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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Anticipated Influenza/SARS-CoV-2 “Twindemic” Has Not Developed, Says CDC, Much to the Relief of the Nation’s Medical Laboratories

The remarkably low number of influenza diagnoses makes it possible for clinical laboratories to stay focused on COVID-19

One positive note for clinical laboratories this winter is the fact that the number of biological samples being submitted for influenza (flu) testing have dropped significantly. This has given medical laboratories more resources for processing COVID-19 tests.

Dark Daily’s sister publication The Dark Report covered this phenomenon in “Surprise! Many Fewer Cases of Flu in Us, Canada, Europe,” December 7, 2020.

According to a feature published in Nature, the number of samples being submitted to medical laboratories for flu testing has dropped by 61%. More surprisingly, the number of positives has dropped by 98%. The combined flu/COVID-19 “twindemic” that some medical experts feared could crush our healthcare system has not materialized—yet, the Washington Examiner reported.

“In any given winter, hospitals are taxed by the flu,” Brian Garibaldi, MD, a pulmonologist and critical care specialist and Medical Director of the Johns Hopkins Biocontainment Unit told the Washington Examiner. “There’s always a concern that our emergency departments will be overwhelmed, and ICU capacity will be strained [due to the concurrence of flu and COVID-19 outbreaks], particularly with people who have coexisting conditions that then get influenza.”

The 2019-2020 flu season ended earlier than usual, likely because of precautions put in place in the spring to combat the coronavirus pandemic. Most years, the seasonal flu in the US peaks in February and trails off by May, Nature reported in “How Coronavirus Lockdowns Stopped Flu in Its Tracks.”

“Seasonal flu cases in the northern hemisphere usually peak in February and tail off by the end of May,” Nature wrote. “This year, unusually, lab-confirmed cases of influenza dropped precipitously in early April, a few weeks after the coronavirus pandemic was declared on 11 March. The data comes from tests of more than 150,000 samples from national influenza laboratories in 71 countries that report data to FluNet, a global surveillance system.”

Government Leaders and Health Experts Remain Concerned

Despite that encouraging data point, public health experts and political leaders were still concerned. In September, Arizona Governor Doug Ducey said, “The overlap of COVID-19 and flu season presents a perfect storm, and we aren’t taking any chances. We are approaching this fall with a proactive mindset and plan of action to limit the impact of the flu and preserve hospital resources,” the Washington Examiner reported.

The caution was certainly warranted. A normal flu season strains resources, but a severe flu season coupled with a global pandemic could have been disastrous. Luckily, Ducey’s “perfect storm” did not materialize.

chart of flu-season during COVID-19 and years 2016 - 2020 with 4 years of flu data charted by FluNet Response System
Data from the World Health Organization’s FluNet Global Influenza Surveillance and Response System was used by Nature to develop the graphic above. It illustrates how the number of positive Influenza specimens in 2019-2020 declined compared to the previous two years. Some experts believe this is due to protocols implemented to combat the COVID-19 coronavirus by hospitals and clinical laboratories. (Graphic copyright: Nature.)

Why Is There Less Influenza?

So, why is there less flu and other respiratory infections?

Epidemiologist Lisa Lockerd Maragakis, MD, MPH, Associate Professor of Medicine and Senior Director of Infection Prevention at Johns Hopkins Health System, told U.S. News, widespread business and school closures provide fewer opportunities for influenza to spread. “We commonly see flu spread in communities, schools, businesses and through travel each year, so those changes are likely keeping the flu away.”

However, this may have a negative effect as well. Eili Klein, PhD, Associate Professor of Emergency Medicine at Johns Hopkins School of Medicine, warns that “Because of the current restrictions and precautions everyone is taking this season, far fewer people will be infected or exposed to the flu virus, and therefore won’t become immune to certain strains of the virus. So, the number of people who may have more severe infections next year is likely to be greater because immunity will be lower,” the Washington Examiner reported.

Other Viral Infections Also in Decline Due to COVID-19 Precautions, Vaccines

Masking, frequent handwashing, and social distancing certainly played a role in reducing the number of cases of flu reported this year. But influenza is not the only disease that saw reductions. “In Hong Kong, compared with previous years, the number of chickenpox cases dropped by about half to three-quarters,” Nature reported. “In April, cases of measles and rubella were their lowest, globally, since at least 2016, according to data available so far.”

Early in the COVID-19 pandemic, some public health officials were concerned that the decline in influenza cases was actually related to a lack of testing. “However, renewed efforts by public health officials and clinicians to test samples for influenza resulted in adequate numbers tested and detection of little to no influenza virus,” the Centers for Disease Control and Prevention (CDC) reported.

Another factor in the lower numbers of flu cases could be due to the fact that more people have gotten vaccinated this year. More than 188 million flu vaccines were distributed in 2020, an increase compared to the 169 million given in 2019.

“Flu vaccination in the community started earlier this year, as recommended by the CDC, and our community physicians report that vaccine uptake has been higher than usual,” Marie-Louise Landry, MD, Clinical Virologist, Professor of Laboratory Medicine and of Medicine (Infectious Diseases), and Director of the Clinical Virology Laboratory at Yale School of Medicine, told Healthline.

It may also be that influenza diagnoses are fewer because people are not seeking treatment. Hospitals at or beyond capacity due to the pandemic, or fear of contracting COVID-19, may have motivated people with flu-like symptoms to stay home rather than seek treatment. However, most healthcare experts agree that public health measures to fight COVID-19 are likely the larger reason there is less flu.

“Public health measures such as movement restrictions, social distancing, and increased personal hygiene likely had an effect on decreasing influenza and other respiratory virus transmissions,” the World Health Organization (WHO) told Nature.

What About the Next Flu Season?

Experts are more conflicted regarding what all of this means for coming flu seasons. Some experts think that because there’s less flu this year, there will be less immunity next year, and severe illness will result. Others are more optimistic and hope that some strains of flu will disappear, which could mean less flu in the immediate future. It’s not a simple prediction to make.

“A lot of different flus have been circulating in recent years. Are they all going to make it out of this or not? It’s possible that what this season will do is actually make the virological picture a lot simpler. That may be permanent, potentially,” Richard Webby, PhD, an infectious disease scientist at St. Jude Children’s Research Hospital and Director of the World Health Organization Collaborating Center for Studies on the Ecology of Influenza in Animals and Birds, told Nature in “How COVID-19 is Changing the Cold and Flu Season.”

Even if the low flu numbers this year mean some strains do not survive, it is unlikely that will remain the case. “I am sure that flu will come back with a vengeance at some stage in the future,” Robert Ware, PhD, a biostatistician, clinical epidemiologist, and Professor of Biostatistics with Griffith University in Queensland, Australia, told Nature.

Thus, clinical laboratories should remain vigilant for future influenza outbreaks. Hopefully by then the COVID-19 pandemic will have peaked and labs will be able to reallocate testing resources appropriately.

—Dava Stewart

Related Information:

How COVID-19 Is Changing the Cold and Flu Season

How Coronavirus Lockdowns Stopped Flu in Its Tracks

CDC Reports Record-Low Positive Flu Tests

What Happened to the Flu This Year?

Decreased Influenza Activity During the COVID-19 Pandemic—United States, Australia, Chile, and South Africa, 2020

Why Flu Cases Are Down During a Massive Pandemic

Scientists at St. Jude Children’s Research Hospital Create 3D Map of Mouse Genome to Study How Genes Respond to Disease

The scientist also employed machine learning “to gauge how easily accessible genes are for transcription” in research that could lead to new clinical laboratory diagnostic tests

Anatomic pathologists and clinical laboratories are of course familiar with the biological science of genomics, which, among other things, has been used to map the human genome. But did you know that a three-dimensional (3D) map of a genome has been created and that it is helping scientists understand how DNA regulates its organization—and why?

The achievement took place at St. Jude Children’s Research Hospital (St. Jude) in Memphis, Tenn. Scientists there created “the first 3D map of a mouse genome” to study “the way cells organize their genomes during development,” a St. Jude news release noted.

Some experts predict that this new approach to understanding how changes happen in a genome could eventually provide new insights that anatomic pathologists and clinical laboratory scientists could find useful when working with physicians to diagnose patients and using the test results to identify the most appropriate therapy for those patients.

The St. Jude researchers published their findings in the journal Neuron in a paper titled “Nucleome Dynamics during Retinal Development.” 

Machine Learning Provides Useful Genomic Data

In addition to 3D modeling, the researchers applied machine learning to data from multiple sources to see how the organization of the genome changed at different times during development. “The changes are not random, but part of the developmental program of cells,” Dyer said in the news release.

The St. Jude study focused on the rod cells in a mouse retina. That may seem like a narrow scope, but there are more than 8,000 genes involved in retinal development in mice, during which those genes are either turned on or off.

To see what was happening among the cells, the researchers used HI-C analysis, an aspect of ultra-deep chromosome conformation capture, in situ. They found that the loops in the DNA bring together regions of the genome, allowing them to interact in specific ways.

Until this study, how those interactions took place was a mystery.

“Understanding the way cells organize their genomes during development will help us to understand their ability to respond to stress, injury and disease,” Michael Dyer, PhD (above), Chair of St. Jude’s Developmental Neurobiology Department, co-leader of the Developmental Biology and Solid Tumor Program, and Investigator at Howard Hughes Medical Institute (HHMI), said in the news release. (Photo copyright: St. Jude Children’s Research Hospital.)

The scientists also discovered there were DNA promoters, which encourage gene expression, and also DNA enhancers that increase the likelihood gene expression will occur.

“The research also included the first report of a powerful regulator of gene expression, a super enhancer, that worked in a specific cell at a specific stage of development,” the news release states. “The finding is important because the super enhancers can be hijacked in developmental cancers of the brain and other organs.”

St. Jude goes on to state, “In this study, the scientists determined that when a core regulatory circuit super-enhancer for the VSX2 gene was deleted, an entire class of neurons (bipolar neurons) was eliminated. No other defects were identified. Deletion of the VSX2 gene causes many more defects in retinal development, so the super-enhancer is highly specific to bipolar neurons.”

The St. Jude researchers developed a genetic mouse model of the defect that scientists are using to study neural circuits in the retina, the news release states.

Research Technologist Victoria Honnell (left); Developmental Neurobiologist Jackie Norrie, PhD (center); and Postdoctoral Researcher Marybeth Lupo, PhD (right), work in the St. Jude clinical laboratory of Michael Dyer, PhD, using 3D genomic mapping to study gene regulation during development and disease. (Photo copyright: St. Jude Children’s Research Hospital.)

DNA Loops May Matter to Pathology Sooner Rather than Later

Previous researcher studies primarily used genomic sequencing technology to locate and investigate alterations in genes that lead to disease. In the St. Jude study, the researchers examined how DNA is packaged. If the DNA of a single cell could be stretched out, it would be more than six feet long. To fit into the nucleus of a cell, DNA is looped and bundled into a microscopic package. The St. Jude scientists determined that how these loops are organized regulates how the cell functions and develops.

Scientists around the world will continue studying how the loops in DNA impact gene regulation and how that affects the gene’s response to disease. At St. Jude Children’s Research Hospital, Dyer and his colleagues “used the same approach to create a 3D genomic map of the mouse cerebellum, a brain structure where medulloblastoma can develop. Medulloblastoma is the most common malignant pediatric brain tumor,” noted the St. Jude’s news release.

In addition to providing an understanding of how genes function, these 3D studies are providing valuable insight into how some diseases develop and mature. While nascent research such as this may not impact pathologists and clinical laboratories at the moment, it’s not a stretch to think that this work may lead to greater understanding of the pathology of diseases in the near future.

—Dava Stewart

Related Information:

Researchers Move Beyond Sequencing and Create a 3D Genome

Nucleome Dynamics During Retinal Development

Whole Genome Sequencing

HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples

Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates

An Overview of Methods for Reconstructing 3D Chromosome and Genome Structures from Hi-C Data

Apple Updates Its Mobile Health Apps, While Microsoft Shifts Its Focus to Artificial Intelligence. Both Will Transform Healthcare, But Which Will Impact Clinical Laboratories the Most?

While Apple recently debuted features to bring personal health records and protected health information to its mobile devices, Microsoft shuttered HealthVault in favor of focusing on AI-powered healthcare advances

As clinical laboratories and anatomic pathology groups know, lab testing data comprise more than 70% of the average patient’s health record. Thus, creating a universal platform on which consumers can share or review health information and medical histories with caregivers is a critical, yet elusive goal for most major tech companies, including tech giants Apple (Nasdaq:AAPL)  and Microsoft (Nasdaq:MSFT).

Apple has big plans for patient health records and is working to bring protected health information (PHI) and healthcare advice to iPhones, iPads, and Apple Watch. Meanwhile, Microsoft is reducing its footprint in the mobile device healthcare market. Instead, it appears to be banking on its Artificial Intelligence (AI) platform. How these two diverging paths play out could have ramifications for the pathology and clinical laboratory industries.

HealthVault Insights versus AI versus Apple Health Mobile Apps

Launched in February 2017, Microsoft’s HealthVault Insights combined machine learning and AI with patients’ PHI and mobile activity tracking. The intent was to create an accessible, interactive platform for patients to monitor important health trends.

However, as of January 2018, Microsoft pulled the mobile app from Android, iOS, and Windows App stores. While summary information that draws on previously collected data is still available from the HealthVault website, new data and detailed insights are no longer available.

“We launched HealthVault Insights as a research project … with the goal of helping patients generate new insights about their health,” states Microsoft’s HealthVault Insights website. “Since then, we’ve learned a lot about how machine learning can be used to increase patient engagement and are now applying that knowledge to other projects.”

According to ZDNet, the closing of HealthVault Insights does not impact the Microsoft Health platform or the HealthVault patient-records system.

However, Microsoft’s shuttering of HealthVault Insights, and Google’s shuttering its Google Health platform in 2012, does seem to make Apple the last major tech company developing apps target at healthcare consumers designed to help them exchange private health information with caregivers through mobile devices. Dark Daily reported on Apple’s update earlier this year. (See, “Apple’s Update of Its Mobile Health App Consolidates Data from Multiple EHRs and Makes It Easier to Push Clinical Laboratory Data to Patients,” March 21, 2018.)

AI Will ‘Dramatically Transform Healthcare’

Shuttering HealthVault highlighted Microsoft’s shift away from consumer-facing health efforts and toward assisting medical laboratories, physicians, and research groups discover and implement treatments driving modern personalized medicine.

In a Microsoft blog post, Peter Lee, Corporate VP of Microsoft Healthcare, stated that Microsoft hopes its Healthcare NeXT platform will “dramatically transform healthcare, will deeply integrate Greenfield research and health technology product development, as well as establish a new model at Microsoft for strategic health industry partnerships.”

HealthVault Insights was one of several projects in Microsoft’s Healthcare NeXT initiative. Run by Microsoft’s AI and Research Group and partnering with major healthcare and research facilities across the country, other projects in the Healthcare NeXT initiative include:

Speaking with Business Insider, Lee noted that healthcare is becoming a “very large business” for Microsoft. “We don’t talk publicly about the dollars, but it’s large,” he concluded.

Microsoft’s EmpowerMD website states the eventual goal is to use the system to connect conversations with the growing trove of healthcare data available. “Our long-term vision is a learning system that incorporates data from longitudinal medical records, medical devices, genomics, population health, research papers, and more.”

AI a ‘Sleeping Giant for Healthcare’

“AI can be viewed as a sleeping giant for healthcare,” Eric Horvitz, PhD, Director of Microsoft Research Labs, told Nasdaq, when discussing Microsoft’s view of technology and healthcare. “AI methods show promise for multiple roles in healthcare. [This includes] inferring and alerting about hidden risks of potential adverse outcomes, selectively guiding attention, care, and interventional programs where [they are] most needed and reducing errors in hospitals.”

One such project involves a strategic partnership with the University of Pittsburg Medical Center (UPMC), which is a “$13-billion Pittsburgh-based system, comprising more than 25 hospitals, a three-million-member health plan, and 3,600 physicians, [that] will be a core partner in our efforts to improve healthcare delivery through a series of projects, beginning with a focus on transforming clinician empowerment and productivity,” according to Microsoft.

“Despite UPMC’s efforts to stay on the leading edge of technology, too often our clinicians and patients feel as though they’re serving the technology rather than the other way around. With Microsoft, we have a shared vision of empowering clinicians by reducing the burden of electronic paperwork and allowing the doctor to focus on the sacred doctor-patient relationship,” Steven D. Shapiro, MD (above), Chief Medical and Scientific Officer of UPMC and President of UPMC’s Health Services division, stated in the Microsoft blog. [Photo copyright: University of Pittsburg Medical Center.]

Today, patients can directly interact with their PHI to analyze trends and take a proactive role in their own healthcare, while researchers tap into the computational power of Cloud computing and correlate data across vast sources using AI. Both trends highlight how technology continues to play a critical role in improving access to healthcare. And how tech researchers continue to develop more efficient and effective treatments.

Medical laboratories and anatomic pathology groups may soon contribute health information to databases that one day will power AI systems. These trends highlight opportunities to both educate physicians on the tools available to utilize patient health data in an effective manner, and on new platforms that clinical laboratories could use to further streamline operations, reduce costs, and boost efficiency.

—Jon Stone

Related Information:

How Microsoft Is Using Advanced Technology in Healthcare

Microsoft Scrapping Personal Health Data App-Based Research Project

An Update on HealthVault Insights

How Microsoft’s Top Scientists Have Built a Big Business in Hacking Healthcare and Helped a Lot of People Along the Way

Microsoft Abandons Its Own HealthVault App: Is This Part of Something Larger?

Here’s How Microsoft Is Investing in AI

Microsoft Rolls Out More AI-Infused Healthcare Services, Software

Microsoft and Partners Combine the Cloud, AI, Research and Industry Expertise to Focus on Transforming Health Care

In Healthcare Push, Microsoft Launches Genomics Service on Azure Cloud

Apple’s Update of Its Mobile Health App Consolidates Data from Multiple EHRs and Makes It Easier to Push Clinical Laboratory Data to Patients