News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

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News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
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University of Maryland Scientists Image World’s First ‘Vampire Virus’

Research could lead to improvements in gene therapy and antiviral resistance medications while also possibly leading to a new class of clinical laboratory tests

Scientists at the University of Maryland, Baltimore County (UMBC) have discovered what may be the scariest virus of all—the Vampire Virus. It’s a term that may inspire “Walking Dead” level horror in the wake of the COVID-19 pandemic, and though virologists and microbiologists might be tempted to dismiss them as imaginary, they are all too real. Even more apropos to the Dracula saga, the UM scientists found them in a soil sample. Yikes!

Happily, this ghoulish discovery could have positive implications for gene editing, gene therapy, and the development of new antiviral medications, according to The Conversation. In turn, these positive implications may eventually trigger the need to create new diagnostic tests that clinical laboratories can offer to physicians.

The UMBC scientists published their findings in the journal ISME, a publication of the International Society for Microbial Ecology, titled, “Simultaneous Entry as an Adaptation to Virulence in a Novel Satellite-Helper System Infecting Streptomyces Species.”

Vampire-like virus photo

The image above, taken from a University of Maryland news release, shows the satellite virus “latched onto its helper virus.” Discovery of vampire-like viruses that attach at the “neck” of other viruses may lead to important discoveries in the development of gene editing and antiviral therapies. Might clinical laboratories one day collect samples for pharmaceutical developers engaged in combating antiviral drug resistance? (Photo copyright: University of Maryland.)

Spotting a Vampire Virus

According to IFLScience, these tiny vampire viruses were first discovered by undergraduates who believed they were looking at sample contamination when analyzing sequences of bacteriophages from environmental soil samples. But upon repeating the experiment they realized it was no mistake.

In the UMBC news release, bioinformatician Ivan Erill, PhD, Professor of Biological Sciences at the University of Maryland, noted that “some viruses, called satellites, depend not only on their host organism to complete their life cycle, but also on another virus, known as a helper.

“The satellite virus needs the helper either to build its capsid, a protective shell that encloses the virus’ genetic material, or to help it replicate its DNA,” he added. “These viral relationships require the satellite and the helper to be in proximity to each other at least temporarily, but there were no known cases of a satellite actually attaching itself to a helper—until now.”

Although scientists have witnessed viruses working together before, this is the first known instance of a virus directly latching onto another virus’ capsid—rather like a vampire going for the neck.

“When I saw it, I was like, I can’t believe this,” said Tagide deCarvalho, PhD, Assistant Director of Natural and Mathematical Sciences at the University of Maryland and first author of the study, in a UM news release, “No one has ever seen a bacteriophage—or any other virus—attach to another virus.”

Visualizing the tiny viruses was only possible through the use of the transmission electron microscope (TEM) at UMBC’s Keith R. Porter Imaging Facility (KPIF), to which deCarvalho had access.

“Not everyone has a TEM at their disposal. [With the TEM] I’m able to follow up on some of these observations and validate them with imaging. There’s elements of discovery we can only make using the TEM,” said deCarvalho in the UMBC news release.

Using Vampire Viruses to Develop Better Gene Therapies

Spookily, the comparisons to Dracula and his parasitic brethren do not stop with their freeloading tendencies. The researchers found that some viruses without a satellite attached still showed signs of having been leeched onto before. Those viruses had the equivalent of “bite marks” showing evidence of encountering vampiric viruses in the past.

“It’s possible that a lot of the bacteriophages that people thought were contaminated were actually these satellite-helper systems,” said deCarvalho in the ISME paper.

But what does UMBC’s breakthrough mean for the greater scientific and medical community? Do we need to arm host viruses with silver crosses and necklaces of garlic? Jokes aside, this discovery could lead to further development in research of how to genetically alter viruses and deliver therapeutic elements into cells.

According to Healthline, some gene therapy or “gene editing” already involves the use of viruses. Scientists switch out the programming on a virus and trick it into healing, instead of harming the cells it infiltrates. Therefore, UMBC’s discovery could lead to new breakthroughs battling deadly viruses by using their own parasitic tricks to infiltrate other viruses.

Although groundbreaking and extremely interesting, the research is still in early stages. Any developments from this discovery aren’t likely to impact clinical laboratories any time soon. But after the past few years of battling the COVID-19 variants, this exciting discovery could help find new ways to prevent the next pandemic.  

—Ashley Croce

Related Information:

Vampire Viruses Prey on Other Viruses to Replicate Themselves and May Hold the Key to New Antiviral Therapies

Virus Seen Latching onto Another Virus (Like A Tiny Vampire) for First Time

UMBC Team Makes First-Ever Observation of a Virus Attaching to Another Virus

The First Discovered Vampire Virus Hooks Onto other Viruses—Meet the ‘MiniFlayer’

Simultaneous Entry as an Adaptation to Virulence in a Novel Satellite-Helper System infecting Streptomyces Species

Your Guide to Gene Therapy: How It Works and What It Treats

Bizarre First: Viruses Seen ‘Biting’ onto Other Viruses Like Tiny Vampires

What Key Laboratory Leaders Will Learn at This Week’s 2023 Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management

Executives and pathologists from many of the nation’s most prominent clinical laboratories are on their way to the Crescent City today to share best practices, hear case studies from innovative labs, and network

NEW ORLEANS—This afternoon, more than 900 lab CEOs, administrators, and pathologists will convene for the 28th Annual Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management conference. Three topics of great interest will center around adequate lab staffing, effective cost management, and developing new sources of lab testing revenue.

Important sessions will also address the explosion in next-generation sequencing and genetic testing, proposed FDA regulation of laboratory-developed tests (LDTs), and innovative ways that clinical laboratories and pathology groups can add value and be paid for that additional value.

All this is happening amidst important changes to healthcare and medicine in the United States. “Today, the US healthcare system is transforming itself at a steady pace,” explained Robert L. Michel, Editor-in-Chief of The Dark Report and Founder of the Executive War College. “Big multi-hospital health systems are merging with each other, and payers are slashing reimbursement for many medical lab tests, even as healthcare consumers want direct access to clinical laboratory tests and the full record of their lab test history.

“Each of these developments has major implications in how clinical laboratories serve their parent organizations, offer services directly to consumers, and negotiate with payers for fair reimbursement as in-network providers,” Michel added. “Attending the Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management equips lab leaders with the tools they’ll need to make smart decisions during these challenging times.”

Executive War College

Now in its 28th year, the Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management convenes April 25-26 in New Orleans. Executive War College extends to a third day with three full-day workshops: LEAN fundamentals for lab leaders, a genetic testing program track, and a digital pathology track. Learn more at www.ExecutiveWarCollege.com. (Photo copyright: The Dark Intelligence Group.)

Challenges and Opportunities for Clinical Laboratories

With major changes unfolding in the delivery and reimbursement of clinical services, clinical laboratory and pathology practice leaders need effective ways to respond to the evolving needs of physicians, patients, and payers. As The Dark Report has often covered, three overlapping areas are a source of tension and financial pressure for labs:

  • Day-to-day pressures to manage costs in the clinical laboratory or pathology practice.
  • The growing demand for genetic testing, accompanied by reimbursement challenges.
  • Evolving consumer expectations in how they receive medical care and interact with providers.

Addressing all three issues and much more, the 2023 Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management features more than 80 sessions with up to 125 lab managers, consultants, vendors, and in vitro diagnostic (IVD) experts as speakers and panelists.

Old-School Lab Rules Have Evolved into New-School Lab Rules

Tuesday’s keynote general sessions (to be reported exclusively in Wednesday’s Dark Daily ebriefing) will include four points of interest for clinical laboratory and pathology leaders who are managing change and pursuing new opportunities:

  • Positioning the lab to prosper by serving healthcare’s new consumers, new care models, new payment models, and more, with Michel at the podium.
  • How old-school lab rules have evolved into new-school lab rules and ways to transition the lab through today’s disrupters in healthcare and the clinical laboratory marketplace, with Stan Schofield, Managing Principal of the Compass Group.
  • The growing trend of clinical laboratory-pharmacy relationships with David Pope, PharmD, CDE, Chief Pharmacy Officer at OmniSYS, XIFIN Pharmacy Solutions.
  • Generating value by identifying risk signals in longitudinal lab data and opportunities in big data from payers, physicians, pharma, and bioresearch, with Brad Bostic, Chairman and CEO of hc1.

Wednesday’s keynote sessions (see exclusive insights in Friday’s Dark Daily ebriefing) explore:

Wednesday’s keynotes conclude with a panel discussion on delivering value to physicians, patients, and payers with lab testing services.

Clinical Labs, Payers, and Health Plans Swamped by Genetic Test Claims

Attendees of the 2023 Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management may notice a greater emphasis on whole genome sequencing and genetic testing this year.

As regular coverage and analysis in The Dark Report has pointed out, clinical laboratories, payers, and health plans face challenges with the explosion of genetic testing. Several Executive War College Master Classes will explore critical management issues of genetic and genomic testing, including laboratory benefit management programs, coverage decisions, payer relations, and best coding practices, as well as genetic test stewardship.

This year’s Executive War College also devotes a one-day intensive session on how community hospitals and local labs can set up and offer genetic tests and next-generation sequencing services. This third-day track features more than a dozen experts including:

During these sessions, attendees will be introduced to “dry labs” and “virtual CLIA labs.” These new terms differentiate the two organizations that process genetic data generated by “wet labs,” annotate it, and provide analysis and interpretation for referring physicians.

State of the Industry: Clinical Lab, Private Practice Pathology, Genetic Testing, IVD, and More

For lab consultants, executives, and directors interested in state-of-the-industry Q/A and discussions concerning commercial laboratories, private-practice pathology, and in vitro diagnostics companies, a range of breakout sessions, panels, and roundtables will cover:

  • Action steps to protect pathologists’ income and boost practice revenue.
  • Important developments in laboratory legal, regulatory, and compliance requirements.
  • New developments in clinical laboratory certification and accreditation, including the most common deficiencies and how to reach “assessment ready” status.
  • An update on the IVD industry and what’s working in today’s post-pandemic market for lab vendors and their customers.
  • Federal government updates on issues of concern to clinical laboratories, including PAMA, the VALID Act, and more.

Long-time attendees will notice the inclusion of “Diagnostics” into the Executive War College moniker. It’s an important addition, Michel explained for Dark Daily.

“In the recent past, ‘clinical laboratory’ and ‘anatomic pathology’ were terms that sufficiently described the profession of laboratory medicine,” he noted. “However, a subtle but significant change has occurred in recent years. The term ‘diagnostics’ has become a common description for medical testing, along with other diagnostic areas such as radiology and imaging.”

Key managers of medical laboratories, pathology groups, and in vitro diagnostics have much to gain from attending the Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management, now in its 28th year. Look for continued coverage through social media channels, at Dark Daily, and in The Dark Report.

Clinical laboratories are invited to continue the conversations by joining the Executive War College Discussion Group and The Dark Report Discussion Group on LinkedIn.

Liz Carey

Related Information:

Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management Agenda

Six Important Themes to Help Labs Succeed

Executive War College Press

The Dark Report

Dark Daily eBriefings

The Dark Report Discussion Group

Executive War College Discussion Group

Stanford Medicine Scientists Sequence Patient’s Whole Genome in Just Five Hours Using Nanopore Genome Sequencing, AI, and Cloud Computing

And in less than eight hours, they had diagnosed a child with a rare genetic disorder, results that would take clinical laboratory testing weeks to return, demonstrating the clinical value of the genomic process

In another major genetic sequencing advancement, scientists at Stanford University School of Medicine have developed a method for rapid sequencing of patients’ whole human genome in as little as five hours. And the researchers used their breakthrough to diagnose rare genetic diseases in under eight hours, according to a Stanford Medicine news release. Their new “ultra-rapid genome sequencing approach” could lead to significantly faster diagnostics and improved clinical laboratory treatments for cancer and other diseases.

The Stanford Medicine researchers used nanopore sequencing and artificial intelligence (AI) technologies in a “mega-sequencing approach” that has redefined “rapid” for genetic diagnostics. The sequence for one study participant—completed in just five hours and two minutes—set the first Guinness World Record for the fastest DNA sequencing to date, the news release states.

The Stanford scientists described their new method for rapid diagnosis of genetic diseases in the New England Journal of Medicine (NEJM) titled, “Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting.”

Euan Ashley, MD, PhD

“A few weeks is what most clinicians call ‘rapid’ when it comes to sequencing a patient’s genome and returning results,” said cardiovascular disease specialist Euan Ashley, MD, PhD (above), professor of medicine, genetics, and biomedical data science, at Stanford University in the news release. “The right people suddenly came together to achieve something amazing. We really felt like we were approaching a new frontier.” Their results could lead to faster diagnostics and clinical laboratory treatments. (Photo copyright: Stanford Medicine.)

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Need for Fast Genetic Diagnosis 

In their NEJM paper, the Stanford scientists argue that rapid genetic diagnosis is key to clinical management, improved prognosis, and critical care cost savings.

“Although most critical care decisions must be made in hours, traditional testing requires weeks and rapid testing requires days. We have found that nanopore genome sequencing can accurately and rapidly provide genetic diagnoses,” the authors wrote.

To complete their study, the researchers sequenced the genomes of 12 patients from two hospitals in Stanford, Calif. They used nanopore genome sequencing, cloud computing-based bioinformatics, and a “custom variant prioritization.”

Their findings included:

  • Five people received a genetic diagnosis from the sequencing information in about eight hours.
  • Diagnostic rate of 42%, about 12% higher than the average rate for diagnosis of genetic disorders (the researchers noted that not all conditions are genetically based and appropriate for sequencing).
  • Five hours and two minutes to sequence a patient’s genome in one case.
  • Seven hours and 18 minutes to sequence and diagnose that case.

How the Nanopore Process Works

To advance sequencing speed, the researchers used equipment by Oxford Nanopore Technologies with 48 sequencing units called “flow cells”—enough to sequence a person’s whole genome at one time.

The Oxford Nanopore PromethION Flow Cell generates more than 100 gigabases of data per hour, AI Time Journal reported. The team used a cloud-based storage system to enable computational power for real-time analysis of the data. AI algorithms scanned the genetic code for errors and compared the patients’ gene variants to variants associated with diseases found in research data, Stanford explained.

According to an NVIDIA blog post, “The researchers accelerated both base calling and variant calling using NVIDIA GPUs on Google Cloud. Variant calling, the process of identifying the millions of variants in a genome, was also sped up with NVIDIA Clara Parabricks, a computational genomics application framework.”

Rapid Genetic Test Produces Clinical Benefits

“Together with our collaborators and some of the world’s leaders in genomics, we were able to develop a rapid sequencing analysis workflow that has already shown tangible clinical benefits,” said Mehrzad Samadi, PhD, NVIDIA Senior Engineering Manager and co-author of the NEJM paper, in the blog post. “These are the kinds of high-impact problems we live to solve.”

In their paper, the Stanford researchers described their use of the rapid genetic test to diagnose and treat an infant who was experiencing epileptic seizures on arrival to Stanford’s pediatric emergency department. In just eight hours, their diagnostic test found that the infant’s convulsions were attributed to a mutation in the gene CSNK2B, “a variant and gene known to cause a neurodevelopmental disorder with early-onset epilepsy,” the researchers wrote.

“By accelerating every step of this process—from collecting a blood sample to sequencing the whole genome to identifying variants linked to diseases—[the Stanford] research team took just hours to find a pathogenic variant and make a definitive diagnosis in a three-month-old infant with a rare seizure-causing genetic disorder. A traditional gene panel analysis ordered at the same time took two weeks to return results,” AI Time Journal reported.

New Benchmarks

The Stanford research team wants to cut the sequencing time in half. But for now, the five-hour rapid whole genome sequence can be considered by clinical laboratory leaders, pathologists, and research scientists a new benchmark in genetic sequencing for diagnostic purposes.

Stories like Stanford’s rapid diagnosis of the three-month old patient with epileptic seizures, point to the ultimate value of advances in genomic sequencing technologies.

Donna Marie Pocius

Related Information:

Fastest DNA Sequencing Technique Helps Undiagnosed Patients Find Answers in Mere Hours

Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting

Stanford Researchers Use AI to Sequence and Analyze DNA in Five Hours

World Record-Setting DNA Sequencing Technique Helps Clinicians Rapidly Diagnose Critical Care Patients

Ultima Genomics Delivers the $100 Genome

UCSD Scientists Discover a Person’s Skin Microbiome May Make Some Individuals More Attractive to Biting Insects than Others

Research could lead to clinical laboratory tests in service of precision medicine therapies to reduce a person’s susceptibility to being targeted by blood-sucking insects

Ever wonder why some people attract mosquitoes while others do not? Could biting insects pick their victims by smell? Scientists in California believe the answers to these questions could lead to new precision medicine therapies and clinical laboratory tests.

The research revealed evidence that some blood-sucking insects may identify their prey by homing in on the “scent” of chemicals produced by bacteria located in the skin microbiome of animals and humans.  

This is yet another example of research into one area of the human microbiome that might someday lead to a new clinical laboratory test, in this case to determine if a person is more likely to attracts biting insects. If there were such a test, precision medicine therapies could be developed that change an individual’s microbiome to discourage insects from biting that individual.

Then, the clinical laboratory test would have value because it helped diagnose a health condition that is treatable.

Researchers from the University of California San Diego (UCSD) School of Medicine, Department of Pediatrics, and Scripps Institution of Oceanography examined blood-sucking flies that are attracted to bats to learn how the insects choose which bats to feed on. One of the authors of the study, Holly Lutz, PhD, had previously encountered multitudes of bats while performing malaria research in bat caves in Kenya and Uganda.

Lutz is an Assistant Project Scientist, Department of Pediatrics, in the Center for Microbiome Innovation at the UCSD School of Medicine. She is also a Scientific Affiliate at the Field Museum of Natural History.

The researchers published their findings in the scientific journal Molecular Ecology, titled, “Associations Between Afrotropical Bats, Eukaryotic Parasites, and Microbial Symbionts.”

Holly Lutz, PhD

Curiosity regarding why mosquitoes seem to gravitate towards some humans over others was the original catalyst for the UCSD Medical School research. “You know when you go to a barbeque and your friend is getting bombarded by mosquitos, but you’re fine? There is some research to support the idea that the difference in mosquito attraction is linked to your skin microbiome—the unique community of bacteria living on your skin,” said Holly Lutz, PhD (above), first author of the UCSD study. “Keeping in mind that some people are more attractive to mosquitoes than others, I wondered what makes insects attracted to some bats but not others.” Lutz’s research could lead to clinical laboratory tests that drive precision medicine therapies to alter human skin microbiomes and make people less attractive to biting insects. (Photo copyright: The Field Museum of Natural History.)

Biting Flies Prefer Specific Bats

“In these caves, I’d see all these different bat species or even taxonomic families roosting side by side. Some of them were loaded with bat flies, while others had none or only a few,” Lutz said in Phys.org. “And these flies are typically very specific to different kinds of bats—you won’t find a fly that normally feeds on horseshoe bats crawling around on a fruit bat. I started wondering why the flies are so particular. Clearly, they can crawl over from one kind of bat to another, but they don’t really seem to be doing that.”

The researchers suspected that the bacteria contained in the skin microbiomes of individual bats could be influencing which bats the flies selected to bite. The bacteria produce a distinctive odor which may make certain bats more attractive to the flies.

The type of fly assessed for the study are related to mosquitoes and most of them are incapable of flight.

“They have incredibly reduced wings in many cases and can’t actually fly,” Lutz explained. “And they have reduced eyesight, so they probably aren’t really operating by vision. So, some other sensory mechanisms must be at play, maybe a sense of smell or an ability to detect chemical cues.”

To test their hypothesis, the research team collected skin and fur samples from the bodies and wings of a variety of bat species located in various caves around Kenya and Uganda. They collected their samples at 14 field sites from August to October in 2016. They then examined the DNA of the bats as well as the microbes residing on the animals’ skin and searched for the presence of flies.

“The flies are exquisitely evolved to stay on their bat,” said Carl Dick, PhD, a professor of biology at Western Kentucky University and one of the study’s authors. “They have special combs, spines, and claws that hold them in place in the fur, and they can run quickly in any direction to evade the biting and scratching of the bats, or the efforts by researchers to capture them,” he told Phys.org.

“You brush the bats’ fur with your forceps, and it’s like you’re chasing the fastest little spider,” Lutz said. “The flies can disappear in a split second. They are fascinatingly creepy.”

Genetic Sequencing DNA of Bat Skin Bacteria

After collecting their specimens, the researchers extracted DNA from the collected bacteria and performed genetic sequencing on the samples. They created libraries of the bacteria contained in each skin sample and used bioinformatics methods to identify the bacteria and compare the samples from bats that had flies versus those that did not.

“How the flies actually locate and find their bats has previously been something of a mystery,” Dick noted. “But because most bat flies live and feed on only one bat species, it’s clear that they somehow find the right host.”

The scientists discovered that different bat families did have their own distinctive skin microbiome, even among samples collected from different locations. They found that differences in the skin microbiomes of certain bats does contribute to whether those bats have parasites. But not all their questions were answered.

“We weren’t able to collect the actual chemicals producing cue—secondary metabolites or volatile organic compounds—during this initial work. Without that information, we can’t definitively say that the bacteria are leading the flies to their hosts,” Lutz said.

Next Steps

“So, next steps will be to sample bats in a way that we can actually tie these compounds to the bacteria. In science, there is always a next step,” she added.

This research illustrates that there may be a reason why certain animals and humans tend to be more attractive to insects than others. It is also possible that an individual’s skin microbiome may explain why some people are more prone to mosquito and other types of insect bites.

More research and clinical studies on this topic are needed, but it could possibly lead to a clinical laboratory test to determine if an individual’s skin microbiome could contribute to his or her potential to being bitten by insects. Such a test would be quite beneficial, as insects can carry a variety of diseases that are harmful to humans.

Perhaps a precision medicine therapy could be developed to alter a person’s microbiome to make them invisible to blood-sucking insects. That would be a boon to regions of the world were diseases like malaria are spread by insect bites.

—JP Schlingman

Related Information:

Blood-sucking Flies May Be Following Chemicals Produced by Skin Bacteria to Locate Bats to Feed on

Associations Between Afrotropical Bats, Eukaryotic Parasites, and Microbial Symbionts

The Human Skin Microbiome

McMaster University Researchers Develop Bioinformatics ‘Shortcut’ That Speeds Detection and Identification of Pathogens, including Sepsis, SARS-CoV-2, Others

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.

Hendrik Poinar, PhD

“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 National Human Genome Research Institute defines a “probe” in genetics as a “single-stranded sequence of DNA or RNA used to search for its complementary sequences in a sample genome.”

The McMaster scientists call their unique probe design process, HUBDesign, or Hierarchical Unique Bait Design. “HUB is a bioinformatics pipeline that designs probes for targeted DNA capture,” according to their paper published in the journal Cell Reports Methods, titled, “Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets.”

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.

—Donna Marie Pocius

Related Information:

DNA Researchers Develop Critical Shortcut to Detect and Identify Known and Emerging Pathogens

Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets

New Tool Designs Probes for Targeted DNA Capture

Novel Tool Developed to Detect and Identify Pathogens

Hospitals Worldwide are Deploying Artificial Intelligence and Predictive Analytics Systems for Early Detection of Sepsis in a Trend That Could Help Clinical Laboratories Microbiologists

Penn Medicine Informatics Taps Medical Laboratory Data and Three Million Patient Records Over 10 Years to Evaluate Patients’ Sepsis Risk and Head Off Heart Failure

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