Molecular probes designed to spot minute amounts of pathogens in biological samples may aid clinical laboratories’ speed-to-answer
Driven to find a better way to isolate minute samples of pathogens from among high-volumes of other biological organisms, researchers at Canada’s McMaster University in Hamilton, Ontario, have unveiled a bioinformatics algorithm which they claim shortens time-to-answer and speeds diagnosis of deadly diseases.
Two disease pathogens the researchers specifically targeted in their study are responsible for sepsis and SARS-CoV-2, the coronavirus causing COVID-19. Clinical laboratories would welcome a technology which both shortens time-to-answer and improves diagnostic accuracy, particularly for pathogens such as sepsis and SARS-CoV-2.
Their design of molecular probes that target the genomic sequences of specific pathogens can enable diagnosticians and clinical laboratories to spot extremely small amounts of viral and bacterial pathogens in patients’ biological samples, as well as in the environment and wildlife.
“There are thousands of bacterial pathogens and being able to determine which one is present in a patient’s blood sample could lead to the correct treatment faster when time is very important,” Zachery Dickson, a lead author of the study, told Brighter World. Dickson is a bioinformatics PhD candidate in the Department of Biology at McMaster University. “The probe makes identification much faster, meaning we could potentially save people who might otherwise die,” he added.
Sepsis is a life-threatening response to infection that leads to organ failure, tissue damage, and death in hospitals worldwide. According to Sepsis Alliance, about 30% of people diagnosed with severe sepsis will die without quick and proper treatment. Thus, a “shortcut” to identifying sepsis in its early stages may well save many lives, the McMaster researchers noted.
And COVID-19 has killed millions. Such a tool that identifies sepsis and SARS-CoV-2 in minute biological samples would be a boon to hospital medical laboratories worldwide.
“We currently need faster, cheaper, and more succinct ways to detect pathogens in human and environmental samples that democratize the hunt, and this pipeline does exactly that,” Hendrik Poinar, PhD (above), McMaster Professor of Anthropology and a lead author of the study, told Brighter World. Poinar is Director of the McMaster University Ancient DNA Center. Hospital medical laboratories could help save many lives if sepsis and COVID-19 could be detected earlier. (Graphic copyright: McMaster University.)
Is Bioinformatics ‘Shortcut’ Faster than PCR Testing?
The researchers say their probes enable a shortcut to detection—even in an infection’s early stages—by “targeting, isolating, and identifying the DNA sequences specifically and simultaneously.”
The probes’ design makes possible simultaneous targeted capture of diverse metagenomics targets, Biocompare explained.
But is it faster than PCR (polymerase chain reaction) testing?
The McMaster scientists were motivated by the “challenges of low signal, high background, and uncertain targets that plague many metagenomic sequencing efforts,” they noted in their paper.
They pointed to challenges posed by PCR testing, a popular technique used for detection of sepsis pathogens as well as, more recently, for SARS-CoV-2, the coronavirus causing COVID-19.
“The (PCR) technique relies on primers that bind to nucleic acid sequences specific to an organism or group of organisms. Although capable of sensitive, rapid detection and quantification of a particular target, PCR is limited when multiple loci are targeted by primers,” the researchers wrote in Cell Reports Methods.
According to LabMedica, “A wide array of metagenomic study efforts are hampered by the same challenge: low concentrations of targets of interest combined with overwhelming amounts of background signal. Although PCR or naive DNA capture can be used when there are a small number of organisms of interest, design challenges become untenable for large numbers of targets.”
Detecting Pathogens Faster, Cheaper, and More Accurately
As part of their study, researchers tested two probe sets:
one to target bacterial pathogens linked to sepsis, and
another to detect coronaviruses including SARS-CoV-2.
They were successful in using the probes to capture a variety of pathogens linked to sepsis and SARS-CoV-2.
“We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 [Human coronavirus NL 63] in a human RNA background and seven bacterial strains in human blood. HUBDesign has broad applicability wherever there are multiple organisms of interest,” the researchers wrote in Cell Reports Methods.
The findings also have implications to the environment and wildlife, the researchers noted.
Of course, more research is needed to validate the tool’s usefulness in medical diagnostics. The McMaster University researchers intend to improve HUBDesign’s efficiency but note that probes cannot be designed for unknown targets.
Nevertheless, the advanced application of novel technologies to diagnose of sepsis, which causes 250,000 deaths in the US each year, according to the federal Centers for Disease Control and Prevention, is a positive development worth watching.
The McMaster scientists’ discoveries—confirmed by future research and clinical studies—could go a long way toward ending the dire effects of sepsis as well as COVID-19. That would be a welcome development, particularly for hospital-based laboratories.
Because air travel volumes are low, experts believe it is timely to develop COVID-19 testing systems and gain insight on which protocols are most effective
As the COVID-19 pandemic surges on, several international airlines now require customers to complete at-home COVID-19 testing before they can travel. This is triggering unusual business practices. For example, one airline allows its passengers to use frequent flier miles to purchase mail-in COVID-19 test kits.
Frequent Flyer Miles for COVID-19 Testing
Across the United States, Hawaii has one of the lowest rates of infection, partly thanks to the state’s strict quarantine regulations. In a state, however, that depends on tourism for its economic health, the pandemic has caused serious financial difficulties. In an effort to prevent spread of the coronavirus while also encouraging tourism, Hawaiian Airlines now offers “Pre-travel COVID-19 Test Options” on its website.
To be allowed to skip the state’s mandatory 14-day self-quarantine before arriving on the islands, flyers can take a pre-travel coronavirus test with the following conditions:
The test must be from a state-approved testing provider.
The test must be administered no more than 72 hours prior to the scheduled departure time of the final leg to Hawaii.
For trans-pacific travel, test results must be received prior to flight departure.
Additionally, the airline accepts frequent flyer miles to pay for mail-in COVID-19 tests. In exchange for 14,000 HawaiianMiles, a passenger receives a test kit in the mail. The kit features a video call during which a healthcare professional guides the consumer on taking a saliva sample. The user then ships the sample to a qualified clinical laboratory. Results are returned electronically within 24 hours of the lab receiving the sample.
Hawaii’s COVID-19 portal states, “The state of Hawaii will ONLY accept Nucleic Acid Amplification Test (NAAT) from a certified Clinical Laboratory Improvement Amendment (CLIA) lab test results from Trusted Testing and Travel Partners” that are participating in the state’s pre-travel testing program. Honolulu and Maui are the only two arrival airports allowed. A negative result must have come from a test performed within 72 hours prior to the final leg of the passenger’s trip to Hawaii, according to the portal.
“A negative pre-travel test is an alternative to two weeks in self-isolation for arrivals to the archipelago,” the UK’s Independent reported.
JetBlue and Vault Health Partner to Offer COVID Testing to Airline Passengers
In another instance of an airline getting involved in at-home testing, JetBlue (NASDAQ:JBLU) is partnering with Vault Health to offer at-home testing. The process is similar to the Hawaiian Airlines program. However, rather than purchasing the test with frequent flyer miles, JetBlue offers polymerase chain reaction (PCR) tests at a discount.
Business Travel News reported that passengers must provide a confirmation code while ordering the $119 test from Vault Health’s webpage. “Vault provides a kit for an at-home saliva test, and users administrate it while on a video chat supervised by Vault to ensure the test is done properly. The user sends it overnight to a clinical laboratory and the results are provided within 72 hours,” Business Travel News stated.
“We continue to hear from health officials that [COVID-19] testing is incredibly important in the fight against the coronavirus, and we want to make sure our customers have options for testing, especially prior to travel,” said Joanna Geraghty, President and Chief Operating Officer, JetBlue, in a press release. “As more and more regions reopen, many are requiring test results to enter. Now with easier testing options, those safety requirements may not be a deterrent for travel, but rather provide greater public health and peace of mind with little inconvenience.” (Photo copyright: Spectrum News NY1.)
In addition to airlines such as Hawaii Airlines and JetBlue instituting programs for coronavirus testing, some airports are as well. Tampa International Airport, for example, test-piloted a voluntary testing program for all arriving and departing passengers from October 1st to October 31st. The airport partnered with BayCare, a 15-hospital Tampa area healthcare network, to provide both rapid antigen and PCR tests.
“Testing services will be offered on a walk-in basis … seven days a week from 8 a.m. until 2 p.m. The pilot will be open to all ticketed passengers who are flying or have flown within three days and can show proof of travel. The PCR COVID-19 test costs $125 and the antigen test costs $57,” a press release stated.
Tampa Airport CEO Joe Lopano told the Washington Post, “This could be—especially if adopted by other airports—another way to instill confidence.”
COVID-19 Testing by Retailers Expanding as Well
Travelers aren’t the only people who need testing. Some employers also are requiring negative tests before employees can return to work.
As with all at-home kits, the consumer collects their own specimen and sends it off to a qualified clinical laboratory for processing. AZOVA, a telehealth company, supplies the kits to Costco for resale and provides a smartphone app where customers can check and display the test results.
P23 Labs’ TaqPath SARS-CoV-2 assay is the test being used, which, according to P23, “has a 98% sensitivity and 99% specificity,” Business Insider reported.
The researchers found that “All seven SARS-CoV-2 genomes were genetically identical, with the exception of a single mutation in one case, and all genomes had five signature mutations seen in only six other genomes from the >155,000 genomes sequenced globally. Four of these six related genome sequences were from Switzerland, the country of origin of the suspected index case.”
They added, “By combining information on disease progression, travel dynamics, and genomic analysis, we conclude that at least four in-flight transmission events of SARS-CoV-2 likely took place.”
At-home test kits for COVID-19 are here to stay. That large businesses in multiple industries are now partnering with COVID-19 test developers and clinical laboratory companies to accomplish testing of customers and employees means independent labs that process coronavirus testing can look forward to increasing COVID-19 testing business.
“We need to be using the time now, when [travel] volumes are relatively low, to test the systems and gain insight on which protocols are most effective,” Mara Aspinall, biomedical diagnostics professor at Arizona State University, President and CEO of the Health Catalysts Group, an investment and advisory firm, and former President/CEO of Ventana Medical Systems (now Roche Tissue Diagnostics), a billion-dollar division of Swiss pharmaceutical and diagnostics manufacturer Roche, told the Washington Post.
Even more impressive is that the automated testing lab can reportedly process (with results in four hours) up to 3,000 patient samples daily for SARS-CoV-2, the coronavirus that causes the COVID-19 illness.
“All of our laboratories do PCR every day. But for this test we need to go above and beyond to ensure accurate detection,” said Jennifer Doudna, PhD, IGI Executive Director and UC Berkeley Professor of Molecular and Cell Biology, in an IGA news release.
“We put in place a robotic pipeline for doing thousands of tests per day,” she continued, “with a pipeline for managing the data and getting it back to clinicians. Imagine setting that up in a couple of weeks. It’s really extraordinary and something I’ve never seen in my career.”
Robert Sanders, UC Berkeley’s Manager Science Communications, told Dark Daily the COVID-19 lab performs about 180 tests per day and has tested 1,000 people so far—80% of the samples came from the campus community. About 1.5% to 4% of the tests were found to be positive for the SARS-CoV-2 coronavirus among the groups tested.
“We hope other academic institutions will set up testing labs too,” he said.
How Did Berkeley Set Up a COVID-19 Diagnostic Lab So Fast?
To get up and running quickly, university officials drew from the campus and surrounding business community to equip and operate the laboratory, as well as, train researchers to do clinical analysis of patient samples.
Though the methodology to test for the coronavirus—isolating RNA from a biological sample and amplifying it with PCR—is standard fare in most research labs worldwide, including at UC Berkeley, the campus’ research labs were shuttered due to the spread of the coronavirus.
IGI reached out to the idle labs for their high-throughput PCR systems to start-up the lab. Through its partnership with University Health Services and local and national companies, IGI created an automated sample intake and processing workflow.
Additionally, several research scientists who were under government-mandated stay-at-home orders made themselves available. “My own research is shut down—and there’s not very much I can do other than stay in my home … finally I’m useful,” said PhD candidate Holly Gildea in a Berkeleyside article which noted that about 30 people—mostly doctoral students and postdoctoral researchers—are being trained to oversee the process and monitor the automated equipment.
Postdoctoral fellows Jenny Hamilton (left) and Enrique Shao (right) with an automated liquid-handling robot (Hamilton Microlab STAR), which will be used to analyze swabs from patients to diagnose COVID-19. Hamilton and Shao volunteered to train to become CLIA certified so as to process patient samples. When analyzing real samples from patients, they would be wearing full personal protective equipment (PPE), including mask, face shield, gown and gloves. (Photo and caption copyright: Max and Jules Photography/UC Berkeley.)
Federal and State Authorities Remove Hurdles
In her article, “Blueprint for a Pop-up SARS-CoV-2 Testing Lab,” published on the medRxiv servers, Doudna summarized “three regulatory developments [that] allowed the IGI to rapidly transition its research laboratory space into a clinical testing facility.
“The second was California Governor Newsom’s Executive Order N-25-20, which modified the requirements for clinical laboratory personnel running diagnostic tests for SARS-CoV-2 in a certified laboratory.
“The third was increased flexibility and expediency at the state and federal levels for certification and licensure requirements for clinical laboratory facilities under the Clinical Laboratory Improvement Amendments (CLIA) program. Under these emergency conditions, the California Department of Public Health (CDPH) was willing to temporarily extend—once the appropriate regulatory requirements have been fulfilled—an existing CLIA certificate for high-complexity testing to a non-contiguous building on our university campus.”
“These developments,” wrote Doudna, “enabled us to develop and validate a laboratory-developed test (LDT) for SARS-CoV-2, extend the UC Berkeley Student Health Center’s clinical laboratory license to our laboratory space, and begin testing patient samples.”
Lessons Learned Implementing a Pop-Up COVID-19 Testing Laboratory
“Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to others in setting up similar testing centers,” she wrote.
Learned strategies Doudna says could aid other academic research labs transform to a “SARS-CoV-2 Diagnostic Testing Laboratory include:
Leveraging licenses from existing CLIA-certified labs;
Following FDA authorized testing procedures;
Using online HIPAA training;
Managing supply chain “bottlenecks” by using donated equipment;
Adopting in-house sample barcoding;
Adapting materials, such as sampling tubes, to work with donated equipment;
Cost of equipment and supplies (not including staff) was $550,000, with a per test cost of $24, Doudna noted.
“As the COVID-19 pandemic continues, our intention is to provide both PCR-based diagnostic testing and to advance research on asymptomatic transmission, analyze virus sequence evolution, and provide benchmarking for new diagnostic technologies,” she added.
Medical laboratory leaders understand that the divide between clinical and research laboratories is not easy to surmount. Nevertheless, UC Berkley’s IGI pulled it off. The lab marshaled resources as it took on the novel coronavirus, quickly developed and validated a test workflow, and assembled and trained staff to analyze tests with fast TAT to providers, students, and area residents. There’s much that can be learned from UC Berkeley IGI’s accomplishments.
Media reports in the United Kingdom cite bad timing and centralization of public health laboratories as reasons the UK is struggling to meet testing goals
Clinical pathologists and medical laboratories in UK and the US function within radically different healthcare systems. However, both countries faced similar problems deploying widespread diagnostic testing for SARS-CoV-2, the novel coronavirus that causes COVID-19. And the differences between America’s private healthcare system and the UK’s government-run, single-payer system are exacerbating the UK’s difficulties expanding coronavirus testing to its citizens.
The Dark Daily reported in March that a manufacturing snafu had delayed distribution of a CDC-developed diagnostic test to public health laboratories. This meant virtually all testing had to be performed at the CDC, which further slowed testing. Only later that month was the US able to significantly ramp up its testing capacity, according to data from the COVID Tracking Project.
However, the UK has fared even worse, trailing Germany, the US, and other countries, according to reports in Buzzfeed and other media outlets. On March 11, the UK government established a goal of administering 10,000 COVID-19 tests per day by late March, but fell far short of that mark, The Guardian reported. The UK government now aims to increase this to 25,000 tests per day by late April.
This compares with about 70,000 COVID-19 tests per day in
Germany, the Guardian reported, and about 130,000 per day in the US
(between March 26 and April 14), according to the COVID Tracking Project.
“Ministers need to explain why the NHS [National Health Service] is not testing to capacity, why we are falling behind other countries, and what measures they will put in place to address this situation as a matter of urgency,” MP Keir Starmer (above) said in Parliament in late March, The Guardian reported. (Photo copyright: The Guardian.)
What’s Behind the UK’s Lackluster COVID-19 Testing
Response
In January, when the outbreak first hit, Public Health England (PHE) “began a strict program of contact tracing and testing potential cases,” Buzzfeed reported. But due to limited medical laboratory capacity and low supplies of COVID-19 test kits, the government changed course and de-emphasized testing, instead focusing on increased ICU and ventilator capacity. (Scotland, Wales, and Northern Ireland each have separate public health agencies and national health services.)
Later, when the need for more COVID-19 testing became
apparent, UK pathology laboratories had to contend with global shortages of
testing kits and chemicals, The Guardian reported. At present, COVID-19 testing
is limited to healthcare workers and patients displaying symptoms of pneumonia,
acute
respiratory distress syndrome, or influenza-like illness, PHE stated in “COVID-19:
Investigation and Initial Clinical Management of Possible Cases” guidance.
Another factor that has limited widespread COVID-19 testing is the country’s highly-centralized system of public health laboratories, Buzzfeed reported. “This has limited its ability to scale and process results at the same speed as other countries, despite its efforts to ramp up capacity,” Buzzfeed reported. Public Health England, which initially performed COVID-19 testing at one lab, has expanded to 12 labs. NHS laboratories also are testing for the SARS-CoV-2 coronavirus, PHE stated in “COVID-19: How to Arrange Laboratory Testing” guidance.
Sharon Peacock, PhD, PHE’s National Infection Service Interim Director, Professor of Public Health and Microbiology at the University of Cambridge, and honorary consultant microbiologist at the Cambridge clinical and public health laboratory based at Addenbrookes Hospital, defended this approach at a March hearing of the Science and Technology Committee (Commons) in Parliament.
“Laboratories in this country have largely been merged, so we have a smaller number of larger [medical] laboratories,” she said. “The alternative is to have a single large testing site. From my perspective, it is more efficient to have a bigger testing site than dissipating our efforts into a lot of laboratories around the country.”
Writing in The Guardian, Paul Hunter, MB ChB MD, a microbiologist and Professor of Medicine at University of East Anglia, cites historic factors behind the testing issue. The public health labs, he explained, were established in 1946 as part of the National Health Service. At the time, they were part of the country’s defense against bacteriological warfare. They became part of the UK’s Health Protection Agency (now PHE) in 2003. “Many of the laboratories in the old network were shut down, taken over by local hospitals or merged into a smaller number of regional laboratories,” he wrote.
US Facing Different Clinical Laboratory Testing Problems
Meanwhile, a few medical laboratories in the US are now contending with a different problem: Unused testing capacity, Nature reported. For example, the Broad Institute of MIT and Harvard in Cambridge, Mass., can run up to 2,000 tests per day, “but we aren’t doing that many,” Stacey Gabriel, PhD, a human geneticist and Senior Director of the Genomics Platform at the Broad Institute, told Nature. Factors include supply shortages and incompatibility between electronic health record (EHR) systems at hospitals and academic labs, Nature reported.
Politico
cited the CDC’s narrow testing criteria, and a lack of supplies for collecting
and analyzing patient samples—such as swabs and personal protective equipment—as
reasons for the slowdown in testing at some clinical laboratories in the US.
Challenges Deploying Antibody Tests in UK
The UK has also had problems deploying serology tests designed to detect whether people have developed antibodies against the virus. In late March, Peacock told members of Parliament that at-home test kits for COVID-19 would be available to the public through Amazon and retail pharmacy chains, the Independent reported. And, Politico reported that the government had ordered 3.5 million at-home test kits for COVID-19.
However, researchers at the University of Oxford who had been charged with validating the accuracy of the kits, reported on April 5 that the tests had not performed well and did not meet criteria established by the UK Medicines and Healthcare products Regulatory Agency (MHRA). “We see many false negatives (tests where no antibody is detected despite the fact we know it is there), and we also see false positives,” wrote Professor Sir John Bell, GBE, FRS, Professor of Medicine at the university, in a blog post. No test [for COVID-19], he wrote, “has been acclaimed by health authorities as having the necessary characteristics for screening people accurately for protective immunity.”
He added that it would be “at least a month” before suppliers could develop an acceptable COVID-19 test.
In the United States, the Cellex COVID-19 test is intended for use by medical laboratories. As well, many research sites, academic medical centers, clinical laboratories, and in vitro diagnostics (IVD) companies in the US are working to develop and validate serological tests for COVID-19.
Within weeks, it is expected that a growing number of such
tests will qualify for a Food and Drug Administration (FDA) Emergency Use
Authorization (EUA) and become available for use in patient care.
Using precision genomics, Mayo researchers hope to develop improved medical laboratory tools for screening, diagnosing, and treating patients with inherited genetic disorders such as accelerated aging
Telomeres increasingly are on the radars of physicians and healthcare consumers alike, as researchers gain more knowledge about these critical nucleotides, and doctors continue to indicate their belief that telomeres could make useful diagnostic tools. If so, that would open up a new channel of precision medicine testing for clinical laboratories and anatomic pathology groups.
Telomeres are DNA strands that protect chromosome end points from degrading as people age. Their job is similar to the way plastic tips keep shoelaces from fraying, researchers at the Mayo Clinic explained in a news release. They have been using precision genomics in their assessment of 17 patients with short telomere syndrome (STS) to uncover the genetic causes of the condition.
Using Genetic Sequencing to Find Causes of Short Telomeres
People with STS could develop conditions including bone marrow failure, liver disease, and lung disease earlier in life than others, the news release pointed out.
However, according to the researchers’ paper, “Management of STSs is fraught with significant challenges such as delayed diagnoses, lack of routinely available diagnostics modalities, and standardized treatment guidelines.”
Nevertheless, some physicians are already leveraging information about telomeres in patient treatment. And many consumers have been turning to telomere diagnostic testing companies to learn the lengths of their own telomeres. They’ve learned that the longer the telomeres the better, as shorter telomeres are associated with accelerated aging.
“The length of certain telomeres gives a history of all the assaults a person has been subject to over the course of her lifetime,” a Wired article noted, quoting Joseph Raffaele, MD, co-founder of PhysioAge Medical Group, a clinical practice in New York City that specializes in “proactive” medicines. He goes on to call telomeres “the new cholesterol.” (Photo copyright: drraffaele.com.)
More Study into STS is Needed
GenomeWeb summarized the Mayo study’s methodology as follows:
“An analysis of data from 17 patients with STS confirmed by flow-FISH (fluorescence in situ hybridization) occurred;
Two were of unknown significance in TERT and RTEL1
Study authors concluded that while some genetic mutations are common to short telomeres, they were found in only about 40% of the people in their study. So, more research is needed to discover other causes of short telomeres.
The study found that when compared to people with normal blood telomeres, people with shorter telomere lengths and more rapidly aging blood cells:
Were 50% more likely to develop new or increasing respiratory symptoms;
Were nine times more likely to die; and,
Had worse health status and quality of life.
“It is known that short telomeres are associated with common morbidities of COPD, but it was not known if there is a relationship between blood telomeres and patient-related outcomes in COPD,” Don Sin, MD, a chest physician who led the research at the Centre for Heart Lung Innovation at St. Paul’s Hospital, stated in a news release.
Other Takes on Telomeres
A Harvard Medical blog noted, however, that short telomeres do not necessarily mean disease is imminent, nor that long ones guarantee optimal health.
“There is mounting evidence that a healthy lifestyle buffers your telomeres,” stated Immaculata De Vivo, PhD, a Harvard Medical School Professor and Genetics Researcher at the Dana-Farber/Harvard Cancer Center, in the blog post.
However, another expert questions the value of measuring telomeres for disease risk.
“In short, telomere lengths are too variable within a population, too variable within an individual, and too sensitive to environmental factors to offer any reliable information for common disease risk,” wrote Ricki Lewis, PhD, in PLOS.
Although there are many pitfalls to overcome, some doctors are pushing to use telomere information in patient treatment, and these studies from the Mayo Clinic and other researchers have contributed important data for diagnostic test developers.
In the end, vast and varied content about telomeres exists and clinical laboratory professionals may be called on to help clarify and assess the information. And that’s the long and the short of it.
