Zombie cells in the sea: Viruses keep the most common marine bacteria in check

MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

 

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SUNSET OVER THE ISLAND OF HELGOLAND IN THE GERMAN BIGHT, WHERE THE RESEARCHERS FROM THE MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY OBTAINED THEIR SAMPLES.

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CREDIT: JAN BRÜWER/MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY

The ocean waters surrounding the German island of Helgoland provide an ideal setting to study spring algae blooms, a focus of research at the Max Planck Institute for Marine Microbiology since 2009. In a previous study, the Max Planck scientists observed a group of bacteria called SAR11 to grow particularly fast during these blooms. However, despite their high growth rates, the abundance of SAR11 decreased by roughly 90% over five days. This suggested that the cells were quickly decimated by predators and/or viral infections. Now, the Max Planck researchers investigated what exactly lies behind this phenomenon.

Finding the phages infecting SAR11

“We wanted to find out if the low numbers of SAR11 were caused by phages, that is viruses that specifically infect bacteria”, explains Jan Brüwer, who conducted the study as part of his doctoral thesis. “Answering this seemingly simple question was methodologically very challenging”.

How does phage infection work? Phages infect bacteria by introducing their genetic material into them. Once there, it replicates, and utilizes the bacterial ribosomes to produce the proteins it needs. Researchers from Bremen used a technology that enabled them to “follow” the phage’s genetic material inside the cell. “We can stain the specific phage genes and then see them under the microscope. Since we can also stain the genetic material of SAR11, we can simultaneously detect phage-infected SAR11 cells”, explains Jan Brüwer.

While this might seem straightforward, the low brightness and small size of the phage genes made it challenging for researches to detect them. Nonetheless, thousands of microscope images were successfully analyzed, bringing some exciting news.  

“We saw that SAR11 bacteria are under massive attack by phages”, says Jan Brüwer. “During periods of rapid growth, such as those associated with spring algae blooms, nearly 20% of the cells were infected, which explains the low cell numbers. So, phages are the missing link explaining this mystery.”

Zombie cells: A global phenomenon

To the surprise of the scientists, the images revealed even more. "We discovered that some of the phage-infected SAR11 cells no longer contained ribosomes. These cells are probably in a transitional state between life and death, thus we called them 'zombie' cells”, Brüwer explains.

Zombie cells represent a novel phenomenon observed not only in pure SAR11 cultures but also in samples collected off Helgoland. Furthermore, analysis of samples from the Atlantic, Southern Ocean, and Pacific Ocean revealed the presence of zombie cells, indicating this phenomenon occurs worldwide.

“In our study, zombie cells make up to 10% of all cells in the sea. The global occurrence of zombie cells broadens our understanding of the viral infection cycle”, Brüwer emphasizes. “We suspect that in zombie cells, the nucleic acids contained in the ribosomes are being broken down and recycled to make new phage DNA.”

Brüwer and his colleagues hypothesize that not only SAR11 bacteria, but also other bacteria, can be turned into zombies. Thus, they want to further investigate the distribution of zombie cells and their role in the viral infection cycle.

“This new finding proves that the SAR11 population, despite dividing so fast, is massively controlled and regulated by phages”, stresses Brüwer. “SAR11 is very important for global biogeochemical cycles, including the carbon cycle, therefore their role in the ocean must be redefined. Our work highlights the role of phages in the marine ecosystem and the importance of microbial interactions in the ocean”.

Infected cells and zombie cells 

Under the microscope, scientists identified SAR11 zombie cells by their distinct lack of ribosomes. In an example comparing a live, infected SAR11 cell to an infected zombie cell: blue indicates bacterial DNA, yellow shows ribosomes, and purple highlights phage genes. The live cell (upper pictures) displays all three colors, while the zombie cell (lower pictures) lacks the yellow ribosome signal. The final column of images on the right merges these colors, clearly distinguishing the two cell types.

CREDIT

Jan Brüwer/Max Planck Institute for Marine Microbiology

JOURNAL

Nature Communications

DOI

10.1038/s41467-024-48172-w 

ARTICLE TITLE

Globally occurring pelagiphage infections create ribosome-deprived cells

LA REVUE GAUCHE - Left Comment: Search results for BACTERIOPHAGE 

 

Developing a vaccine for the “zombie drug” xylazine

Scripps Research chemical biologists design an early “proof-of-concept” vaccine that could lead to the first effective treatment of xylazine overdose in people

SCRIPPS RESEARCH INSTITUTE

LA JOLLA, CA—Xylazine is an FDA-approved sedative and pain reliever for use in animals, but it has severe adverse effects when used in humans. It is now illicitly being added to opioids, like fentanyl and heroin, as well as cocaine—leading to a sharp rise in overdose deaths.

Now, Scripps Research chemical biologists have developed a vaccine to block the effects of xylazine’s toxicity. The vaccine works by training the immune system to attack the drug, which is described in a new paper published in Chemical Communications on April 1, 2024.

“We demonstrated that a vaccine can reverse the symptoms of a xylazine overdose in rodents,” says study senior author Kim D. Janda, PhD, the Ely R. Callaway, Jr. Professor of Chemistry at Scripps Research. “There is currently no remedy for xylazine poisoning other than supportive care, thus, we believe our research efforts and the data we have provided will pave the way for an effective treatment in humans.”

The rapid increase in lethal drug overdoses attributed to xylazine combined with fentanyl prompted the White House Office of National Drug Control Policy to declare this combination an emerging threat to the United States. Xylazine intoxication presents similarly to opioid overdose, causing respiratory and central nervous system depression, and it can heighten the effects of opioids. However, naloxone—typically administered to reverse the effects of opioids—does not tackle the impact of xylazine, highlighting the need for effective measures to treat acute toxicity caused by xylazine.

Researchers suspect xylazine works by reducing blood flow to the brain, among other areas of the body. The drug also causes non-healing skin lesions and wounds, often located on the forearms and lower legs, that can require amputation in some cases—giving it the nickname “zombie drug.”

Although no treatment currently exists, targeted vaccines may offer a solution. Vaccines nudge the immune system to create antibodies to fend off invaders. Antibodies can target viruses, bacteria and toxins. However, sometimes molecules are too small to initiate an immune response, as is the case with xylazine. So, to circumvent this problem, the researchers created a vaccine using a design principle that Janda pioneered, which relies on pairing the drug molecule (called a hapten) with a larger carrier molecule (a protein) and an adjuvant.

In this study, the scientists combined a xylazine hapten with multiple different protein types, to see which combination would create a robust immune response against xylazine. The team tested three vaccine formulations (termed TT, KLH and CRM197, based on the protein involved) to see which vaccine cocktail could help rodents after being challenged with xylazine. One of the three vaccines (TT) significantly increased movement in mice given xylazine after 10 minutes, while two of the three vaccines (TT and KLH) led to an improvement in breathing.

The scientists also examined how these vaccines would limit xylazine blood brain barrier, (BBB) permeation, a filtering mechanism that scrutinizes drug penetration. When xylazine was injected, it immediately crossed into the brain to bind with receptors. Antibodies typically cannot navigate the BBB; however, two of the three vaccines (TT and KLH) showed a strong ability to stop xylazine from reaching its receptors in the brain, limiting its detrimental effects.

A provisional patent has been filed on the research. In the future, his team will build off this work to create a bifunctional antibody that will reverse both fentanyl and xylazine’s toxicity simultaneously, something that naloxone cannot do.

“A monoclonal antibody treatment could be given in tandem with the vaccine to provide both immediate and long-term protection from both opioid substance use disorders as well as opioid-xylazine overdoses,” says Janda. “This strategy could make a significant impact on the opioid epidemic.”  

“Evaluation of a Hapten Conjugate Vaccine Against the ‘Zombie Drug’ Xylazine” was co-authored by Mingliang Lin, Lisa M. Eubanks, Bin Zhou, and Kim D. Janda, all of Scripps Research.

Funding for the study was provided by the Shadek family and Pearson Foundation.

 

About Scripps Research

Scripps Research is an independent, nonprofit biomedical institute ranked one of the most influential in the world for its impact on innovation by Nature Index. We are advancing human health through profound discoveries that address pressing medical concerns around the globe. Our drug discovery and development division, Calibr, works hand-in-hand with scientists across disciplines to bring new medicines to patients as quickly and efficiently as possible, while teams at Scripps Research Translational Institute harness genomics, digital medicine and cutting-edge informatics to understand individual health and render more effective healthcare. Scripps Research also trains the next generation of leading scientists at our Skaggs Graduate School, consistently named among the top 10 US programs for chemistry and biological sciences. Learn more at www.scripps.edu.

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DOI

10.1039/D4CC00883A 

The couple trying to keep killer ‘zombie viruses’ at bay – and protect us from another pandemic

Simon Usborne
Sun, 18 February 2024 

Jean-Michel Claverie and Chantal Abergel in their laboratory just outside Marseille - Jeremy Suyker

Jean-Michel Claverie was already at retirement age when he travelled to Siberia to hunt for ancient viruses in the Arctic. After a long career as a research scientist – and 25 years since he had set up a laboratory outside Marseille with his wife Chantal Abergel – he could have put his feet up. He and Abergel, who is 62, commute to their lab from a comfortable house near the pretty harbour town of Cassis. But Claverie, who was about to turn 70, had no intention of hanging up his lab coat.

It took days, several flights and a ride in a rickety boat made from old war plane parts to reach the banks of the Kolyma river west of Chersky, a remote town not far from the East Siberian Sea. Once a transit hub for Soviet Gulags, Chersky and its river had become a magnet for scientists trying to unearth secrets from the frozen deep.

At a tight bend in the river he set up a makeshift research station inside a tent and from there, he and a small team began removing soil from the steep-sided riverbank to expose earth that has been frozen for 30,000 years.

A layer of this hardened soil and sand, known as permafrost, lies beneath the earth’s surface across vast areas of the northern hemisphere, largely in Arctic regions of Russia, Scandinavia and North America. In places such as Chersky, the permafrost stays below freezing even while the summers are hot and the surface landscape verdant. In some Arctic regions, life in this layer has been suspended for around 700,000 years.

But climate change and rising temperatures mean that permafrost is now thawing. As a result, powers including Russia, China and the US are stepping up efforts to drill and dig through it in pursuit of precious metals and fossil fuels.

Suspended within this thinning layer, however, are the preserved remnants of prehistoric life. Some of it – including viruses – may yet return from the dead with unknown consequences.

I meet Claverie, who is now 73 and wears blue jeans and running shoes, in the genomic and structural information lab at Aix-Marseille University, where he is now a professor emeritus. He and Abergel, an experimental biologist who runs the lab, lead an international team of a dozen researchers in a stout concrete building on a hilltop campus between Marseille and Cassis.

Claverie (pictured) points out that we still don’t know for certain what role viruses might have played in the demise of major species such as Neanderthals or woolly rhinos - Jeremy Suyker

Inside a small lab with a yellow biohazard danger sign on the door, alongside the logo for the Back to the Future film, Claverie pulls a small plastic bag out of a freezer. It contains what looks like the damp remains of a sandcastle. It is in fact thawed Siberian permafrost. During his two-week field trip, Claverie’s team used a drill with a cup-shaped coring bit to prize more than 20 such samples from the banks of the Kolyma. He brought them back to the French Riviera in his suitcase.

The team study these, as well as permafrost samples already stored in scientific institutes, in a race to understand the microbes suspended within them. While virology research tends to focus on threats lurking in more tropical climates, Claverie and Abergel are searching for potential dangers now emerging from the frozen north, including what have become known as ‘zombie viruses’.

‘The real danger would be to be confronted with viruses we’ve never seen before,’ Claverie tells me in the lab, where a low winter sun streams through a high window. He points out that we still don’t know for certain what role viruses might have played in the demise of major species such as Neanderthals or woolly rhinos.

And consider, he says, the huge efforts required to suppress pathogens already familiar to science, such as the coronaviruses. ‘So think about a totally new virus that might have caused [an] extinction. What happens if it comes back?’

Claverie and Abergel fell in love at a science conference in a French ski resort in 1987. They were both interested in the then emerging field of bioinformatics – the use of computers to make sense of biological data. In 1995, after working in the US for five years, the couple settled in Marseille, where Abergel had grown up, to establish their lab. They now have two grown-up sons – a chef and an engineer.

The couple occupy neighbouring offices above the labs. ‘We had to work together at home in the pandemic and Jean-Michel was upset because I was making too much noise,’ Abergel tells me at her desk, which is next to a vast potted Flamboyant tree she planted as a seed. ‘It is very capricious and has never flowered,’ she adds with a smile.

Abergel: 'We’re both stubborn and, like all scientists, we always think we’re right' - Jeremy Suyker

Claverie had enjoyed an early career as a nomadic researcher in multiple fields, including theoretical physics. The lab’s early work involved the sequencing of bacterial genomes – the genetic information that defines organisms. The switch to virus research was accidental. A sample that had originally come from a hospital in Bradford as part of a search for the origins of a pneumonia outbreak contained what scientists had assumed was a new type of bacteria. On closer inspection in Marseille, the bacteria turned out to be a virus that broke all the rules.

There are more viruses than stars in the universe and most remain undiscovered. They lurk anywhere there is life – in the sea, soil and air – but only replicate when they meet a host. They were always thought to be tiny and genetically simple, containing only what they needed to invade cells, replicate and move on. The new microbe from Bradford was orders of magnitude larger and more complex than any known virus. ‘I can still remember when we got the image from the microscope,’ Claverie recalls. ‘I said, “Jesus, what is this?!”’

They named it Mimivirus. The discovery stunned the field of virology, which was concerned largely with diseases caused by viruses in humans, livestock and agriculture. Viruses existing in the wild without a known host had flown under the radar. Mimivirus opened a new field of research. ‘This was the start of environmental virology,’ says Claverie, who quickly refocused his lab’s work.

For several years, the team discovered more giant viruses, which they helped detect by introducing amoebas to samples; if the single-cell organisms died, it signalled the presence of a virus and the need for further research. This work, which added to wider understanding of viruses and how they interact with hosts, found a new avenue in 2013 when Claverie read a Russian paper about the regeneration of a plant from fruit tissue that had been frozen in the Siberian permafrost for 30,000 years. ‘I thought, if they can revive a plant, can we revive a virus?’

The ground floor of the building in Marseille is divided into a series of modest labs, many cluttered with microscopes, chemicals, glass flasks and beakers. While Claverie is the de facto chief virus hunter, Abergel has led the development of the techniques used to isolate and study them. ‘We complement each other well, even if we sometimes fight,’ she says. ‘We’re both stubborn and, like all scientists, we always think we’re right.’

Machines and air-conditioning units hum in the background, maintaining climates for each stage of the process. One of the machines, called a ‘mosquito robot’, incorporates 96 needles capable of inserting virus proteins into wells containing different culture conditions. In another room, the amoebas that are used as bait to catch viruses are grown and stored. When a virus is detected in a sample, technicians purify and amplify it before its DNA can be sequenced.

Claverie can’t remember who first used the word ‘zombie’ in relation to his virus work. Certainly it did not appear in his landmark paper in 2014, which detailed the first revival of a virus preserved in permafrost. He named the microbe, which he found in an existing, 30,000-year-old sample taken from ground not far from Chersky, ‘Pithovirus sibericum’. Not long after the discovery, a specialist toy company made a stuffed Pithovirus, added a cute smile, and called it Zombie Virus. ‘The whole thing started going crazy,’ Claverie says.

A permafrost sample - Jeremy Suyker

The sci-fi name challenged Claverie’s academic instincts but it has also amplified his and Abergel’s research over a decade in which the climate crisis has become more urgent. The couple have continued to revive more than a dozen distinct viruses from permafrost, including in the last meals found in the frozen stomachs of woolly mammoths. In one case they reanimated a virus that had hibernated for 50,000 years.

None of these viruses would pose a risk to humans even beyond the controlled environment of the Marseille lab; they are specific to their amoeba hosts. But the scientists are anxious to raise awareness of potential threats that may still emerge. ‘If there are viruses that have been preserved for 50,000 years, there will probably be others from long before that,’ Claverie says. ‘The human species is only 200,000 years old. We don’t know what kind of viruses existed before that and we’re certain our immune systems were never exposed to them.’

There have been early warning signs of the health effects of climate change in the Arctic. In 2016, a young boy and thousands of livestock died in the Yamal-Nenets region of Russia when a reindeer that had been dead for decades thawed in a record heatwave, releasing the anthrax bacteria.

Scientists fear that centuries-old shallow graves that herders used for livestock (firewood being too scarce to burn carcasses) may become anthrax infection sites, although the disease is not contagious between people. Meanwhile, the DNA of the smallpox and influenza viruses has been detected in human corpses that had been frozen for over a century. Those samples were not revived and even the deadliest virus poses no threat if it remains locked in permafrost. But Claverie fears that this may be about to change.

Over the past four decades, the Arctic has warmed up four times faster than the global average – and up to seven times faster in parts of Norway and Russia. A doom loop known as Arctic amplification involves the absorption of more sunlight as a result of the loss of reflective ice, leading to further warming and melting.

View from Chersky stone hill, Siberia - Alamy Stock Photo

Melting ice is bad news for polar bears and other Arctic fauna but there is perhaps less awareness of the effects of thawing permafrost. Earth that has been frozen solid is turning to mud, causing giant sinkholes to open up. Phone lines, roads, airport runways and whole towns are at risk.

Meanwhile, the thawing of organic matter within permafrost is releasing vast quantities of methane, creating a second vicious cycle as the potent greenhouse gas exacerbates global warming. These effects strike fear into the hearts of scientists, but present opportunities to businesses and nations still struggling to break bad habits. Melting sea ice is opening up shipping routes to support growing industrial exploitation of thawing ground that is becoming more viable as a source of minerals and fuel.

Russian nuclear-powered icebreakers are supplying plants that make up the growing Yamal liquified natural gas project. In Norway, Canada and the US, prospectors are eyeing up Arctic ground for the precious and rare metals and minerals needed to power technology such as batteries for electric vehicles. As workforces the size of large towns gather at these sites, Claverie worries about the potential threat of exposure to viruses that may be churned up in the course of drilling and digging.

‘There are a lot of sharks in Australia, but if you don’t go surfing, that’s fine,’ he says, reaching for a metaphor from an even warmer climate to illustrate the point that there is no danger without exposure to an underlying hazard. ‘But now, with the development of industrial activities in the Arctic, we are going to have contact with these things.’

Then there are the effects of Covid. The pandemic has been positive for investment in viral research, but Claverie is also concerned that this is bringing us closer to danger. Parts of the scientific community are going out in search of exotic viruses that they know are deadly to humans. Yet one bite from a bat in the field, or a slip of a needle, is all it can take for a disastrous outbreak to occur.

Claverie shows me two photos from an Arctic research centre in which a baby mammoth carcass is laid out on a slab. In the official image, scientists wear masks and full-body protective suits. In another snap taken privately, a small crowd in everyday clothing gathers around the animal as if it were an item on Antiques Roadshow. ‘There are scientists in Russia who are already trying to revive viruses that infected mammoths and woolly rhinos,’ the professor adds. ‘This is totally stupid and dangerous. You do not revive viruses that infect animals.’

Jean-Michel Claverie was nearly 70 when he travelled to Siberia to study 'zombie viruses' - Jeremy Suyker

Claverie is part of an increasingly vocal campaign within the science community to prioritise surveillance over prospecting, finding sick patients early rather than investing millions in the risky search for pathogens in the wild. The Marseille lab is now part of UArctic, a consortium of educational institutes that is working to establish a monitoring network and quarantine protocols in the event of an infection from a permafrost virus. ‘The idea is that you capture the virus before it becomes a pandemic.’

Yet scientific cooperation with Russia, which has the largest share of permafrost (two-thirds of the country sits above it), has been on ice since the invasion of Ukraine in 2022, blocking access to researchers and samples. Claverie is worried about this collaborative breakdown, as well as Putin’s disregard for climate targets and rush to exploit Arctic resources. ‘My trip was funded partly by the Russian Academy of Sciences,’ he says. ‘Those things don’t exist any more, they are frozen.’

Up in Claverie’s own office, fragments of mammoth bones sit on a bookshelf. The professor smuggled them out of Russia along with his permafrost samples in 2019. He is glad he was able to make it to Siberia before the pandemic and the Ukraine invasion. Either way, he sees no reason to return now he has proved his point: that the world should be alert to the viruses that may be released from thawing permafrost.

He has grave concerns about the future but does not come across as a doomsayer; he is driven by a natural curiosity and passion for science. Work at the lab goes on to find viruses in existing samples, including thousands stored at a polar research institute near Hamburg. Meanwhile, he has expanded his interest south to Antarctica.

He tells me he has already made promising discoveries in samples of sediment he asked scientists on an Italian research vessel to retrieve from beneath the Ross Sea in 2022. Only a last-minute change of the expedition’s budget prevented him from travelling to the frozen south himself. As he sails through his notional retirement in Marseille, he says Abergel’s relative youth, apart from anything else, keeps him working. ‘Perhaps when she retires I will stop, but until then I’m not going to go on a cruise by myself,’ he says, before returning to his screen.

 

It's award season: let's celebrate microbes in movies

A review in FEMS Microbiology Letters by Professor Manuel Sanchez from UMH (Spain) reveals how movies can raise public awareness and appreciation of the world of microbiology

Peer-Reviewed Publication

UNIVERSIDAD MIGUEL HERNANDEZ DE ELCHE

 

IMAGE: 

DEAD ANT INFECTED WITH OPIOCORDYCEPS UNILATERALIS, BY DAVID P. HUGHES, MAJ-BRITT PONTOPPIDAN. WIKIMEDIA COMMONS / PEDRO PASCAL AND BELLA RAMSEY IN THE HBO SERIES "THE LAST OF US" (2023).

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CREDIT: UMH

Elche (Spain), January 22, 2024. Usually, show business depicts viruses, bacteria, and other microorganisms as one of the worst menaces to humankind. Entertainment movies influence the way audiences understand and perceive these topics. Yet, few films accurately portray the science of microbiology and its social implications. Movies and TV series often feature outbreaks of deadly diseases and the efforts of scientists and medical professionals to contain them. However, entertainment movies can also educate the public about the importance and the impact those microorganisms have on our lives. A new publication in FEMS Microbiology Letters provides insights and examples to teach microbiology concepts to undergraduate students. Manuel Sanchez is a Microbiology professor at the Miguel Hernandez University of Elche. He's been using movies in class for many decades. He finds students can learn complex scientific concepts easily when integrated into a story. The expert has recently published a review in FEMS Microbiology Letters to show the relationship between movies and microbiology, from the fight against diseases such as AIDS or tuberculosis to the zombie apocalypse. "Maybe one day the Academy of Motion Picture Arts and Sciences will honor an Oscar award for microbes", writes Sanchez. According to the Internet Movie Database (IMDB), as of June 2023, there were 2,502 titles related to the keyword' virus', 184 related to 'bacteria', and 760 to 'infection'. For example, without viruses, we would not have such cinematic characters as the zombies that try to eat Brad Pitt and his family in "World War Z" or the cool vampires from the "Blade" saga. But are microbes villains, or are they heroes? Although microbes do much more good than harm in nature, this aspect is rarely represented on screen. Professor Sanchez explains that some film productions, especially recent ones, take great care in enrolling scientific advisors to have the most plausible and realistic scripts. However, in most occasions, that situation does not occur, so making a virtue out of necessity, movie goofs such as the scene from "Mission: Impossible II" where a flu virus infects a red blood cell, can be seen as an opportunity to explain the concept and conditions of viral host recognition to undergraduate students. Movies can be used in the classroom in two ways, depending on the time available. Students can watch the whole film as an external activity and then discuss its content in class. Another option is to use clips of selected scenes related to the subject to be addressed. For example, in minute 19 of "Dallas Buyers Club", a medical doctor (Jennifer Garner) explains to her AIDS patient (Matthew McConaughey) what is a double-blind clinical trial. This scene can be used as an introduction to a class about bioethics and/or drug development. Another example is the sequence at minute 74 from the movie "Panic in the Streets", which can be used to explain the 'One Health' concept, thanks to the following dialogue: Community? What community? Do you think you're living in the Middle Ages? Anybody that leaves here can be in any city in the country within 10 hours. I could leave here today and be in Africa tomorrow. And whatever disease I had would go with me… Then think of it when you're talking about communities! We're all in a community…the same one! Professor Sanchez's review can be helpful for teachers looking for such learning material. The paper is organized into three major sections, providing insights and examples of movies and TV/streaming series telling stories involving real diseases, others about the role of scientists, and feature films about the apocalyptic results of microbial infection. The first section is dedicated to the real infectious diseases represented on the screen. Commercial movies are better known to the general public than documentaries, so they could be used to explain the symptoms of the illness and other aspects, such as the care of the sick or the impact of the disease in a particular historical moment or in our current society. For example, in "The African Queen" (John Huston, 1951), Charlie, Humphrey Bogart's character, is bitten by a mosquito and is affected by malaria. Spoiler alert: he survives, unlike Giovanni de Medici in "Il mestiere delle armi" ("The Profession of Arms, Ermanno Olmi, 2001). A second section is dedicated to movies where the protagonists are the scientists and medical doctors who fight against microbial diseases. In this case, the main concepts to be explained are scientific methods and biocontainment measures. For example, "Outbreak" (Wolfgang Petersen, 1995) is so full of scientific mistakes that it's actually amusing to dissect. Also, the stereotype of the scientist has evolved from the solitary, dedicated hero of the 1930s to today's interdependent groups of highly technical researchers. Finally, the last part deals with the films in which microbes manage to defeat humanity, creating a dystopian world. Movies and series like "I Am Legend" (Danny Boyle, 2002), "28 Days Later", or "The Last of Us" (Neil Druckmann and Craig Mazin, 2023) are well known by the public and can be used to explain key concepts in epidemiology and disease transmission but also how to deal with highly stressful situations. Professor Sanchez is a microbiologist and science communicator. He has written several books regarding this subject and articles about microbiology in popular culture for The Conversation.

JOURNAL FEMS Microbiology Letters

DOI https://doi.org/10.1093/femsle/fnad129

ARTICLE TITLE Microbial pathogens in the movies

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JOURNAL

FEMS Microbiology Letters

DOI

10.1093/femsle/fnad129 

METHOD OF RESEARCH

Content analysis

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Microbial pathogens in the movies

ICYMI
Ancient zombie viruses in melting permafrost could cause new pandemic, scientists warn

Andy Gregory
Sun, 21 January 2024 

Ancient “zombie viruses” frozen in melting Arctic permafrost could fuel a new pandemic if unleashed by climate change, scientists have warned.

Global heating is enabling increased human activity in the Earth’s northernmost reaches, as melting sea ice opens up shipping and industrial possibilities, including mining deep into the permafrost which covers a fifth of the northern hemisphere, mainly in Canada, Siberia and Alaska.

But scientists have reportedly started to plan an Arctic monitoring network to watch out for any early cases of a disease sparked by ancient viruses, also known as Methusela microbes.

A cemetery sits on melting permafrost tundra at the Yupik Eskimo village of Quinhagak in Alaska (Mark Ralston/AFP via Getty Images)


Ancient viruses have already been found in Siberian permafrost, including one sample which was 48,500 years old. A team led by geneticist Jean-Michel Claverie has revived several such viruses, capable of infecting only single-cell organisms.

But the scientist fear viruses capable of infecting humans likely also lurk in the permafrost. “We see the traces of many, many, many other viruses,” Professor Claverie told CNN in March, adding: “If the amoeba viruses are still alive, there is no reason why the other viruses will not be still alive, and capable of infecting their own hosts.”

As a result, Prof Claverie is among scientists working with the University of the Arctic network on plans to establish quarantine facilities and provide medical expertise that could pinpoint and attempt to treat any early cases without them leaving the region, according to The Observer.

“At the moment, analyses of pandemic threats focus on diseases that might emerge in southern regions and then spread north,” Prof Claverie, of Aix-Marseille University in France, told the paper. “By contrast, little attention has been given to an outbreak that might emerge in the far north and then travel south – and that is an oversight, I believe.

“There are viruses up there that have the potential to infect humans and start a new disease outbreak.” Among the genomic traces of human pathogens identified already by the team in Siberian permafrost are pox viruses and herpes viruses, he said.

According to scientists, Alaska has been warming twice as fast as the global average (Mark Ralston/AFP via Getty Images)

Virologist Marion Koopmans agreed, telling the paper: “We don’t know what viruses are lying out there in the permafrost but I think there is a real risk that there might be one capable of triggering a disease outbreak – say of an ancient form of polio. We have to assume that something like this could happen.”

With forecasts suggesting the Arctic Sea will be ice-free as early as 2040 due to climate breakdown, it is the prospect of increased human activity in the Arctic, as opposed to melting permafrost, which most concerns Prof Claverie.

“Huge mining operations are being planned, and are going to drive vast holes into the deep permafrost to extract oil and ores,” he said. “Those operations will release vast amounts of pathogens that still thrive there. Miners will walk in and breath the viruses. The effects could be calamitous.”

“Our immune systems may have never been in contact with some of those microbes, and that is another worry,” said Prof Claverie. “The scenario of an unknown virus once infecting a Neanderthal coming back at us, although unlikely, has become a real possibility.”

Prof Koopmans added: “If you look at the history of epidemic outbreaks, one of the key drivers has been change in land use. Nipah virus was spread by fruit bats who were driven from their habitats by humans. Similarly, monkeypox has been linked to the spread of urbanisation in Africa.

“And that is what we are about to witness in the Arctic: a complete change in land use, and that could be dangerous, as we have seen elsewhere.”

LA REVUE GAUCHE - Left Comment: Search results for permafrost 

LA REVUE GAUCHE - Left Comment: Search results for melting permafrost 

LA REVUE GAUCHE - Left Comment: Search results for ZOMBIE VIRUSES 

‘Resurrection biology’ scientists work to bring back extinct dodo, study ancient ‘zombie viruses’

By Patrick Reilly
Published Dec. 26, 2023, 

Scientists around the world are working to revive ancient ice-capsulated cells to find new sources of life-saving medicine and possibly bring back a long-extinct species, like the dodo bird.

The science, called resurrection biology, has made immense progress over the past year as researchers in the field turn to the past for solutions for the future, CNN reported.

While the scientists aren’t looking to bring back the dinosaurs à la Jurassic Park — although some have goals to resurrect lost plant and animal species — they hope studying the prehistoric cells can reveal new sources for drugs as well as ways to thwart dangerous long-dormant pathogens.

The research also offers a look into human history and how our ancestors lived and died thousands of years ago, according to CNN.

Resurrection biology scientists work on “zombie viruses” found in ancient ice, including the ancient “pandora” virus from thawing permafrost pictured here.

Jean-Michel Claverie/IGS/CNRS-AM

Jean-Michel Claverie, a professor emeritus of medicine and genomics at the Aix-Marseille University School of Medicine in Marseille, France, has been identifying possible “zombie viruses” lurking in the permafrost of Siberia.

Viruses that have been buried for tens of thousands of years could come back and potentially devastate life on Earth as global temperatures rise and the ice melts.

In 2014, Claverie isolated a virus researchers found in the permafrost and revived it by inserting it into cultured cells — making it infectious for the first time in 30,000 years, according to CNN.

Then this past February, he and his team isolated several strains of an ancient virus from multiple samples of Earth representing five new families of previously unknown viruses. They only infected single-cell organisms with the virus in their research as a safety precaution. The samples dated between 48,500 and 27,000 years old.

These zombie viruses pose a significant threat to humanity, Claverie told CNN.

“We view these amoeba-infecting viruses as surrogates for all other possible viruses that might be in the permafrost,” the professor said.

Environmental virologist Jean-Michel Claverie has been identifying viruses dormant for years in the arctic ice. SVFU

“Our reasoning is that if the amoeba viruses are still alive, there is no reason why the other viruses will not be still alive, and capable of infecting their own hosts.”

Other “resurrection biologists” are studying the ancient specimens as a potential source for antibiotics to fight pathogens that have become increasingly resistant to overused conventional treatments.

César de la Fuente, Presidential Assistant Professor at the University of Pennsylvania, and his team of researchers are analyzing genetic information from Neanderthals and extinct animal species to find small protein or peptide molecules they believe to have bacteria-fighting powers.

“Bacteria from today have never faced those molecules so they may give us a better opportunity at targeting the pathogens that are problematic today,” de la Fuente told CNN.

More ambitiously, biotechnology and genetic engineering startup Colossal Biosciences announced this year its plan to revive the dodo — a flightless bird that has been extinct since the 17th century — and reintroduce it to its natural habitat on the island of Mauritius in the Indian Ocean.

Scientists have located viruses tens of thousands of years old in the Siberian permafrost.

AFP via Getty Images

The company is also using groundbreaking DNA sequencing, gene-editing technology and synthetic biology to try to bring back the ice age giant woolly mammoth and the Tasmanian tiger, which went extinct from Australia in the last century.

In their efforts to resurrect the dodo, geneticists discovered cells that act as progenitors for reproductive organs — known as primordial germ cells, or PGCs — of the Nicobar pigeon, the dodo’s closest living relative, that can grow successfully in a chicken embryo, according to CNN.

Scientists will compare the genomes of the dodo and the also-extinct Rodrigues solitaire, a close relative to the dodo, and see how they differ. They will then edit the PGCs of a Nicobar pigeon to give it the physical characteristics of a dodo.

The cells will then be inserted into the embryos of a chicken and rooster, who will theoretically have offspring resembling the dodo.

“Physically, the restored dodo will be indiscernible from what we know of the dodo’s appearance,” Matt James, chief animal officer of Colossal Biosciences, told CNN last month.

If successful, the offspring will not be a true dodo — but rather a hybrid impression of the bird.

“Because of the complexity of recreating a species from DNA, even if it was possible, [it] can only result in a dodo-esque creature,” said Julian Hume, an avian paleontologist and research associate at London’s Natural History Museum.

“It will then take years of selective breeding to enhance a small pigeon into a large flightless bird. Remember, nature took millions of years for this to happen with the dodo,” he told CNN.

Watch drone delve into Siberia's growing 'gateway to the underworld,' the largest permafrost depression in the world

Jennifer Nalewicki
Tue, July 25, 2023 

A giant crater in Siberia covered in snow and ice.

A massive crater in Siberia dubbed the "gateway to the underworld" by locals is continuing to grow larger, new drone footage reveals.

The footage, which was released on July 12, offers viewers a bird's-eye view of the Batagay (also spelled Bagatayka and Batagaika) crater, considered to be the largest permafrost depression in the world, according to Ruptly.tv.

Covering approximately 0.3 square miles (0.8 square kilometers) — equivalent to the area of about 145 football fields — the deep scar cutting through the east Siberian woodlands was likely triggered by deforestation during the 1940s. This led to erosion, which then exacerbated seasonal melting of the permafrost and created a "megaslump," or the massive crater in the ground. Because the permafrost in this region is comprised of 80% ice, the large amounts of melting forced sediment on the hillside to collapse, revealing what looks like a giant gash slashing through the landscape in Russia's Sakha Republic.

Related: Zapotec 'entrance to the underworld' discovered under Catholic church in Mexico

And it's not just drone imagery that shows that the crater continues to expand. Over the years, satellite imagery has also confirmed that the megaslump has grown in size. As the land has retreated, it has revealed "tens of thousands of years of frozen remains," dating as far back as the Middle Pleistocene, which ended 126,000 years ago.

In one study, the melt allowed scientists to access bison meat that had been frozen for roughly 8,000 years, giving researchers new insight into animals and plants that once inhabited the region.

Scientists aren't sure exactly how quickly the crater is expanding. However, locals claim that in the last several years, it has grown between 66 feet and 98 feet (20 and 30 m) at certain points, according to NDTV, a TV station in New Delhi.

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"This is something very rare," Alexey Lupachev, a senior researcher at the Institute of Physicochemical and Biological Problems of Soil Science at the Russian Academy of Sciences, told Ruptly.tv. "This is a unique object of nature, which allows us to see the history of Earth over a period of half a million years preserved in permafrost."

Eight terrifying ancient 'zombie viruses' are spreading thanks to climate change

Some of the world's top scientists have banded together to warn about the impact climate change is having in releasing dangerous "zombie viruses" into the modern world

NEWS
By Adam Cailler

Journalist and wrestling lead

DAILY STAR, ZA

 4 JUN 2023

Jean-Michel Claverie (right) has warned of the dangers of the zombie viruses (Image: BBC)

Several top scientists are sounding the alarm bells after it emerged that eight potentially deadly “zombie viruses” are running rampant – without us even knowing about it.

And it is all down to climate change.

According to boffins in Russia, Germany and France, who got together to pen a new study into what happens when permafrost thaws, it was found that several deadly viruses are being released into the open air despite being trapped there since prehistoric times, various outlets report.

Speaking to Live Sciene, Jean-Michel Claverie, a computational biologist at Aix-Marseille University in France said: “We do not have formal proof that viruses other than amoeba-specific viruses could survive as long, but there would be no reason why not, because all viruses basically have the same property of being inert particles while outside their host cells.

Experts are analysing melted permafrost and the findings are worrying (stock) (Image: Nina Sleptsova / NEFU Press Service)
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“We do not wish to take the immense risk of starting a new pandemic with unknown 'zombie' viruses from the distant past just to demonstrate that we are right.

“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.”

The eight viruses experts believe are now posing a threat to the world are Pithovirus Sibericum, Mollivirus Sibericum, Pithovirus Mammoth, Pandoravirus Mammoth, Pandoravirus yedoma, Megavirus Mammoth, Pacmanvirus Lupus and Cedratvirus Lena.

Many of the zombie viruses can be traced back around 30,000 years (stock) (Image: UIG via Getty Images)

READ MORE Fresh pandemic fears as scientists chillingly try to awaken ancient viruses

Of those, the Pithovirus Sibericum is one of the biggest viruses ever found, measuring in at 1.5 micrometres long.

It was found in 2014, and is thought to be around 30,000 years old.

Mr Claverie said: “This is the first time we've seen a virus that's still infectious after this length of time.

“The ease with which these new viruses were isolated suggests that infectious particles of viruses specific to many other untested eukaryotic hosts [including humans and animals] probably remain abundant in ancient permafrost.”

Pithovirus sibericum is one of several zombie viruses found in the permafrost 

(Image: Jean-Michel Claverie/IGS/CNRS-AM)

READ MORE Coldest places in the world with -55C temperatures and polar bears by the pub

The virus is thought to be harmless to humans, but its impact on wildlife could be dangerous.

The Mollivirus Sibericum poses a significant risk to humans, as it is thought that it had a huge impact on ancient Siberian humans.

Mr Claverie said: “We cannot rule out that distant viruses of ancient Siberian human (or animal) populations could re-emerge as arctic permafrost layers melt and/or are disrupted by industrial activities.”

Melting permafrost is posing a huge danger to the world (Image: Getty Images)

READ MORE 'Rage zombie outbreak plausible' after 48,000-year-old virus revived in Russia

Pandoravirus Yedoma has previously been found to kill amoeba cells, and is thought to be around 48,500 years old, while Megavirus Mammoth is another that infects amoebas.

No human cases of these viruses have been found yet, but the experts are under the impression that the more permafrost thaws, the greater the chances of that happening are.

Does the revival of 'Zombie Viruses' pose a legitimate health threat?


As global temperatures rise, permafrost is melting rapidly, unearthing a host of ancient viruses and bacteria — a troubling scenario that poses a risk to public health.

Zombie viruses from permafrost may sound like the plot of a horror movie, but they are a real public health threat as the Arctic thaws due to climate crisis.

Scientists have revived ancient viruses from permafrost and discovered they could still infect living single-celled amoebae.

While it is unclear whether these viruses could infect animals or humans, the researchers assert that permafrost viruses should be considered a public health threat.

Permafrost is a layer of soil that remains completely frozen year-round, covering 15 percent of the land in the Northern Hemisphere. However, due to human activities, global temperatures are rising, causing permafrost to melt rapidly.

This phenomenon is unearthing a host of ancient relics from viruses and bacteria to woolly mammoths and an impeccably preserved cave bear.

READ MORE: NASA: Antarctica losing ice faster than thought

'Reviving zombie viruses'

In 2014, French professor Jean-Michel Claverie started publishing research on reviving ancient viruses, or "zombie viruses" as he calls them.

He found strains of the frozen virus from a few permafrost sites in Siberia.

The oldest strain, which dated back 48,500 years, came from a sample of soil from an underground lake, while the youngest samples were 27,000 years old.

One of the young samples was discovered in the carcass of a wooly mammoth.

Claverie and his team were able to revive several new strains of "zombie" viruses and found that each one could still infect cultured amoebas.

He said this should be regarded as both a scientific curiosity and a concerning public health threat.

READ MORE: 'Climate change 'multiplies' Siberian heatwave 600 times


Risk of ancient bacteria

It's not just viruses. Ancient bacteria, too, could be released and reactivated for the first time in up to two million years as permafrost thaws.

That's what happened, scientists think, when outbreaks of the bacterial infection anthrax appeared in humans and reindeer in Siberia in 2016.

That may be a "more immediate public health concern," according to Claverie.

The current research on frozen viruses like Claverie's 'zombie' virus is helping scientists understand more about how these ancient viruses function and whether, or not, they could potentially infect animals or humans.

Their findings make it clear that it is crucial that action is taken to address the climate crisis, in order to prevent the release of more ancient viruses and bacteria from the permafrost, which could have serious implications for global public health.

READ MORE: Billionaires turn to reap benefits from melting glaciers

Uh-Oh: ‘Zombie’ Viruses Hidden in Permafrost Now Revived


Tim Newcomb
Thu, March 9, 2023 

Ed Reschke - Getty Images

A French scientist is searching Siberian permafrost for “zombie viruses” and testing their abilities.


Viruses and chemical waste currently locked in permafrost could pose danger to humans if thaw releases them.


There’s also the potential for finding lost flowers and animals as permafrost recedes.

The Arctic tundra’s permafrost layer of soil has frozen long-lost animals and species of flowers. It has also preserved viruses for nearly 50,000 years. French scientist Jan-Michel Claverie is studying the world of viruses frozen in time has found “zombie viruses” that could be revived—and become infectious again—under the right conditions.

Claverie revived his first ancient virus in 2014, making it infectious again for the first time in tens of thousands of years. Don’t worry, the experiment posed no danger to humans—Claverie selected a virus only able to invade single-celled amoebas.


And he hasn’t stopped since. He and his team have continued to take frozen amoeba-infecting viruses from the permafrost soil layer and bring them back to an infectious stage. The most ancient of these viruses, based on carbon dating, was 48,500 years old.

This work highlights a serious issue the world will face if the arctic permafrost—which not only preserves the viruses by keeping them cold, but by protecting them from the destructive effects of oxygen and light—continues to dissipate. And considering the arctic is currently warming up to four times as fast as the rest of the world, it’s not a possibility that can be easily dismissed.

“We view these amoeba-infecting viruses as surrogates for all other possible viruses that might be in the permafrost,” Claverie tells CNN. “Our reasoning is that if the amoeba viruses are still alive, there is no reason why the other viruses will not be still alive, and capable of infecting their own hosts.”

In all, Claverie has revived seven families of viruses, and there’s evidence that viruses and bacteria able to infect humans also reside in the permafrost.

“If there is a virus hidden in the permafrost that we have not been in contact with for thousands of years, it might be that our immune defense is not sufficient,” Birgitta Evengård, professor emerita at Umea University’s Department of Clinical Microbiology in Sweden, tells CNN. “It is correct to have respect for the situation and be proactive and not just reactive.”

The dangers of these viruses are unknown, and there’s no real way of guessing just how a thawed virus or bacteria would fare upon release from deep freeze. “It’s not really an experiment,” Kimberley Miner, a climate scientist at the NASA Jet Propulsion Laboratory tells CNN, “that I think any of us want to run.”

With one-fifth of the Northern Hemisphere covered by permafrost, viruses aren’t the only concern if the rate of thaw continues. Scientists know that manmade problems, whether chemicals or even radioactive waste, could get liberated in a thaw as the climate changes.

“There’s a lot going on with the permafrost that is of concern,” Miner says, “and [it] really shows why it’s super important that we keep as much of the permafrost frozen as possible.”

Scientists revived a 'zombie' virus frozen for 48,500 years in ice. They learned it could still infect other cells.

Some experts believe climate change may increase the emergence of new animal-to-human transmitted diseases like COVID-19


Chris Panella,Morgan McFall-Johnsen
Thu, March 9, 2023 

A man walks through a tunnel formed from crystals of permafrost outside the village of Tomtor.

Maxim Shemetov/REUTERS

Scientists revived a 48,500-year-old 'zombie' virus from permafrost and found it was still infectious.


The virus was tested on amoebae but could indicate more dangerous viruses are lurking in permafrost.


Some scientists are concerned that climate change thawing permafrost could reawaken ancient viruses.

From a horror movie plot to real life: Scientists have revived ancient "zombie" viruses from permafrost and discovered they could still infect living single-celled amoebae. The chances of these viruses infecting animals or humans are unclear, but the researchers say permafrost viruses should be considered a public health threat.

Permafrost is a layer of soil that remains completely frozen year-round — at least it used to, before human activities started raising global temperatures. It covers 15% of land in the Northern Hemisphere.

Because of climate change, though, permafrost is thawing rapidly, unearthing a host of ancient relics from viruses and bacteria to wooly mammoths and an impeccably preserved cave bear.

A carcass of an Ice Age cave bear found on Great Lyakhovsky Island, in northern Russia, unearthed by thawing permafrost.North-Eastern Federal University via AP

According to CNN, French professor Jean-Michel Claverie found strains of the 48,000-year-old frozen virus from a few permafrost sites in Siberia. The oldest strain, which dated back 48,500 years, came from a sample of soil from an underground lake, while the youngest samples were 27,000 years old. One of the young samples was discovered in the carcass of a wooly mammoth.

Some scientists fear that as climate change warms the Arctic, thawing permafrost could release ancient viruses that haven't been in contact with living things for thousands of years. As such, plants, animals, and humans might have no immunity to them.

"You must remember our immune defense has been developed in close contact with microbiological surroundings," Birgitta Evengård, professor emerita at Umea University's Department of Clinical Microbiology in Sweden, told CNN.

"If there is a virus hidden in the permafrost that we have not been in contact with for thousands of years, it might be that our immune defense is not sufficient," she added. "It is correct to have respect for the situation and be proactive and not just reactive. And the way to fight fear is to have knowledge."
How 'zombie' viruses could infect hosts once they emerge

This isn't the first time Claverie has revived ancient viruses, or "zombie viruses" as he calls them. He's been publishing research on this topic since 2014 and says that beyond his work, very few researchers are taking these viruses seriously.

"This wrongly suggests that such occurrences are rare and that 'zombie viruses' are not a public health threat," Claverie and his colleagues report in their latest paper published February 18 in the journal Viruses.

In that study, Claverie and his team were able to revive several new strains of "zombie" viruses and found that each one could still infect cultured amoebas — a feat, Claverie said, that should be regarded as both a scientific curiosity and a concerning public health threat.

Erosion, caused by thawing permafrost and the disappearance of sea ice which formed a protective barrier, threatens houses from the Yupik Eskimo village of Quinhagak in Alaska.

Mark Ralston/AFP/Getty Images

"We view these amoeba-infecting viruses as surrogates for all other possible viruses that might be in permafrost," he told CNN. "We see the traces of many, many, many other viruses. So we know they are there. We don't know for sure that they are still alive. But our reasoning is that if the amoeba viruses are still alive, there is no reason why the other viruses will not be still alive, and capable of infecting their own hosts."

The current research on frozen viruses like Claverie's 'zombie' virus is helping scientists understand more about how these ancient viruses function and whether, or not, they could potentially infect animals or humans.
Ancient bacteria like anthrax may already be thawing back to life

It's not just viruses. Ancient bacteria, too, could be released and reactivated for the first time in up to two million years as permafrost thaws.

That's what happened, scientists think, when outbreaks of the bacterial infection anthrax appeared in humans and reindeer in Siberia in 2016.

That may be a "more immediate public health concern," according to Calverie's paper.