Viruses are between 27,000 to 48,500 years old and not dangerous, but researchers say thawing permafrost may one day release pathogens capable of infecting humans
Last fall, European researchers working with virologists and genetic scientists at the Aix-Marseille University in France reported having revived and characterized 13 previously unknown “zombie” viruses isolated from Siberian permafrost samples, including one that was almost 50,000 years old. This will be of particular interest to microbiologists and clinical laboratory managers since these organisms are new to science and may be precursors to infectious agents active in the world today.
The work of the European scientists demonstrates how advancements in genome sequencing and analysis of DNA data are becoming, faster, less expensive, and more precise. That’s good because the researchers warned that, should the permafrost continue to thaw, other previously dormant viruses could be released, posing potential risks for public health.
The pathogens isolated by the researchers are so-called “giant viruses” that infect Acanthamoeba, a commonly found genus of amoeba, and thus are not likely to pose an immediate health threat, the researchers wrote.
However, the scientists expressed concern. “We believe our results with Acanthamoeba-infecting viruses can be extrapolated to many other DNA viruses capable of infecting humans or animals. It is thus likely that ancient permafrost … will release these unknown viruses upon thawing,” they stated in their Viruses paper.
It’s unknown how long the viruses “could be infectious once exposed to outdoor conditions (UV light, oxygen, heat), and how likely they will be to encounter and infect a suitable host in the interval,” they added. However, “the risk is bound to increase in the context of global warming, in which permafrost thawing will keep accelerating, and more people will populate the Arctic in the wake of industrial ventures.”
“In nature we have a big natural freezer, which is the Siberian permafrost,” virologist Paulo Verardi, PhD (above), head of the Department of Pathobiology and Veterinary Science at the University of Connecticut, told The Washington Post. “And that can be a little bit concerning.” However, “if you do the risk assessment, this is very low. We have many more things to worry about right now.” Nevertheless, clinical laboratories may want to remain vigilant. (Photo copyright: University of Connecticut.)
Extremely Old, Very Large Viruses
The newly discovered viruses were found in seven different permafrost samples. Radiocarbon dating determined that they had been dormant for 27,000 to 48,500 years. But viruses contained in permafrost could be even older, the researchers wrote, as the time limit is “solely dictated by the validity range of radiocarbon dating.”
In their Viruses paper, the researchers noted that most of the 13 viruses are “at a preliminary stage of characterization,” and others have been isolated in the research laboratory “but not yet published, pending their complete genome assembly, annotation, or detailed analysis.”
“Every time we look, we will find a virus,” study co-author Jean-Michel Claverie, PhD, told The Washington Post. “It’s a done deal. We know that every time we’re going to look for viruses—infectious viruses in permafrost—we are going to find some.”
Claverie is a professor emeritus of genomics and bioinformatics in the School of Medicine at Aix-Marseille Université in Marseille, France. He leads a university laboratory known for its work in “paleovirology,” and in 2003, discovered the first known giant virus, dubbed Mimivirus. The research team included scientists from Germany and Russia.
According to CNN, unlike regular viruses that generally require an electron microscope to be viewed, giant viruses can be seen under a standard light (optical) microscope. Claverie’s laboratory previously isolated giant viruses from permafrost in 2014 and 2015.
Protecting Against Accidental Infection
To demonstrate the infectious potential of the viruses, the researchers inserted the microbes into cultured amoeba cells, which the researchers describes as “virus bait,” The Washington Post reported. One advantage of using Acanthamoeba cultures is to maintain “biological security,” the researchers wrote in their paper.
“We are using [the amoeba’s] billion years of evolutionary distance with human and other mammals as the best possible protection against an accidental infection of laboratory workers or the spread of a dreadful virus once infecting Pleistocene mammals to their contemporary relatives,” the paper noted. “The biohazard associated with reviving prehistorical amoeba-infecting viruses is thus totally negligible compared to the search for ‘paleoviruses’ directly from permafrost-preserved remains of mammoths, woolly rhinoceros, or prehistoric horses.”
The paper cites earlier research noting the presence of bacteria in ancient permafrost samples, “a significant proportion of which are thought to be alive.” These include relatives of contemporary pathogens such as:
“We can reasonably hope that an epidemic caused by a revived prehistoric pathogenic bacterium could be quickly controlled by the modern antibiotics at our disposal,” the researchers wrote, but “the situation would be much more disastrous in the case of plant, animal, or human diseases caused by the revival of an ancient unknown virus.”
However, according to The Washington Post, “Virologists who were not involved in the research said the specter of future pandemics being unleashed from the Siberian steppe ranks low on the list of current public health threats. Most new—or ancient—viruses are not dangerous, and the ones that survive the deep freeze for thousands of years tend not to be in the category of coronaviruses and other highly infectious viruses that lead to pandemics.”
Cornell University virologist Colin Parrish, PhD, President of the American Society for Virology, told The Washington Post that an ancient virus “seems like a low risk compared to the large numbers of viruses that are circulating among vertebrates around the world, and that have proven to be real threats in the past, and where similar events could happen in the future, as we still lack a framework for recognizing those ahead of time.”
Anthony Fauci, MD, former Director of the National Institute of Allergy and Infectious Diseases (NIAID), responded to an earlier study from Claverie’s lab by outlining all the unlikely events that would have to transpire for one of these viruses to cause a pandemic. “The permafrost virus must be able to infect humans, it must then [cause disease], and it must be able to spread efficiently from human to human,” he told The Washington Post in 2015. “This can happen, but it is very unlikely.”
Thus, clinical laboratories probably won’t see new diagnostic testing to identify ancient viruses anytime soon. But it’s always best to remain vigilant.
End of social distancing, masking, and other COVID-19 pandemic mitigations may lead to more severe flu-like infections in northern hemisphere, experts say
Clinical laboratory professionals in the United States and Canada should prepare now for a severe flu season. That is according to infectious disease experts at Johns Hopkin’s Center for Health Security who predict the rise in influenza (flu) cases in Australia signals what will likely be higher than normal numbers of flu-like infections starting this fall in the Northern Hemisphere.
As a Southern Hemisphere nation, Australia experiences winter from June through August. The land down under just concluded its worst flu season in five years. The flu arrived earlier than usual and was severe. Surveillance reports from the Aussie government’s Department of Health and Aged Care noted that influenza-like illness (ILI) peaked in May and June, but that starting in mid-April 2022 the weekly number of flu cases exceeded the five-year average.
If the same increase in flu cases happens here, healthcare systems and clinical laboratories already burdened with continuing COVID-19 testing and increasing demand for monkeypox testing could find the strain unbearable.
Amesh Adalja, MD (above), Infectious Disease Expert and Senior Scholar at the Johns Hopkin’s Center for Health Security, told Prevention that Australia’s flu season is typically a harbinger of what will follow in the US, Canada, and other Northern Hemisphere countries. “The planet has two hemispheres which have opposite respiratory viral seasons,” he said. “Therefore, Australia’s flu season—which is just ending—is often predictive of what will happen in the Northern Hemisphere.” Clinical laboratories in the United States should review their preparations as North America enters its influenza season. (Photo copyright: Johns Hopkins Bloomberg School of Public Health.)
Consequences of Decline in Flu Vaccinations and Social Distancing, Masks
The New York Times noted that in 2017, when Australia suffered through its worst flu season since modern surveillance techniques were adopted, the US experienced a deadly 2017-2018 flu season a half-year later that took an estimated 79,000 lives.
While the number of flu cases in this country is currently low, according to the weekly US Centers for Disease Control and Prevention’s (CDC) “Flu View,” that is expected to change as temperatures cool.
During the height of the COVID-19 pandemic in the US, influenza was nearly nonexistent. Pandemic-mitigation efforts such as masking, social distancing, and quarantining slowed the spread of the annual respiratory illness. But pandemic mitigation efforts are no longer the norm.
“Many have stopped masking,” said Abinash Virk MD, an Infectious Diseases Specialist at Mayo Clinic College of Medicine and Science, in a Mayo Clinic news blog that urged patients to get vaccinated for flu. “For the large part, we will see the re-emergence of influenza in the winter. In comparison, in 2020 winter … there was literally no influenza. But now that has all changed.”
Diminished Immunity Will Lead to More Severe Flu Cases
A CDC report published in July also noted that last winter’s flu season broke from the traditional pattern of arrival of the flu in the fall followed by a peak in cases in February.
During the 2021-22 season, influenza activity began to increase in November and remained elevated until mid-June. It featured two distinct waves, with A(H3N2) viruses predominating for the entire season. But the overall case counts were the lowest in at least 25 years preceding the COVID-19 pandemic.
Thomas Russo, MD, Professor and Chief of Infectious Disease at the University at Buffalo in New York, said the past two mild flu seasons could set the stage for a difficult year in 2022-23.
“Immunity to respiratory viruses, including the flu, wanes over time,” Russo told Prevention. “People have not seen the virus naturally for a couple of years and many individuals don’t get the flu vaccine.” That, he says, raises the risk that people who are unvaccinated against the flu will develop more severe cases if they do happen to get infected.
“People are interacting closely again and there are very few mandates,” he added. “That’s a set-up for increased transmission of influenza and other respiratory viruses.”
“The Southern Hemisphere has had a pretty bad flu season, and it came on early,” Fauci, told Bloomberg in late August. “Influenza, as we all have experienced over many years, can be a serious disease, particularly when you have a bad season.”
CNN reported that US government modeling predicts flu will peak this year in early December.
CDC Advises Public to Get Flu Vaccine
Because COVID-19 and Influenza have many symptoms in common, such as fever, cough, shortness of breath, fatigue, sore throat, runny nose, headache, and muscle aches, the Mayo Clinic points out on its blog that testing is the only way to discern between the two when symptoms overlap.
According to the CDC, the best way to reduce risk from seasonal flu and its potentially serious complications is to get vaccinated every year. The best time to get vaccinated for the flu is in September and October before the flu starts spreading in communities, the CDC states. However, vaccination after October can still provide protection during the peak of flu season.
Yet, many people fail to get the flu vaccine even though it is recommended for everyone over the age of six months. CNN reported that just 45% of Americans got their flu shots last season. Flu vaccination rates fell for several at-risk groups, including pregnant women and children.
Though flu seasons are often unpredictable, clinical laboratories should prepare now for an influx of influenza test specimens and higher case rates than the past two pandemic-lightened flu seasons. Coupled with COVID-19 and monkeypox testing, already strained supply lines may be disrupted.
Clinical laboratory scientists should also know experts warn that ‘herd resistance’ is more likely than ‘herd immunity’ due to low vaccination rates in many parts of the world
Scientists estimate 73% of the US population may be immune to the SARS-CoV-2 omicron variant. Whether the nation is approaching “herd immunity” against the disease, however, remains open to debate, the Associated Press (AP) reported. These estimates are relevant to medical laboratories doing serology tests for COVID-19, as different individuals will have different immune system responses to COVID-19 infections and vaccines.
More than two years into the COVID-19 pandemic in the United States, the CDC’s COVID Data Tracker shows the number of daily cases dropped to fewer than 50,000 as of March 4, 2022, after reaching a high of 928,125 on January 3, 2022.
Meanwhile, the seven-day death rate per 100,000 people stands at 2.78. That’s significantly above the seven-day death rate reached last July of .45, but well below the 7.21 mark recorded on January 13, 2021.
“We’re clearly entering a new phase of the pandemic,” William Morice, II, MD, PhD, Department of Laboratory Medicine and Pathology at Mayo Clinic in Rochester, Minn., told KARE11, an NBC affiliate.
Is Herd Immunity Achievable?
According to the AP, an estimated 73% of the US population is likely to be immune to the Omicron variant due to vaccination or natural immunity from contracting the disease. That calculation was done for the media outlet by the Institute for Health Metrics and Evaluation (IHME) at the University of Washington in Seattle. The IHME anticipates immunity to Omicron could rise to 80% this month, as more people receive vaccination booster shots or become vaccinated.
“Herd immunity is an elusive concept and doesn’t apply to coronavirus,” he told the Associated Press (AP).
Milton maintains populations are moving toward “herd resistance,” rather than “herd immunity.” This will transform COVID-19 into a permanent fixture with seasonal outbreaks similar to influenza.
Epidemiologist, Ali Mokdad, PhD (above), Chief Strategy Officer for Population Health and Professor of Health Metrics Science at the University of Washington in Seattle, believes the US is now much better positioned to withstand the next wave of COVID-19 cases. “I am optimistic even if we have a surge in summer, cases will go up, but hospitalizations and deaths will not,” he told the Associated Press (AP). Mokdad worked on the IHME model that calculated the 73% Omicron-immunity figure for the AP. However, he recommends continued vigilance toward COVID-19. “We’ve reached a much better position for the coming months, but with waning immunity we shouldn’t take it for granted,” he added. And so, clinical laboratories can expect to continue to play a vital role in the fight against the spread of the SARS-CoV-2 coronavirus. (Photo copyright: University of Washington.)
Herd Immunity Varies, according to the WHO
Because antibodies that developed from vaccines—or natural immunity from a previous infection—diminish over time, waning protection means even those boosted or recently recovered from COVID-19 could be reinfected. In addition, vaccination rates vary widely around the world. Our World in Data estimates only 13.6% of people in low-income countries had received one dose of the COVID-19 vaccine as of March 7, 2022.
The World Health Organization (WHO) points out that herd immunity levels vary with different diseases. Herd immunity against measles requires about 95% of a population to be vaccinated, while the threshold for polio is about 80%.
“The proportion of the population that must be vaccinated against COVID-19 to begin inducing herd immunity is not known. This is an important area of research and will likely vary according to the community, the vaccine, the populations prioritized for vaccination, and other factors,” the WHO website states.
Living with COVID-19
Nonetheless, the US appears to be moving into a new “normal” phase of living with the disease.
In an interview with Reuters, US infectious disease expert Anthony Fauci, MD, Director of the National Institute of Allergy and Infectious Diseases (NIAID) acknowledged a need for returning to normal living even though portions of the population—immunocompromised individuals and the unvaccinated, including children under age five who are not eligible for vaccination—remain vulnerable to more severe COVID-19.
“The fact that the world and the United States—and particularly certain parts of the United States—are just up to here with COVID, they just really need to somehow get their life back,” Fauci said. “You don’t want to be reckless and throw everything aside, but you’ve got to start inching towards that. There’s no perfect solution to this.”
Most states have lifted coronavirus-related restrictions, including masking requirements. As COVID-19 cases drop in California, Gov. Gavin Newsom put in motion a plan called SMARTER (Shots, Masks, Awareness, Readiness, Testing, Education, and Rx) that no longer responds to COVID-19 as a crisis, but instead emphasizes prevention, surveillance, and rapid response to future variant-based surges in cases.
“We have all come to understand what was not understood at the beginning of this crisis, that there’s no ending, that there’s not a moment where we declare victory,” Newsom told USA Today.
Mayo Clinic’s Morice agrees. “It can’t be out of sight, out of mind, per se, but it at least gives us hope that we can get back to some level of normalcy here over the course of the year,” he said.
Since clinical laboratories played a critical role in assay development and COVID-19 testing, medical laboratory leaders should continue monitoring COVID-19 as it moves from pandemic to endemic status due to high vaccination rates and advances in treatment options.
The COVID-19 pandemic has raised awareness among healthcare consumers as well, about the critical role laboratory medicine plays in modern medicine and healthcare. Medical laboratory leaders and pathologists would be wise to amplify this message and stress the importance of clinical laboratory testing for many diseases and healthcare conditions.
A New York Times report suggests that frequent testing is still the best approach to controlling spread of the SARS-CoV-2 coronavirus
Many colleges and universities go to great lengths to screen their students for signs of COVID-19 using technologies that include fever scanners, heart-rate monitors, and symptom-checking apps. But a recent report in The New York Times, titled, “Colleges That Require Virus-Screening Tech Struggle to Say Whether It Works,” suggests that academic institutions would be better off adopting frequent clinical laboratory testing for the SARS-CoV-2 coronavirus, even if it is more expensive than symptom screening.
This shouldn’t be a surprise to pathologists and other medical laboratory professionals who have followed news and research about the pandemic. Back in Sept. 2020, the federal Centers for Disease Control and Prevention (CDC) in a media statement noted that “symptom-based screening has limited effectiveness because people with COVID-19 may have no symptoms or fever at the time of screening, or only mild symptoms.”
That same month, Medscape reported that presidential advisor Anthony Fauci, MD, said, “It is now clear that about 40%-45% of infections are asymptomatic.”
But this hasn’t prevented educational institutions from investing in costly screening technologies. One cited by The New York Times (NYT) was the University of Idaho, where 9,000 students live on or near campus. The university has spent $90,000 on fever scanners resembling airport metal detectors, the paper reported, but as of early March, the units had identified fewer than 10 people with high skin temperatures.
“Even then, university administrators could not say whether the technology had been effective because they have not tracked students flagged with fevers to see if they went on to get tested for the virus,” the NYT reported, adding that many other institutions that adopted screening technologies have failed to systematically measure the effectiveness of these approaches.
“The moral of the story is you can’t just invest in this tech without having a validation process behind it,” infectious-disease epidemiologist Saskia Popescu PhD, MPH, of George Mason University told The New York Times.
Rising COVID-19 Infections on College Campuses
These efforts have come amid increasing COVID-19 infection rates on many US campuses. In “Cases Rise, Restrictions Begin,” Inside Higher Ed reported that large universities were doing better than they had in the fall 2020 semester, but that “other campuses—including those that kept cases low in the fall—are seeing numbers rise.” One such campus was Boston College, which cast blame on students who were not following safety protocols.
For its story, The New York Times surveyed more than 1,900 US colleges and universities as part of an effort to track outbreaks on campus. Respondents reported more than 120,000 campus-related COVID-19 cases between Jan. 1 and March 2, 2021, but because institutions measure outbreaks in different ways, the NYT reported that this is likely an undercount. Overall, institutions reported more than 535,000 cases since the pandemic began, according to the survey.
Clinical Laboratory Testing Still Ongoing on College Campuses
School administrators told The New York Times that despite questions about the usefulness of screening tools, this approach is still worthwhile as reminders for students to follow other protocols, such as mask wearing.
And universities have not abandoned testing for COVID-19. For example, The New York Times noted that students at the University of Idaho are tested at least twice each semester, and the school is also testing wastewater to identify outbreaks of SARS-CoV-2.
The Ohio State News, a publication of Ohio State University, reported in late February that it had tested 30,000 people in a single week, accounting for 12% of the COVID-19 tests conducted in Ohio. At the start of the fall semester, the university was sending test samples to a private company in New Jersey, but later it began processing samples at the on-campus Applied Microbiology Services Lab (AMSL).
“By the start of spring semester, the AMSL was processing about 85% of Ohio State’s COVID-19 tests,” the university reported, for a likely savings of $30 million to $40 million. Leaders of the testing program expect that they can realistically conduct 35,000 tests per week.
Chris Marsicano, PhD (above), a professor and researcher at Davidson College, told Inside Higher Ed that many institutions are relying on antigen testing, which is less costly but also less reliable than PCR (polymerase chain reaction) tests. “PCR tests are expensive,” he said. “Just because you’re testing multiple times a week doesn’t mean you’re catching all the cases.” Marsicano leads the institution’s College Crisis Initiative. Clinical laboratory leaders can attest to Marsicano’s statement. (Photo copyright: Twitter.)
Using Technology for COVID-19 Contact Tracing
In addition to symptom screening, some universities have adopted technologies that track student movement on campus for contact-tracing purposes. But again, the benefits are questionable. For example, Bridgewater State University in Bridgewater, Mass. asked students to scan QR codes at various locations, but only one-third were doing so, The New York Times reported. Another system at the university records entry to campus buildings when students swipe their IDs.
“We found what we need is tests and more tests,” clinical psychologist Christopher Frazer, Psy.D., Executive Director of the university’s wellness center, told The New York Times. He said that students on campus are tested once a week. When they have tested positive, contact tracers “often learned much more about infected students’ activities by calling them than by examining their location logs,” the NYT reported.
Colleges and universities are also banking on vaccination to reduce the spread of the virus, Inside Higher Ed reported. Some will require all students to be vaccinated for the fall semester, but such mandates are facing legal and political hurdles. For example, executive orders by Texas Governor Greg Abbott and Florida Governor Ron DeSantis may prohibit institutions in those states from imposing vaccination requirements.
As colleges and universities struggle to deal with the challenges of COVID-19, clinical laboratories have resources for staying up to date on current testing and tracking technologies in use on campuses. For example, the CDC is funding a program to facilitate sharing of best practices and other information. Inside Higher Ed reported that the Higher Education COVID-19 Community of Practice (CoP) will include a discussion board, webinars, and a searchable database of info uploaded by participating institutions.
Gene sequencing is enabling disease tracking in new ways that include retesting laboratory specimens from before the SARS-CoV-2 outbreak to determine when it arrived in the US
On February 26 of this year, nearly 200 executives and employees of neuroscience-biotechnology company Biogen gathered at the Boston Marriott Long Wharf hotel for their annual leadership conference. Unbeknownst to the attendees, by the end of the following day, dozens of them had been exposed to and become infected by SARS-CoV-2, the coronavirus that causes the COVID-19 illness.
Researchers now have hard evidence that attendees at this meeting returned to their communities and spread the infection. The findings of this study will be relevant to pathologists and clinical laboratory managers who are cooperating with health authorities in their communities to identify infected individuals and track the spread of the novel coronavirus.
This “superspreader” event has been closely investigated and has led to intriguing conclusions concerning the use of genetic sequencing to revealed vital information about the COVID-19 pandemic. Recent improvements in gene sequencing technology is giving scientists new ways to trace the spread of COVID-19 and other diseases, as well as a method for monitoring mutations and speeding research into various treatments and vaccines.
Genetic Sequencing Traces an Outbreak
“With genetic data, a record of our poor decisions is being captured in a whole new way,” Bronwyn MacInnis, PhD, Director of Pathogen Genomic Surveillance at the Broad Institute of MIT and Harvard, told The Washington Post (WaPo) during its analysis of the COVID-19 superspreading event. MacInnis is one of many Broad Institute, Harvard, MIT, and state of Massachusetts scientists who co-authored a study that detailed the coronavirus’ spread across Boston, including from the Biogen conference.
What they discovered is both surprising and enlightening. According to WaPo’s report, at least 35 new cases of the virus were linked directly to the Biogen conference, and the same strain was discovered in outbreaks in two homeless shelters in Boston, where 122 people were infected. The variant tracked by the Boston researchers was found in roughly 30% of the cases that have been sequenced in the state, as well as in Alaska, Senegal, and Luxembourg.
“The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission,” the researchers noted in their study abstract.
“The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into [Massachusetts] early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data,” they concluded.
The use of genetic sequencing to trace the virus could inform measures to control the spread in new ways, but currently, only about 0.33% of cases in the United States are being sequenced, MacInnis told WaPo, and that not sequencing samples is “throwing away the crown jewels of what you really want to know.”
Another role that genetic sequencing is playing in this pandemic is in tracking viral mutations. One of the ways that pandemics worsen is when viruses mutate to become deadlier or more easily spread. Scientists are using genetic sequencing to monitor SARS-CoV-2 for such mutations.
A group of scientists at Texas A&M University led by Yue Xing, PhD, published a paper titled, “MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences,” which explains that “Although most mutations are expected to be selectively neural, it is important to monitor if SARS-CoV-2 will eventually evolve to be a stronger or weaker infectious agent as time goes on. Therefore, it is vital to track mutations from newly sequenced SARS-CoV-2 genome.”
Korber’s findings are important because the mutation the scientists identified appears to have a fitness advantage. “Our data show that, over the course of one month, the variant carrying the D614G Spike mutation became the globally dominant form of SARS-CoV-2,” they wrote. Additionally, the study noted, people infected with the mutated variant appear to have a higher viral load in their upper respiratory tracts.
Genetic Sequencing, the Race for Treatments, Vaccines, and Managing Future Pandemics
If, as Fauci and Morens predict, future pandemics are likely, improvements in gene sequencing and analysis will become even more important for tracing, monitoring, and suppressing outbreaks. Clinical laboratory managers will want to watch this closely, as medical labs that process genetic sequencing will, no doubt, be part of that operation.
