As a deployable medical laboratory, the 1st AML is designed to run field-based clinical laboratory diagnostics and conduct health threat assessments
Clinical laboratory professionals may be surprised to learn that the US Army has a deployable medical laboratory that is equipped to perform the same menu of basic lab tests as their labs here in the United States, but in support of army units deployed in the field. At the same time, the Army’s deployable medical lab has the added responsibility of testing for infectious diseases and chemicals/agents that could be used by terrorists or enemy forces.
“The 1st Area Medical Laboratory identifies and evaluates health hazards through unique medical laboratory analyses and rapid health hazard assessments of nuclear, biological, chemical, endemic disease, occupational, and environmental health threats,” according to an Army new release.
A recent visit by the leaders of this lab unit to meet with their counterparts in Poland highlights the important diagnostic work the military prepares for by using this one-of-a-kind clinical laboratory model.
Col. Matthew Grieser (left), Commander of the 1st Area Medical Laboratory (AML) is shown above meeting with Col. Przemysław Makowski, MD, (right), Deputy Commander of the Military Preventive Medicine Center in Wrocław, Poland. Leaders from the US Army’s 1st AML visited military and medical officials in Poland. “It was a great opportunity to meet our Polish counterparts and to learn from one another,” said Grieser in an Army news release. “We intend to continue to strengthen this relationship … Poland is a great ally, and it was an honor to visit our counterpart organizations.” (Photo copyright: US Army.)
Role and Makeup of the 1st Area Medical Laboratory
The 1st AML traces its roots back to World War II, where it was one of 19 field laboratories spun up in 1944. It was deactivated after the Vietnam War and then reactivated in 2004. It is currently the Army’s only deployable field laboratory, according to the National Library of Medicine.
This specialized unit deploys worldwide to conduct threat detection and medical surveillance, according to the Army. For example, the military can send the 1st AML to locations where samples cannot quickly be transported to a fixed facility, or where there is a need for immediate hazard identification due to chemical or biological contamination or epidemic disease.
During the Ebola outbreak in Liberia in 2014-2015, the 1st AML operated four blood-testing laboratories and helped oversee two others manned by Navy personnel. The goal was to perform quick turnaround times to identify local residents who carried the disease, all while operating with extensive safety measures. More than 4,500 samples were tested during a six-month stay, Army Times reported.
Commanders from the 1st AML recently met with medical officials and chemical, biological, radiological, and nuclear experts from the Polish Armed Forces in the Warsaw area of Poland, the Army news release noted.
“It was a great opportunity to meet our Polish counterparts and to learn from one another,” said Col. Matthew Grieser, Commander of the 1st AML.
Maj. Suzanne Mate, the Chief of chemical threat assessment for the 1st AML, said meeting with allies helps to keep NATO ready for any contingency.
“It’s better to know your partners before you have to work together in a high-consequence situation,” said Mate in the Army news release. “We learned the strengths in different mobility platforms for laboratories and the capabilities within fixed scientific institutions to maintain standards and currency in chemical, biological, and radiological [CBR] investigations.
“This knowledge is invaluable when determining how to move a sample quickly and efficiently to characterize a suspected CBR threat when airlift resources are constrained or country treaties prevent movement activities,” she added.
Observant clinical laboratory managers will note similarities between their own jobs and those of the 1st AML. The military needs lab-based capabilities to perform a menu of diagnostic tests in support of Army units in the field and traditional clinical laboratories do the same in support of the healthcare providers they service.
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.
Screening and analysis of ocean samples also identified a possible missing link in how the RNA viruses evolved
An international team of scientists has used genetic screening and machine learning techniques to identify more than 5,500 previously unknown species of marine RNA viruses and is proposing five new phyla (biological groups) of viruses. The latter would double the number of RNA virus phyla to 10, one of which may be a missing link in the early evolution of the microbes.
Though the newly-discovered viruses are not currently associated with human disease—and therefore do not drive any current medical laboratory testing—for virologists and other microbiologists, “a fuller catalog of these organisms is now available to advance scientific understanding of how viruses evolve,” said Dark Daily Editor-in-Chief Robert Michel.
“While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively unstudied,” wrote four microbiologists from Ohio State University (OSU) who participated in the study in an article they penned for The Conversation.
In contrast to the better-understood DNA virus, an RNA virus contains RNA instead of DNA as its genetic material, according to Samanthi Udayangani, PhD, in an article she penned for Difference Between. Examples of RNA viruses include:
One major difference, she explains, is that RNA viruses mutate at a higher rate than do DNA viruses.
The OSU scientists identified the new species by analyzing a database of RNA sequences from plankton collected during a series of ocean expeditions aboard a French schooner owned by the Tara Ocean Foundation.
“Plankton are any aquatic organisms that are too small to swim against the current,” the authors explained in The Conversation. “They’re a vital part of ocean food webs and are common hosts for RNA viruses.”
The team’s screening process focused on the RNA-dependent RNA polymerase (RdRp) gene, “which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells,” according to the OSU news story.
“RdRp is supposed to be one of the most ancient genes—it existed before there was a need for DNA,” Zayed said.
The RdRp gene “codes for a particular protein that allows a virus to replicate its genetic material. It is the only protein that all RNA viruses share because it plays an essential role in how they propagate themselves. Each RNA virus, however, has small differences in the gene that codes for the protein that can help distinguish one type of virus from another,” the study authors explained.
The screening “ultimately identified over 44,000 genes that code for the virus protein,” they wrote.
Identifying Five New Phyla
The researchers then turned to machine learning to organize the sequences and identify their evolutionary connections based on similarities in the RdRp genes.
“The more similar two genes were, the more likely viruses with those genes were closely related,” they wrote.
The technique classified many of the sequences within the five previously known phyla of RNA viruses:
But the researchers also identified five new phyla—including two dubbed “Taraviricota” and “Arctiviricota”—that “were particularly abundant across vast oceanic regions,” they wrote. Taraviricota is named after the Tara expeditions and Arctiviricota gets its name from the Arctic Ocean.
They speculated that Taraviricota “might be the missing link in the evolution of RNA viruses that researchers have long sought, connecting two different known branches of RNA viruses that diverged in how they replicate.”
In addition to the five new phyla, the researchers are proposing at least 11 new classes of RNA viruses, according to the OSU story. The scientists plan to issue a formal proposal to the International Committee on Taxonomy of Viruses (ICTV), the body responsible for classification and naming of viruses.
Studying RNA Viruses Outside of Disease Environments
“As the COVID-19 pandemic has shown, RNA viruses can cause deadly diseases. But RNA viruses also play a vital role in ecosystems because they can infect a wide array of organisms, including microbes that influence environments and food webs at the chemical level,” wrote the four study authors in The Conversation. “Mapping out where in the world these RNA viruses live can help clarify how they affect the organisms driving many of the ecological processes that run our planet. Our study also provides improved tools that can help researchers catalog new viruses as genetic databases grow.”
This remarkable study, which was partially funded by the US National Science Foundation, will be most intriguing to virologists and microbiologists. However, clinical laboratories also should be interested in the fact that the catalog of known viruses has just expanded by 5,500 types of RNA viruses.
On top of everything else during this pandemic, drug-resistant infections are threatening the most vulnerable patients in COVID-19 ICUs
New study by researchers at the University of Minnesota highlights the continuing need for microbiologists and clinical laboratories to stay alert for COVID-19 patients with drug-resistant infections. In their study, researchers highlighted CDC statistics about the number of Candida auris (C. auris) infections reported in the United States during 2020, for example.
Candida auris is a particularly nasty fungus. It spreads easily, is difficult to remove from surfaces, and can kill. Worst of all, modern drugs designed to combat this potentially deadly fungus are becoming less effective at eradicating it, and COVID-19 ICU patients appear especially vulnerable to C. auris infections.
COVID-19 and C. auris a Potentially Devastating Combination
Hospitals in many areas are at a critical capacity. Thus, hospital-acquired infections such as sepsis can be particularly dangerous for COVID-19 patients. Adding to the problem, C. auris requires special equipment to identify, and standard medical laboratory methods are not always enough. Misidentification is possible, even probable.
A paper in the Journal of Global Antimicrobial Resistance (JGAR), titled, “The Lurking Scourge of Multidrug Resistant Candida Auris in Times of COVID-19 Pandemic,” notes that “A particularly disturbing feature of COVID-19 patients is their tendency to develop acute respiratory distress syndrome that requires ICU admission, mechanical ventilation, and/or extracorporeal membrane oxygenation. … This haunting facet of COVID-19 pandemic has severely challenged even the most advanced hospital settings. Yet one potential confounder, not in the immediate attention of most healthcare professionals, is the secondary transmission of multidrug resistant organisms like the fungus Candida auris in COVID-19 ICUs. … C. auris outbreaks occur in critically ill hospitalized patients and can result in mortalities rates ranging from 30% to 72%. … Both C. auris and SARS-CoV-2 have been found on hospital surfaces including on bedrails, IV poles, beds, air conditioner ducts, windows and hospital floors. Therefore, the standard COVID-19 critical care of mechanical ventilation and protracted ventilator-assisted management makes these patients potentially susceptible to colonization and infections by C. auris.”
One study mentioned in the JGAR paper conducted in New Delhi, India, looked at 596 cases where patients were admitted to the ICU with COVID-19. Fifteen of them had infections caused by C. auris. Eight of those patients died. “Of note, four patients who died experienced persistent fungemia and despite five days of micafungin therapy, C. auris again grew in blood culture,” according to reporting on the study in Infection Control Today (ICT).
Some C. auris mortality rates are as high as 72%. And patients with weakened immune systems are at particular risk, “making it an even more serious concern when 8% to 9% of roughly 530,000 ICU patients in the United States have COVID-19,” ICT reported.
Apparently, the COVID-19 pandemic has created circumstances that are particularly suited for C. auris to spread. “Given the nosocomial transmission of SARS-CoV-2 by those infected, many hospital environments may serve as venues for C. auris transmission as it is a known environmental colonizer of ICUs,” wrote the JGAR paper authors.
CDC Reports and Recommendations
Along with being especially dangerous for people with weakened immune systems, C. auris infections also produce symptoms similar to those of COVID-19, “including fever, cough, and shortness of breath,” according to the CDC’s website. People admitted to ICUs with COVID-19 are especially vulnerable to bacterial and fungal co-infections. “These fungal co-infections are reported with increasing frequency and can be associated with severe illness and death,” says the CDC.
C. auris outbreaks in the United States have mostly been in long-term care facilities, but the pandemic seems to be changing that and more outbreaks have been detected in acute care facilities, the CDC reported. The lack of appropriate personal protective equipment (PPE), changes in infection control routines, and other factors could be to blame for the increase.
Just as community spread is an issue with COVID-19 variants, so too is it a concern with C. auris infections. “New C. auris cases without links to known cases or healthcare abroad have been identified recently in multiple states, suggesting an increase in undetected transmission,” the CDC noted.
As of January 19, 2021, according to the CDC the case count of C. auris infections in the US was 1,625, with California, Florida, Illinois, New Jersey, and New York having more than 100 cases each.
Using Clinical Laboratory Tests to Identify C. Auris
One of the big concerns about C. auris is that it is so difficult to detect, and that medical laboratories in some countries simply do not have the technology and resources to identify and tackle the infection.
“As C. auris diagnostics in resource-limited countries is yet another challenge, we feel that alerting the global medical community about the potential of C. auris as a confounding factor in COVID-19 is a necessity,” wrote the authors of the paper published in the Journal of Global Antimicrobial Resistance.
As if the COVID-19 pandemic has not been enough, drug resistant bacteria, viruses, and deadly fungi are threatening to wreak havoc among SARS-CoV-2 infected patients. Microbiologists and medical laboratory scientists know that testing for all types of infections is vitally important, but especially when it comes to infections caused by antibiotic-resistant bacteria (ARB) and other dangerous organisms that demonstrate antimicrobial resistance (AMR).
Microbiologists and clinical laboratory professionals will want to stay informed about the number of C. auris cases identified in the US and the locations and settings where the fungus was detected. They will want to be on the alert within their hospitals and health networks, as well as with the doctor’s offices served by their labs.
AccuWeather interviewed experts, including pathologists who have analyzed the virus, who say SARS-CoV-2 is susceptible to heat, light, and humidity, while others study weather patterns for their predictions
AccuWeather, as it watched the outbreak of SARS-CoV-2, the novel coronavirus that causes COVID-19, wanted to know what effect that warmer spring temperatures might have on curbing the spread of the virus. There is a good reason to ask this question. As microbiologists, infectious disease doctors, and primary care physicians know, the typical start and end to every flu season is well-documented and closely watched.
As SARS-CoV-2 ravages countries around the world, clinical pathologists and microbiologists debate whether it will subside as temperatures rise in Spring and Summer. Recent analyses suggest it may indeed be a seasonal phenomenon. However, some infectious disease specialists have expressed skepticism.
CNN reported that Nicholls was part of a research team which reproduced the virus in January to study its behavior and evaluate diagnostic tests. Nicholls was also involved in an early effort to analyze the coronavirus associated with the 2003 SARS outbreak involving SARS-CoV, another coronavirus that originated in Asia.
“Sunlight will cut the virus’ ability to grow in half, so the half-life will be 2.5 minutes and in the dark it’s about 13 to 20,” Nicholls told AccuWeather. “Sunlight is really good at killing viruses.” And that, “In cold environments, there is longer virus survival than warm ones.” He added, “I think it will burn itself out in about six months.”
Can Weather Predict the Spread of COVID-19?
Other researchers have analyzed regional weather data to see if there’s a correlation with incidence of COVID-19. A team at the Massachusetts Institute of Technology (MIT) found that the number of cases has been relatively low in areas with warm, humid conditions and higher in more northerly regions. They published their findings in SSRN (formerly Social Science Research Network), an open-access journal and repository for early-stage research, titled “Will Coronavirus Pandemic Diminish by Summer?”
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The MIT researchers found that as of March 22, 90% of the
transmissions of SARS-CoV-2 occurred within a temperature range of three to 17
degrees Celsius (37.4 to 62.6 degrees Fahrenheit) and an absolute humidity
range of four to nine grams per cubic meter. Fewer than 6% of the transmissions
have been in warmer climates further south, they wrote.
“Based on the current data on the spread of [SARS-CoV-2], we
hypothesize that the lower number of cases in tropical countries might be due
to warm humid conditions, under which the spread of the virus might be slower
as has been observed for other viruses,” they wrote.
In the US, “the outbreak also shows a north-south divide,”
with higher incidence in northern states, they wrote. The outliers are Oregon,
with fewer than 200 cases, and Louisiana, where, as of March 22, approximately
1,000 had been reported.
There’s been a recent spike in reported cases from warmer
regions in Asia, South America, and Africa, but the MIT researchers attribute
this largely to increased testing.
Still, “there may be several caveats to our work,” they
wrote in their published study. For example, South Korea has been engaged in
widespread testing that includes asymptomatic individuals, whereas other
countries, including the US, have limited testing to a narrower range of
people, which could mean that more cases are going undetected. “Further, the
rate of outdoor transmission versus indoor and direct versus indirect
transmission are also not well understood and environmental related impacts are
mostly applicable to outdoor transmissions,” the MIT researchers wrote.
Even in warmer, more humid regions, they advocate “proper
quarantine measures” to limit the spread of the virus.
The New York Times (NYT) reported that other recent studies have shown a correlation between weather conditions and the incidence of COVID-19 outbreaks as well, though none of this research has been peer reviewed.
Why the Correlation? It’s Unclear, MIT Says
Though the MIT researchers found a strong relation between
the number of cases and weather conditions, “the underlying reasoning behind
this relationship is still not clear,” they wrote. “Similarly, we do not know
which environmental factor is more important. It could be that either
temperature or absolute humidity is more important, or both may be equally or
not important at all in the transmission of [SARS-CoV-2].”
Some experts have looked at older coronaviruses for clues. “The coronavirus is surrounded by a lipid layer, in other words, a layer of fat,” said molecular virologist Thomas Pietschmann, PhD, Director of the Department for Experimental Virology at the Helmholtz Center for Infection Research in Hanover, Germany, in a story from German news service Deutsche Welle. This makes it susceptible to temperature increases, he suggested.
However, Pietschmann cautioned that because it’s a new
virus, scientists cannot say if it will behave like older viruses. “Honestly
speaking, we do not know the virus yet,” he concluded.
How should pathologists and clinical laboratories in this country prepare for COVID-19? Lipsitch wrote that Influenza does tend to be seasonal, in part because cold, dry air is highly conducive to flu transmission. However, “for coronaviruses, the relevance of this factor is unknown.” And “new viruses have a temporary but important advantage—few or no individuals in the population are immune to them,” which means they are not as susceptible to the factors that constrain older viruses in warmer, more humid months.
So, we may not yet know enough to adequately prepare for
what’s coming. Nevertheless, monitoring the rapidly changing data on COVID-19
should be part of every lab’s daily agenda.