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Clinical Laboratories and Pathology Groups

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FEMA Paid a Just-Formed Company Millions of Dollars for COVID-19 Specimen Collection Tubes That Were Unusable for Clinical Laboratory Testing

The fledgling test-kit company sent plastic preforms that were intended for use in the manufacturing of soda bottles, not clinical laboratory specimen tubes

When is a specimen tube not a specimen tube? When it is a plastic tube made for creating soda bottles. And that may be exactly what the Federal Emergency Management Agency (FEMA) received after paying $7.3 million to a fledgling Florida-based company that won a multi-million-dollar no-bid contract from the federal government for COVID-19 clinical laboratory testing supplies, which FEMA then shipped nationwide to states that had requested the supplies.

FEMA signed the deal with Fillakit, LLC, on May 7, 2020, “just six days after the company was formed,” reported ProPublica, which went on to state that the shipment of unusable Fillakit specimen tubes contributed to delays in rolling out widespread COVID-19 testing in the US.

According to ProPublica, Fillakit supplied “preforms” that are designed to be expanded with heat and pressure into 2-liter soda bottles, not laboratory specimen tubes.

Michelle Forman, a spokesperson for the Association of Public Health Laboratories, told ProPublica one major flaw of the Fillakit tubes is their size. “They are an unusual shape, so they don’t fit racks,” she said, “and we are getting lots of pushback about how difficult it is to work with them from our clinical partners.”

Fillakit image shows the preform tube that is intended to be die-molded into a large soda bottle
The photo of the preform sent by Fillakit above is taken from a Fox23 news report that stated “FEMA sent the Washington State Department of Health nearly 300,000 plastic tubes. They thought they were getting test tubes for coronavirus testing, but instead, they received tiny plastic preforms that can be made into 2-liter soda bottles.” This photograph shows the preform tube that is intended to be die-molded into a large soda bottle. That is why the cap on the tube is appropriate for the tubes intended purpose as a soda bottle.  (Photo copyright: Alison Grande, KIRO7/Fox23.)

Fillakit Employees Describe ‘Unsanitary’ Working Conditions

Ex-employees of Fillakit told the Wall Street Journal (WSJ) the specimen tubes were being handled in unsanitary open-air conditions in a warehouse outside of Houston where the test kits were being assembled.

“There were up to 250 workers crowded in a small warehouse room, shoulder to shoulder … working off of fold-up tables with supplies placed on the floor and handled without gloves,” Teresa Bosworth Green told Community Impact (CI), which reported that Green worked at Fillakit from May 11-20.

“We were told that we would be filling and capping tubes that would be used for COVID testing,” Green told CI.

However, according to CI, Green “expressed concern about the lack of cleanliness and facemasks. Green brought her own mask, but workers were not initially provided any.”

Green told CI, “People were breathing and coughing right over the solution.”

In a letter to FEMA and the Department of Health and Human Services (HHS) after Michigan received more than 322,000 tubes of transport media manufactured by Fillakit, Democrat Senators Debbie Stabenow and Gary Peters wrote, “Even if the tubes themselves were not unsuitable for testing purposes, the contamination risks inherent in such careless handling would cause serious concerns about the reliability of any tests conducted using these materials.”

On July 7, 2020, the Wall Street Journal reported that Fillakit had notified the Florida Secretary of State on June 26 that the company had been dissolved.

Kira Doyle, JD, owner/attorney at Kira Doyle Law in St. Petersburg, FL
Kira Doyle, JD (above), owner/attorney at Kira Doyle Law in St. Petersburg, Fla., who multiple media outlets listed as Fillakit’s manager, told the Tampa Bay Times that media portraits of the company have been unfair. In a series of emails, she said Fillakit was attempting to fill a void in the medical supply chain. “If you are interested in writing an article about empowered female business owners or entrepreneurs creating jobs and helping this great country during an unprecedented pandemic, Fillakit LLC, fits that profile,” Doyle wrote. (Photo copyright: Kira Doyle Law.)

Under Pressure, Feds Award Contracts for COVID-19 Test Supplies to Inexperienced Suppliers

Fillakit as just one example out of “more than 250 companies that got contracts worth more than $1 million without going through a fully competitive bidding process,” NPR reported.

“Government procurement experts say federal officials were trying to move quickly to deliver desperately needed personal protective equipment,” NPR continued. “But they question the need to turn to contractors who have never worked with the government before and lacked experience making or delivering the protective gear.”

Among those receiving contracts were companies with little to no experience in manufacturing clinical laboratory testing supplies, personal protective equipment (PPE), as well as others that had never worked in the medical field. One company imported vodka, while another was a school security consultant. Many of the contractors served as middlemen, securing PPE from Chinese manufacturers, which meant they often were “competing with federal agencies, state governments, and local health systems,” all of which were attempting to buy the same equipment in the global marketplace, NPR reported.

“Giving business to people who don’t have experience is something you don’t want to do in an emergency,” Joshua Schwartz, JD, a professor of Government Contracts Law and co-director of the Government Procurement Law Program at George Washington University School of Law, told NPR.

FEMA Defends Its Contracting Process

A ProPublica analysis of coronavirus contracts found that about 13% of total federal government pandemic spending went to first-time vendors. And in a follow-up article, ProPublica claimed, “many of the new contractors have no experience acquiring medical products.”

FEMA, however, maintains it pays for purchases only after they have been delivered to minimize potential for waste of taxpayer dollars. “FEMA does not enter into contracts unless it has reason to believe they will be successfully executed,” the agency told ProPublica.

The US’ lack of preparedness for the COVID-19 pandemic has resulted in missteps and misspending as federal agencies struggle to provide hospitals, clinical laboratories, and healthcare providers with personal protective gear and test supplies, and to ramp up COVID-19 testing nationwide.

This is yet another instance where federal agencies appear to lack the competencies required to fulfill healthcare requirements with proven products that meet critical specifications. Meanwhile, in every community throughout the United States, independent medical laboratories and hospital-based laboratories are clamoring for adequate supplies of everything from collect swabs and viral transport media to reagents and cuvettes.

—Andrea Downing Peck

Related Information:

The Trump Administration Paid Millions for Test Tubes and Got Unusable Mini Soda Bottles

Conroe-Based Company Made Unusable COVID-19 Test Supplies Using $10-Million FEMA Grant

Covid-19 Test-Tube Firm Awarded U.S. Contract, Is Accused of Unsanitary Workplace

Coronavirus Test-Kit Maker Dissolves Amid Probes

Senators Stabenow and Peters Press Trump Administration for Answers on Rewarding an Unreliable Company to Produce Testing Supplies

How a St. Petersburg Company with No History in Medical Supplies Won a $10 million Coronavirus Contract

A Closer Look at Federal COVID Contractors Reveals Inexperience, Fraud Accusations and a Weapons Dealer Operating Out of Someone’s House

Tracking Federal Purchases to Fight the Coronavirus: Search Contract Descriptions, Companies and Agencies

Feds Spend Billions on COVID-19 Contracts, Often without Fully Competitive Bidding

FEMA: Federal Support to Expand National Testing Capabilities

Instead of Coronavirus Testing Supplies, FEMA Sent 300K Tiny Soda Bottles to Washington

COVID-19 is Mutating and A Scripps Research Study Reveals the Coronavirus May Become Even More Infectious

Researchers found evidence indicating that the virus has—under selection pressure—made itself more stable, giving it a “significant boost in infectivity”

While the COVID-19 pandemic continues to spread across the United States and throughout the world, new research suggests that a coming genetic mutation within the SARS-CoV-2 coronavirus may make it much more dangerous than it already is. This finding has significant implications for clinical laboratories that perform COVID-19 testing and the in vitro diagnostics (IVD) companies that develop and manufacture tests for COVID-19.

The mutation, called D614G, will provide the coronavirus with sturdier spikes that will increase its ability to latch onto and infect cells. That’s according to a study conducted at The Scripps Research Institute (Scripps) in Jupiter, Fla., which found that a mutated coronavirus may be up to 10 times more infectious than the original strain.

“Viruses with this mutation were much more infectious than those without the mutation in the cell culture system we used,” said Hyeryun Choe, PhD, Professor, Department of Immunology and Microbiology, Scripps Research, and senior author of the study, in a Scripps news release.

Choe and Michael Farzan, PhD, co-chair and professor in the Department of Immunology at Scripps Research, co-authored the study, titled, “The D614G Mutation in the SARS-Cov-2 Spike Protein Reduces S1 Shedding and Increases Infectivity.” Their work is currently under peer review and can be downloaded on bioRxiv.

A More Flexible and Potent Coronavirus May Be Coming

The researchers found that coronavirus particles containing the mutation tend to have four to five times more functional spikes than particles without the mutation. The spikes enable the virus to bind to cells more easily. The research suggests that the greater the number of functional spikes on the viral surface the greater the flexibility and potency of the coronavirus.

In the Scripps news release, Farzan said, “more flexible spikes allow newly made viral particles to navigate the journey from producer cell to target cell fully intact, with less tendency to fall apart prematurely.

“Over time, it has figured out how to hold on better and not fall apart until it needs to,” he added. “The virus has, under selection pressure, made itself more stable.”

Scripps Research shows a cryogenic electron microscope image
The image above, taken from the Scripps Research news release, shows “a cryogenic electron microscope image of a SARS-CoV-2 spike protein side view, the S1 section of the spike is shown in green and the S2 portion is shown in purple. This unique two-piece system has shown itself to be relatively unstable. A new mutation has appeared in the viral variant most common in New York and Italy that makes this spike both more stable and better able to infect cells.” (Graphic and caption copyright: Andrew Ward lab, Scripps Research.)

Mutation Makes SARS-CoV-2 Coronavirus ‘Much More Stable’

The two Scripps scientists have studied coronaviruses for nearly 20 years and performed extensive research on the Severe Acute Respiratory Syndrome (SARS) outbreak that occurred in 2003. They noted that there is a difference between spike proteins of SARS, an earlier strain of coronavirus, and the new SARS-CoV-2 strain. 

The protein spikes of both strains were originally tripod shaped. However, the spikes of the SARS-CoV-2 coronavirus are divided into two different segments: S1 and S2. According to the published study: “The S1domain mediates receptor binding, and the S2 mediates downstream membrane fusion.”

This feature originally produced unstable spikes, but with the D614G mutation, the tripod breaks less frequently, which makes more of the spikes fully functional and the virus more infectious.

“Our data are very clear, the virus becomes much more stable with the mutation,” Choe said in the news release.

Is COVID-19 Spread Due to ‘Founder Effect’

The scientists also examined whether the spread of COVID-19 could have been the result of the “Founder Effect,” which is seen when a small number of variants fan out into a wide population by chance. Could the founder effect explain why COVID-19 outbreaks in some areas of the world were more severe than others? The researchers believe their data definitively answered that question. 

“There have been at least a dozen scientific papers talking about the predominance of this mutation,” Farzan said. “Are we just seeing a founder effect? Our data nails it. It is not the founder effect.”

Hyeryun Choe, PhD and Michael Farzan, PhD
Hyeryun Choe, PhD (left), and Michael Farzan, PhD (right), scientists at Scripps Research explained that their research was performed using engineered viruses and that their observations of the virus and its mutation may not translate to increased transmissibility when a virus attaches to a host outside the lab. COVID-19 and its mutation appear to be relatively stable and are mutating at a rate slower than that of the seasonal flu, which may be critical factors in the development of a vaccine. (Photos copyright: Scripps Research.)

Findings Raise ‘Interesting’ Questions about the COVID-19 Coronavirus

Nevertheless, the two scientists are curious about some of their findings. “Our data raise interesting questions about the natural history of SARS-CoV-2 as it moved presumably from horseshoe bats to humans. At some point in this process, the virus acquired a furin-cleavage site, allowing its S1/S2 boundary to be cleaved in virus-producing cells. In contrast, the S1/S2 boundary of SARS-CoV-1, and indeed all SARS-like viruses isolated from bats, lack this polybasic site and are cleaved by TMPRSS2 or endosomal cathepsins in the target cells.

“In summary, we show that an S protein mutation that results in more transmissible SARS-CoV-2 also limits shedding of the S1 domain and increases S-protein incorporation into the virion. Further studies will be necessary to determine the impact of this change on the nature and severity of COVID-19,” the Scripps researchers concluded.

However, not all Scripps researchers agreed with the conclusions of Choe and Farzan’s research.

The Times of Israel reported that Kristian Andersen, PhD, a professor in the Department of Immunology and Microbiology, Scripps California Campus, told the New York Times that “other analyses of virus variants in labs had not found significant differences in infection rates.”

“That’s the main reason that I’m so hesitant at the moment,” Andersen said. “Because if one really was able to spread significantly better than the other, then we would expect to see a difference here, and we don’t.”

Times of Israel also reported that “In late May researchers in University College London said their studies of the genomes of more than 15,000 samples had not shown one strain being more infectious than others.”

So, the jury’s out. Nonetheless, clinical laboratory leaders will want to remain vigilant. A sudden increase in COVID-19 infection rates will put severe strain on already strained laboratory supply chains.

—JP Schlingman

Related Information:

Study: Dominant Form of Virus ‘10 times’ More Infectious than Original Strain

Mutated Coronavirus Shows Significant Boost in Infectivity

The D614G Mutation in the SARS-CoV-2 Spike Protein Reduces S1 Shedding and Increases Infectivity

Banner Health Introduces Virtual Waiting Rooms in 300 Medical Clinics Across Its Nationwide Healthcare System

As digital healthcare continues to gain acceptance and regulatory support, clinical laboratories will need to help patients provide biological samples for virtual doctor visits

Patterns are emerging in healthcare that will likely impact clinical laboratories now and into the future. Trends in telehealth and mobile health (mHealth) that were just beginning to develop before the COVID-19 pandemic have accelerated with the outbreak, and many are predicted to remain once the pandemic is over, reported Healthcare Business and Technology.

Now comes virtual waiting rooms to go along with virtual doctor’s visits. One example is Banner Health of Phoenix, Arizona. The non-profit has more than 50,000 employees in Ariz. and is the state’s largest employer. It operates 28 hospitals and multiple specialty clinics in six states, making it one of the largest health systems in the US as well.

Banner Health is working with LifeLink to deploy virtual waiting rooms in all of its 300 clinics.

What is a Virtual Waiting Room?

The Banner Health System includes 1,500 physicians who work in 300 clinics. More than one million patients in Arizona, California, Colorado, Nebraska, Nevada, and Wyoming are part of the system.

In the not too distant past, when patients visited Banner Health providers and received doctor’s orders for diagnostic tests, they then went to clinical laboratories or the lab’s patient service centers to provide a biological specimen for testing.

Now, because of COVID-19, patients at Banner Health clinics access virtual waiting rooms through a mobile device or computer. They check in virtually for video visits and may not visit a doctor’s office or medical facility at all. Instead, they engage their healthcare provider through a telehealth connection.

The introduction of the virtual waiting rooms is Banner Health’s response to the need for social distancing during the COVID-19 pandemic.

The virtual waiting rooms employ LifeLink chatbots, which interact with patients in a conversational way, and are available for both telehealth and in-person appointments. The chatbots can:

  • provide appointment reminders,
  • guide patients through completing necessary paperwork,
  • provide instructions on using telehealth technology,
  • check patients in for appointments, and
  • direct patients to an exam room for in-person doctor visits.

Banner Health used similar technology for patients visiting their emergency departments.

Jeff Johnson, JD, Vice President of Innovation Banner Health
“The traditional patient experience of walking into an office, filling out paper forms, reading instructions and then waiting for an exam room had to change. LifeLink chatbots have already helped hundreds of thousands of Banner patients navigate emergency room visits, so the concept of digitizing regular doctor appointment visits with a mobile, virtual waiting room chatbot assistant was a natural extension of the technology,” said Jeff Johnson, JD, Vice President of Innovation and Digital Business at Banner Health, in a press release. (Photo copyright: Healthcare IT News.)

Both Patients and Healthcare Providers Need to Adapt

“The COVID-19 pandemic requires an entirely different level of thinking when it comes to providing routine patient services,” said Greg Johnsen, CEO at LifeLink, in the Banner Health press release. “Like the changes we are seeing in retail, healthcare providers need to adapt, and the waiting room experience is one area that will need to change. We take great pride in knowing that LifeLink chatbots are providing peace of mind and convenience for patients that need to see their doctors.”

A significant innovation is that patients can easily engage with the chatbots through a “one-click authentication process and then interact through a standard web browser,” rather than requiring them to download and install a mobile device app, Healthcare IT News reported.

“One of the key benefits of this chatbot technology is the ease of use,” said Banner Health’s Jeff Johnson in the press release. “Interactions that use natural language eliminate the need for user training, and there are no apps or passwords required so it’s simple for patients to interact with us securely, on any device. We have seen high engagement rates as a result.”

One thing seems certain, as COVID-19 causes increased anxiety over social distancing, it is likely that virtual healthcare, telehealth, and digital pathology will continue to be developed in the medical industry.

This has implications for clinical laboratories, because if patients are being scheduled virtually, it is just a small additional step to have the doctor see them virtually via telehealth. In such circumstances, medical laboratories will need to have a way for the patient to provide a specimen for lab testing.

—Dava Stewart          

Related Information:

Banner Health Launches Virtual Waiting Rooms for Telehealth and In-Person Doctor Appointments

Banner Health Innovates with LifeLink Chatbots to Enable Virtual Waiting Rooms for Telehealth and In-Person Appointments

Health Care Isn’t Going Back to Normal After Pandemic

Chatbots are the Future of Healthcare. Here’s why.

Improving the Medicare Patient Experience with Conversational Mobile Technology — The Breakthrough at Banner Health

Mobile Chatbot Tech Improves ER Patient Experience at Banner Health

With Consumer Demand for Ancestry and Genealogy Genetic Tests Waning, Leading Genomics Companies are Investigating Ways to Commercialize the Aggregated Genetics Data They Have Collected

Genomics experts say this is a sign that clinical laboratory genetics testing is maturing into a powerful tool for population health

Faced with lagging sales and employee layoffs, genomics companies in the genealogy DNA testing market are shifting their focus to the healthcare aspects of the consumer genomics data they’ve compiled and aggregated.

Recent analysis of the sales of genetic tests from Ancestry and 23andMe show the market is definitely cooling, and the analysts speculate that—independent of the consequences of the COVID-19 pandemic on consumer behavior—the two clinical laboratory genetic testing companies may already have done testing for the majority of consumers who want to buy these tests.

“I think the consumer market is going to become more integrated into the healthcare experience,” Joe Grzymski, PhD, told GenomeWeb. “Whether that occurs through your primary care doctor, your large integrated health network, or your payor, I think there will be profound changes in society’s tolerance for using genetics for prevention.”

Grzymski is Chief Scientific Officer at Renown Health; Associate Research Professor of Computational Biology at Desert Research Institute, a research campus of the University of Nevada Reno; and Principal Investigator on a large population study called the Healthy Nevada Project.

Layoffs at Genomics Companies Come as No Surprise

In February, Ancestry, the largest company in the home DNA testing space, announced it was laying off 6% of its workforce or approximately 100 people, across different departments due to a decline in sales, CNBC reported. Several weeks earlier, 23andMe, the second largest company in this market, also announced it was laying off about 100 people or 14% of its workforce due to declining sales.

“I wasn’t surprised by the news,” said Linda Avey, a 23andMe co-founder who is now co-founder and Chief Executive Officer at Precisely Inc., a genomics company headquartered in San Francisco. She was commenting to GenomeWeb on the recent restructuring at her former company. “The level of expensive advertising has been insane here in the US. Those [customer acquisition costs] are not a sustainable model.”

CNBC surmised that the lull in at-home genetic testing is due mainly to:

  • A drought of early adopters. Individuals who were interested in the testing for genealogical and health reasons, and who believed in the value of the tests, have already purchased the product.
  • Privacy concerns. Some potential customers may have reservations about having their DNA information collected and stored in a database due to concerns about how that data is safeguarded and its potential uses by outside companies, law enforcement, and governments. 

COVID-19 May or May Not Be a Factor in Declining DNA Testing Sales

The COVID-19 pandemic may be playing a role in the decline in sales of at-home DNA testing kits. However, there are indications that the market was cooling before the virus occurred.

An article in MIT Technology Review reported that 26 million people had purchased at-home DNA testing kits by the beginning of 2019. The article also estimated that if the market continued at that pace, 100 million people were expected to purchase the tests by the end of 2020.

However, data released by research firm Second Measure, a company that analyzes credit and debit card purchases, may show a different story, reported Vox. The data showed a general decline in test kit sales in 2019. Ancestry’s sales were down 38% and 23andMe’s sales were down 54% in November 2019 compared to November 2018. The downward trend continued in December with Ancestry sales declining 15% and 23andMe sales declining 48% when compared to December 2018.

Second Measure, however, compiled data from the two companies’ websites only. They did not include testing kits that may have been purchased through other sources such as Amazon, or at brick and mortar locations.

Nevertheless, the measures being taken by genomics companies to shore up their market indicates the Second Measure data is accurate or very close.

Rise of Population-level Genomics

This decline in genealogical sales seems to be behind DNA-testing companies shifting focus to the healthcare aspects of consumer genomics. Companies like 23andMe and Ancestry are looking into developing health reports based on their customers’ data that can ascertain an individual’s risk for certain health conditions, or how they may react to prescription medications.

Othman Laraki, co-founder and CEO of Color Genomics
“We are seeing the next wave of maturity of the genetics market,” Othman Laraki, co-founder and CEO of Color Genomics, told CNBC. “If expensive diagnostic testing was genomics’ equivalent of mainframe computers, direct to consumer ancestry genetics was the hobbyist use. While the early adopter wave is petering out, we are seeing the real market (the equivalent of a PC in every home and a phone in every pocket), which is population-level use of genetics, taking hold.” (Photo copyright: San Francisco Business Times.)

For some genomics companies like 23andMe, the at-home DNA testing market was never specifically about selling testing kits. Rather, these companies envisioned a market where consumers would pay to have their DNA analyzed to obtain data on their ancestry and health, and in turn the testing companies would sell the aggregated consumer data to other organizations, such as pharmaceutical companies. 

“Remember that 23andMe was never in the consumer genomics business, they were in the data aggregation business,” Spencer Wells, PhD, founder and Executive Director of the Insitome Institute, a US-based 501(c)3 nonprofit think tank focused on key areas in the field of personal genomics, told GenomeWeb. “They created a database that should in principle allow them to do what they promised, which is to improve people’s health through genomic testing.” 

Even with clinical laboratory testing currently focused on COVID-19 testing, there remains an opportunity to sequence large numbers of people through at-home DNA testing and then incorporate those findings into the practice of medicine. The hope is that sales will again accelerate once consumers feel there is a compelling need for the tests.

Pathologists and clinical laboratory managers will want to watch to see if the companies that grew big by selling ancestry and genealogy tests to consumers will start to send sales reps into physicians’ offices to offer genetic tests that would be useful in diagnosing and treating patients.

—JP Schlingman

Related Information:

As Consumer Genomics Market Cools, Providers Ponder Better Ways to Reach Customers

Consumer DNA Testing Has Hit a Lull—Here’s How It Could Capture the Next Wave of Users

Layoffs at Genetic Testing Companies Reflect the Changing Market

Why DNA Tests are Suddenly Unpopular

More than 26 Million People Have Taken an At-home Ancestry Test

Ancestry to Lay Off 6% of Workforce Because of a Slowdown in the Consumer DNA-Testing Market

New Gene Sequencing Method for Studying Circular DNA Found in Viruses, Bacteria, and other Cells, May Lead to Development of New Clinical Laboratory Biomarkers

University of Alberta researchers developed CIDER-Seq tool and protocols for the study, which they have made freely available to all scientists

Here’s another promising new technology which, given more research into effectiveness and safety, may soon lead to improved clinical laboratory cancer diagnostics. Oncology research scientists have focused much attention on understanding the role of extrachromosomal circular DNA (eccDNA) in human cancer. Now, a new gene sequencing method may help expand their knowledge about that and other circular DNA found in the genomes of bacteria, viruses, and other cells.

University of Alberta (UA) researchers have invented a new way for sequencing circular DNA, according to a recent study published in the journal Nature Protocols. As with any new technological method, this new tool—called CIDER-Seq—will need to be time-tested, but it does hold promise for providing valuable insights into the role these “mysterious loops” play not only in human disease, but in agricultural viruses as well.

A New Tool for Understanding DNA

DNA is considered “circular” when it has a closed loop with no ends. It differs from “linear” DNA chromosomes found in human cell nuclei. Circular DNA include:

Devang Mehta, PhD
Devang Mehta, PhD (above), Postdoctoral Fellow in the University of Alberta’s Department of Biological Sciences, and lead author of the UA study, describes the breakthrough in his team’s on-going work researching the role of eccDNA molecules. “We devised a new molecular biology method and a new bioinformatics algorithm to finally obtain full-length sequences of eccDNA,” he said in a news release. “Our method finally allows us to sequence these molecules completely and gives us and other researchers a tool to better understand what they actually do in the cell.” (Photo copyright: ecrLife.)

According to the UA study, circular DNA enrichment sequencing (CIDER-Seq) “is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly.”

CIDER-Seq uses DNA sequencing technology from Pacific Biosciences, Inc. (PacBio) of Menlo Park, Calif. PacBio (NASDAQ:PACB) is an American biotechnology company founded in 2004 that develops and manufactures gene sequencing systems.

Understanding Circular DNA in Any Human or Plant Cell, Including Cancer

Because many viruses that infect crops have circular DNA, Mehta believes the new tool may be particularly helpful to agricultural scientists. His team of researchers, he noted in the UA news release, used an earlier version of CIDER-Seq to study crop plants in Kenya which were genetically engineered to resist circular DNA viruses.

“Our key advance is that, through our method, scientists can finally gain an unbiased, high-resolution understanding of circular DNA in any type of cell. With our invention of CIDER-Seq, we can start to begin to understand the function of these mysterious circular DNAs in human and plant cells,” Mehta said.

However, this technological advance may be equally welcomed by researchers investigating the role of eccDNA in human cancer. Though both healthy and diseased cells may contain circular DNA, the New York Times noted that the “mysterious loops” are “surprisingly common in cancer cells and play a bigger role in many types of cancers than was previously recognized.” The article goes on to state that until now there have not been effective methods for sequencing circular DNA.

In Clinical Chemistry, a panel of eccDNA experts discussed the critical role circular DNA plays in cancer, referred to as extrachromosomal DNA (ecDNA). “Importantly, in cancer cells, ecDNAs seem to be more transcriptionally active than their chromosomal counterparts and have been suspected to confer growth and survival advantage to cancer cells,” the article states.

According to the New York Times, scientists first discovered the existence of circular DNA in the 1960s when “little clumps of DNA” were detected alongside chromosomes. Today, researchers believe circular DNA is more common in the human genome than first realized and could be linked to a variety of conditions and diseases, not solely to cancer.

CIDER-Seq Research May Lead to New Clinical Laboratory Biomarkers

Birgitte Regenberg, PhD, Associate Professor in Ecology and Evolution at the University of Copenhagen, pioneered methods for detecting circular DNA. She told the New York Times, “I think we’re just opening our eyes up.”

Though she says the research has been “cancer-centered,” Regenberg maintains the role circular DNA plays in human biology may prove to be much broader.

“It’s like when a horse has blinders: The blinders focus the science, but they also prevent some things from being understood,” she said.

The University of Alberta news release states the CIDER-Seq data analysis software has been made available online for other scientists to use, along with step-by-step lab and computer protocols for analyzing the DNA sequences.

Clinical laboratory leaders should keep an eye on the use of CIDER-Seq technology. It may lead to the development of new biomarkers for cancer and other diseases.

—Andrea Downing Peck

Related Information:

Scientists Develop Tool to Sequence Circular DNA

Full-length Sequence of Circular DNA Viruses and Extrachromosomal Circular DNA Using CIDER-Seq

Scientists Are Just Beginning to Understand Mysterious DNA Circles Common in Cancer Cells

What is Extrachromosomal Circular DNA and What Does it Do?

Australia Spent $200 Million (AUD) on Chinese COVID-19 Diagnostic Testing Kits That Went into The Country’s Strategic Reserve Rather than Being Used

Australian government heralded April purchase of 10 million clinical laboratory diagnostics tests from BGI, but most of the nation’s states and territories say kits are unneeded or unable to be used by their health departments

While the United States and other nations attempt to bring the COVID-19 outbreak under control, many countries have turned to China to offset shortages of clinical laboratory SARS-CoV-2 test kits needed to diagnose the coronavirus. This did not work out well for the United Kingdom and Spain, each which purchased large volumes of COVID-19 test kits from Chinese companies in April.

Now comes news that Australia spent roughly $130 million US ($200 million AUD) in late April for COVID-19 RT-PCR tests from BGI Genomics. However, those kits are mainly going unused as Australian state governments say they are unneeded or incompatible with existing testing equipment.

This is the latest example of the problems plaguing governments worldwide as they scramble to boost SARS-CoV-2 testing capacity during the evolving pandemic.

At the start of the outbreak, a shortage of rapid molecular COVID-19 tests was compounded by reliability concerns surrounding Chinese-made testing kits. Dark Daily reported on one such fiasco in “Chinese Firm to Replace Clinical Laboratory Test Kits After Spanish Health Authorities Report Tests from China’s Shenzen Bioeasy Were Only 30% Accurate,” Apr 3, 2020.

Since then, concerns among scientists and medical professionals over the accuracy of both molecular and serological antibody tests have only increased. (See Dark Daily, “Multiple Studies Raise Questions About Reliability of Clinical Laboratory COVID-19 Diagnostic Tests,” June 29, 2020.)

The new problem is that COVID-19 testing capacity has increased so much it now exceeds demand for testing. This is true for portions of Australia and in some states in the US.

Demand for Testing in Australia Far Lower than Expected

With a population of roughly 25 million, Australia has a smaller population than Texas, which in 2020 stood at about 28 million. According to the Johns Hopkins COVID-19 Dashboard, Australia had 7,139 confirmed cases of COVID-19 as of May 27 and 103 deaths.

Australian billionaire Andrew “Twiggy” Forrest, former CEO of Fortescue Metals Group, orchestrated the purchase of 10 million COVID-19 RT-PCR testing kits for Australia from BGI. He did so through his philanthropic organization, the Minderoo Foundation, with the understanding that the purchase cost would be refunded by the Australian government.

On April 28, the Australian government heralded Forrest’s purchase as a commercial coup, because it occurred in the midst of sparring between the two countries over China’s handling of the coronavirus outbreak and fierce international competition for COVID-19 diagnostic testing kits.

Australia’s Minister for Health Greg Hunt, MP
“Today we are securing perhaps the most critical step in our testing capability,” Australia’s Minister for Health Greg Hunt, MP (above) stated during a press conference, reported ABC News. “What these 10 million tests will do is allow our state and territory public health units to be able to test right through 2020. [They] provide us with the capacity to contain, suppress and defeat the virus, but also if a case were to emerge, to find it and to find everybody around.” However, demand for testing has not been as great as Australia’s leaders had anticipated. (Photo copyright: ABC News.)

Forrest credited his personal relationship with BGI for his ability to secure the kits for Australia. “Chairman Wang [Jian] and BGI kept to their word and resisted that very clear temptation of a businessman to make a much bigger profit and maintain the integrity of my relationship, and I’m very grateful for that,” Forrest told ABC News.

However, less than a month later, The Guardian Australia reported the taxpayer-funded coronavirus testing kits Forrest brought to Australia were not being used. Instead, the test kits have been added to the country’s strategic reserve. Three of five Australian states and both territories—Queensland, New South Wales, Western Australia, the Northern Territory, and the Australian Capital Territory—all told the newspaper they were not using the BGI tests. Only Victoria reported it was using the BGI tests.

PathWest, Western Australia’s leading pathology laboratory, is not using the BGI-manufactured COVID-19 PCR testing kits,” the Western Australia Department of Health told The Guardian. “PathWest has capacity and sufficient reagent to provide testing throughout the state without the need to use these tests.”

Queensland Health echoed Western Australia’s response.

“Queensland Health does not use the BGI COVID-19 test or its operating platform,” a spokeswoman told The Guardian. “Queensland already has ample testing capacity, illustrated by the world leading figures of 137,000 COVID-19 tests since January.”

According to ABC News, Minderoo also purchased 11 testing machines, which were installed around the country. Six Chinese experts flew to Australia to help oversee the testing machines’ installation.

Testing Capacity Also Exceeds Demand in US

Increased COVID-19 testing capacity has been considered a cornerstone to fully lifting stay-at-home orders and reopening businesses, schools, and entertainment venues. But Australia is not alone in ramping up testing capacity only to have public demand not keep pace. The Washington Post reported in mid-May that in at least a dozen states COVID-19 testing capacity exceeded the number of patients lining up for testing.

Utah Department of Health spokesperson Tom Hudachko is among those questioning why people aren’t getting tested in his state, which has a 9,000-test capacity, but was conducting only 3,500 tests a day.

“Well, that’s the million-dollar question,” Hudachko told the Washington Post. “It could be simply that people don’t want to be tested. It could be that people feel like they don’t need to be tested. It could be that people are so mildly symptomatic that they’re just not concerned that having a positive lab result would actually change their course in any meaningful way.”

Meanwhile, Australia’s federal government has the interesting problem of having purchased $130 million (US) of COVID-19 test kits from a Chinese company—test kits that most of the nation’s states and territories have yet to use. Could this be a sign that many clinical laboratory scientists in Australia have their doubts about the accuracy and reliability of these Chinese-manufactured COVID-19 tests?

—Andrea Downing Peck

Related Information:

Coronavirus Tests Brought to Australia by Andrew Forrest at $200M Cost to Taxpayers Not Being Used

Millions of Coronavirus Tests on the Way after Purchase by Mining Magnate Andrew Forrest

As Coronavirus Testing Expands, a New Problem Arises: Not Enough People to Test

Chinese Firm to Replace Clinical Laboratory Test Kits After Spanish Health Authorities Report Tests from China’s Shenzen Bioeasy Were Only 30% Accurate

Multiple Studies Raise Questions About Reliability of Clinical Laboratory COVID-19 Diagnostic Tests

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