a large degree, on where you live. If it happens to be Iceland, you couldn’t care less. Almost every single individual in Iceland has turned over their DNA voluntarily as part of their Genome project.

It is an admirable undertaking with sound medical goals and a desire to better understand how our genes affect our health and susceptibility to diseases. It also been done with the utmost transparency and the willing engagement of the Icelandic people.

Move across the frozen seas in the direction of America and things change. They change dramatically. There is no transparency, no oversight and a plethora of financially and politically motivated individuals just waiting to screw you over, and in case you didn’t realize, your DNA is ripe for the picking.

You do, in theory, own the right to your DNA in the US. It’s the reason a court order is required to make you hand it over should you be unwilling and the court determines it is in the public interest. There are however a number of huge loopholes in the law. The problem with the current system comes down to the fact that genetic data can have multiple uses beyond its original one.

Say you participate in a research study or clinical trial that generates DNA data. A federal law protecting human subjects, called the US Common Rule, mandates that you be informed of how your data might be shared prior to signing a consent document. In 2016, Congress passed the 21st Century Cures Act, which also provides any federal research subjects with a certificate of confidentiality.

This restricts the researchers collecting your genetic data from releasing it to law enforcement or other government agencies. And if that information were to somehow be illegally obtained, through a hack or some other breach, it would be inadmissible in court.

Great, but say you want to add that genetic information to your electronic health record, so it’s available to your doctor. Now it becomes a piece of personal health data, governed by the Health Insurance Portability and Accountability Act (HIPAA).

Under HIPAA, your genetic data can’t be given to your school or employer, but law enforcement agencies are entitled to access it without a warrant if you’re the victim or suspect of a criminal investigation.

Your insurance provider can also access it. That’s why, in 2008, Congress passed the Genetic Nondiscrimination Act, or GINA, which prevents health insurers from denying coverage or jacking up prices based on someone’s genetic predisposition to various health conditions. (They can still do that if your genes make you actively sick – GINA becomes basically useless once you show symptoms.)

GINA also doesn’t apply to long-term-care insurance, life insurance, or disability insurance, though it does ban employers from using it to decide who gets hired, fired, promoted, or given a raise.

Business and government want your genetic data. They will ensure they get hold of it, one way or another

It is however going to get worse. Much worse, as this recent article from Wired points out.

OF ALL THE provisions of the Affordable Care Act – “Obamacare,” if you’re on a first-name basis – the one that seemed the most uncontroversially humane was the guarantee that insurance companies could not use so-called preexisting conditions to deny coverage. If you had a chronic illness or had recovered from something and lost your insurance, or if you quit or got fired, you could still get onto a plan.

But the odds say that sick people stay sick or get sicker, and insurance companies don’t make a profit by paying out. By voting to repeal the ACA and replace it with … well, with something, not totally clear what, the Republican-led House of Representatives seems to have nuked the preexisting condition guarantee. The new bill, which passed in a close 217–213 vote, allows insurance companies to charge sick people more. According to one nonpartisan analysis, it allocates enough money to cover those higher rates for just 5 percent of people with preexisting conditions.

Think it can’t get worse? The ACA specifically protected against discrimination for preexisting conditions that showed up through genetic tests. You might not be sick yet – in technical terms, the illness has not manifested – but if you, for example, test positive for one of the pathogenic variants (a less X-Manly term than “mutation”) in the BRCA gene that predisposes you to breast cancer, you could still get covered. If the House bill becomes law, that protection vanishes.

The tip of the iceberg

Business and government want your genetic data. They will ensure they get hold of it, one way or another, either in collusion with each other or independently. Their reasons for wanting the data are not to better serve you. Never ever make that mistake.

The information contained in your DNA will be used for social engineering. It is already happening right under our noses. Your DNA will used to “stream” you for careers, health and life insurance premiums, access to services and, depending on the lengths we take it to, possibly even prison, if they ever identify markers associated with criminal behavior.

New biological genetically-based weapons are no doubt already under discussion in the Oval Office. Imagine being able to target a gene unique to a certain population or demographic. It’s a can of worms we can’t close in the hands of individuals we cannot trust and the pandemic has offered them the keys to Aladdin’s cave. We need to ensure they aren’t using them.

So what do we do?

The opportunity to exploit Covid-19 testing clearly exists, but is it happening? There is no hard evidence to confirm it, but sufficient reason to assume it is being done covertly. Under a Trump-led regime that is actively legislating to enable free commercial access to your DNA, why would they intentionally choose to overlook this free goldmine of data?

Can we stop it? Probably not, is the short answer and that of course raises the question of where that leaves you an I? Do we simply accept the inevitability of a society regulated by genes rather than free choice? Or do we raise our hands in united outrage and demand changes? Wholesale changes, to our rights, our freedoms, and our privacy.

A simple legal undertaking by all testing facilities not to perform any tests beyond the scope of the original purpose of a test would be a start. An undertaking to destroy all sample materials provided in a responsible and timely manner and not to share, or allow access to, any of the materials or identifying information provided by the patient. Massive penalties and the prospect of prison would enforce these undertakings.

Were you asked to sign anything when you underwent your Covid-19 test? How long was the document and what information did it require? What was in the fine print and did you read it?

Anyone with access to these testing documents is welcome to email copies or photos of the documents to us. This open invitation extends to the testing laboratories should they wish to actively address the concerns raised above and perhaps highlight how they deal with these issues currently. Submissions can be made anonymously to privacy@medika.life and all submissions will be considered confidential.

You can also reach out to your local government at the state level. Social media in this instance becomes our best friend. Publically highlighting an issue often ensures it is addressed in a transparent and accountable manner and also serves to draw the attention of a noticeably absent media.

The post Is Your Covid Test Being Used to Covertly Harvest Your DNA? appeared first on Medika Life.