Virus World

Large and giant double-stranded DNA viruses within the phylum Nucleocytoviricota are diverse and prevalent in the environment where they substantially affect the ecology and evolution of eukaryotes. Until now, these viruses were only sporadically found in the digestive system of vertebrates. Here, we present the identification and genomic characterization of a proposed third order of viruses within the class Pokkesviricetes that currently consists of poxviruses and asfuviruses. Members of this newly identified order we provisionally named Egovirales are abundant in the digestive system of vertebrates worldwide and occur in high abundances in >10% of livestock animals, >2% of humans, and wild animals. Egoviruses have linear genomes up to 360 kbp in length that likely produce multilayered icosahedral capsids, similar to those of asfuviruses.

The diversity of egoviruses already far exceeds that of all known poxviruses and animal-associated asfuviruses. Phylogenetic analyses and patterns of virus distribution across vertebrates suggest that egoviruses can be either specialists or generalists associated with a single or multiple vertebrate species, respectively. Notably, one egovirus clade is human-specific, evolutionarily constrained, and spread across continents, demonstrating a long-lasting association between Egovirales and the human population on the global scale. Egoviruses not only expand the ecological and evolutionary scope of Pokkesviricetes, but also appear to be the most diverse, widespread, and abundant group of double-stranded DNA viruses infecting eukaryotic cells in the digestive system of vertebrates.

Preprint in bioRxiv  (March 23, 2024):

https://doi.org/10.1101/2024.03.23.586382 

Research into bacteriophages adds to evidence that gut and brain interactions influence our behaviour. Viruses are widely regarded as harmful to our health, but a subset of viruses living in the gut could play a crucial role in regulating stress, research suggests. The discovery adds to mounting evidence that interactions between the gut and brain influence people’s behaviours, and could eventually lead to new treatments for stress-related conditions that target the vast community of viruses living inside us. While previous studies have suggested that the composition of microbes living in the gut changes in response to stress, these have largely focused on bacteria, rather than on this “virome”. “The way the virome interacts with bacteria, and how they affect stress-related health and disease status is largely unexplored,” said Dr Nathaniel Ritz, of the APC Microbiome Ireland research centre at University College Cork. “Our research opens up the potential to target the virome to treat and reduce the effects of stress.”

Ritz and his colleagues focused on a subset of viruses called bacteriophages, which infect bacteria and replicate alongside them. They studied what happened to these viruses when the mice they inhabited were exposed to chronic social stresses, such as being housed alone or in overcrowded conditions, and found that stress exposure led to changes in the composition of the viruses and the bacteria in the animals’ guts. Next, they harvested viruses from the droppings of unstressed healthy animals, and transplanted some of them back in, once the mice had been exposed to chronic social stress. The research, published in Nature Microbiology, suggested these transplants reduced levels of stress hormones and curbed depression- and anxiety-like behaviour in the mice. While further studies are needed to assess whether virus transplants are beneficial to humans suffering from stress-related conditions, the research provides some of the first evidence that gut viruses are involved in the response to stress, and that manipulating them could have therapeutic benefits. “Given that the virome composition varies greatly among individuals, it may open the door for personalised medicine approaches for stress-related disorders in the future,” said Prof John Cryan at APC Microbiome Ireland, who led the research. “One thing for certain, we must acknowledge that not all viruses are bad and they can play a key role in keeping the bad bacteria in our gut at bay especially in times of stress.”

Cited research published in Nature Microbiology (Feb.5, 2024):

https://doi.org/10.1038/s41564-023-01564-y 

Little is known on the landscape of viruses that reside within our cells, nor on the interplay with the host imperative for their persistence. Yet, a lifetime of interactions conceivably have an imprint on our physiology and immune phenotype. In this work, we revealed the genetic make-up and unique composition of the known eukaryotic human DNA virome in nine organs (colon, liver, lung, heart, brain, kidney, skin, blood, hair) of 31 Finnish individuals. By integration of quantitative (qPCR) and qualitative (hybrid-capture sequencing) analysis, we identified the DNAs of 17 species, primarily herpes-, parvo-, papilloma- and anello-viruses (>80% prevalence), typically persisting in low copies (mean 540 copies/ million cells).

We assembled in total 70 viral genomes (>90% breadth coverage), distinct in each of the individuals, and identified high sequence homology across the organs. Moreover, we detected variations in virome composition in two individuals with underlying malignant conditions. Our findings reveal unprecedented prevalences of viral DNAs in human organs and provide a fundamental ground for the investigation of disease correlates. Our results from post-mortem tissues call for investigation of the crosstalk between human DNA viruses, the host, and other microbes, as it predictably has a significant impact on our health.

Published (April 24, 2023)in Nucleic Acids Research:

https://doi.org/10.1093/nar/gkad199 

This year was full of fascinating discoveries. New viruses were identified, and others were associated with new and old diseases. Milestones were reached in the battle against viral diseases, and yet viral outbreaks continued to frighten the world. Scientists uncovered novel technologies to diagnose viral infections, and to deliver gene therapies that achieved results we could not imagine decades ago. Virologists learned more about the role the human microbiome plays in viral infection. This is the year in review with the findings that shaped 2019 in the field of viruses.

New diseases and viruses

A new polio-like disease outbreak (acute flaccid myelitis, or “AFM”) emerged in the United States in the last years, with more than 500 cases reported by CDC. AFM brought us back memories and fears from the early 1940s in the US, where after a few years of small polio outbreaks in American children, many more episodes would come in the following years paralyzing more than 50,000 children at the peak of the1952 epidemic. In 2019, epidemiological and immunological studies associated the new polio-like disease with other picornaviruses, enterovirus D68 and A71. Human herpesviruses 6 (HHV-6) and Epstein-Barr virus (EBV) were associated with multiple sclerosis in humans. HHV-6 and HHV-7 were also linked to Alzheimer’s disease. Adenovirus C was associated with type I diabetes, and human papillomavirus infection correlated with increased odds of breast carcinoma. An entire new family of viruses, the redondoviridae, was found in the human lung during metagenomic analyses. The “medusavirus”, was identified in a hot spring in Japan. The medusavirus infects amoeba cells and its genome is among the largest and more complexed viral genomes ever found, with genes encoding all types of histones. Scientists demonstrated for the first time that a non-enveloped insect RNA virus, “Providence virus”, can also infect plants and mammalian cells, suggesting that plants could act as reservoirs of human viruses. Another study reported that more viruses than previously elucidated (about 30 different viral species) can be found in human semen.  The list included viruses of known routes of sexual transmission, such as HIV or HTLV-1, and also others like Lassa, Zika or Dengue. Proof of sexual transmission of dengue virus was confirmed in 2019 for the first time.

New viral therapies

This was not a great year for FDA approvals for antiviral therapies. 54 new drugs were approved by the FDA in 2019, included 48 new small-molecules. None of them target viral diseases. Xofluza (baloxavir marboxil), an inhibitor of the influenza virus polymerase acidic endonuclease, was approved in October 2018 for the treatment of acute uncomplicated influenza, in healthy people 12 years and older. In October 2019 Xofluza was also approved for the treatment of people at high risk of influenza complications, including those with asthma, chronic lung disease, diabetes, heart disease and obesity. During 2019 we heard great news about the first anti-influenza drug approved in more than 20 years. Therapy with Xofluza was found useful at preventing flu transmission in the household environment, reducing the chances of transmission in individuals under the same house by over 85%. However, in November, results from a study reported alarming rates of baloxavir-resistant strains, especially in children. The appearance of drug-resistance is common among RNA viruses, but the study found the troublesome ability of the virus to mutate without compromising its "viral fitness". Some scientists questioned the use of the antiviral in children, where resistant rates were significantly higher......

Most of the viruses present in people’s guts are bacteriophages, but how they interact with resident bacteria is still an open question. There’s a lot that scientists don’t know about the gut microbiota, and when it comes to the viruses present there they know even less. To learn more, researchers have monitored the gut viromes of nine people for a full year and that of one person for more than two years. They find that many types of bacteriophages are present and that each individual’s virome is stable over time and different from that of the other subjects.

This study “generates an important database for phages in the gut,” says Corrine Maurice, a microbiologist at McGill University who did not participate in the work. “That’s a database that we just didn’t have, and so that data is going to allow us to formulate some really cool hypotheses going forward. It’s really providing us with tools to . . . look further into what these phages may be doing for our health. “It confirms recent reports that there is no such thing as a core gut virome shared between adult individuals, which is in contrast with the bacterial component of our microbiota where there are more members shared between humans,” Evelien Adriaenssens, who studies gut viruses at the Quadram Institute in the UK and was not involved in the work, writes in an email to The Scientist. “We need more studies on the gut virome like these to establish a baseline about what a healthy human gut virome looks like, taking into account differences in for example geography, ethnicity and lifestyle. After we know what is healthy, we can start looking at complex disease syndromes . . . and identify what changes in the virome can be used as a marker for disease.”

There’s a lot that scientists don’t know about the gut microbiota, and when it comes to the viruses present there they know even less. To learn more, researchers have monitored the gut viromes of nine people for a full year and that of one person for more than two years. They find that many types of bacteriophages are present and that each individual’s virome is stable over time and different from that of the other subjects.

This study “generates an important database for phages in the gut,” says Corrine Maurice, a microbiologist at McGill University who did not participate in the work. “That’s a database that we just didn’t have, and so that data is going to allow us to formulate some really cool hypotheses going forward. It’s really providing us with tools to . . . look further into what these phages may be doing for our health.”

“It confirms recent reports that there is no such thing as a core gut virome shared between adult individuals, which is in contrast with the bacterial component of our microbiota where there are more members shared between humans,” Evelien Adriaenssens, who studies gut viruses at the Quadram Institute in the UK and was not involved in the work, writes in an email to The Scientist. “We need more studies on the gut virome like these to establish a baseline about what a healthy human gut virome looks like, taking into account differences in for example geography, ethnicity and lifestyle. After we know what is healthy, we can start looking at complex disease syndromes . . . and identify what changes in the virome can be used as a marker for disease.”

Andrey Shkoporov, a microbiologist at University College Cork, and colleagues set out to establish that baseline. “We thought, ‘Okay, before we embark on comparative studies of the virome in different health conditions, why don’t we look at the longitudinal stability and inter-individual variability of the gut virome between healthy human subjects,’” he tells The Scientist. 

The research team collected fecal samples from 10 adults—four men and six women—every month for a year. From one female subject, they collected three additional samples at months 19, 20, and 26. Then they separated viral particles from fecal matter and cells and isolated and sequenced viral nucleic acids. Because 99 percent of gut viruses are unknown to science, Shkoporov says, it was not possible to rely on existing viral sequence databases to figure out what was there. Instead, the authors assembled the reads into overlapping DNA sequences, predicted protein coding genes, and then tried to detect any similarities between proteins in databases with those likely encoded by the long stretches of DNA. “This can help to get a rough idea what kind of viruses we are dealing with,” Shkoporov adds. The researchers reported yesterday (October 9) in Cell Host & Microbe  that the individual viromes were stable over the 12 or 26 months of the study and diverse, meaning there were many types of bacteriophages present. While the subjects’ viral communities stayed consistent over time, each person’s complement of gut viruses looked different from that of the others.....

Published in Cell Host & Microbe on October 9, 2019:

https://doi.org/10.1016/j.chom.2019.09.009

Perelman School of Medicine team identifies previously unknown viral family that appears to be the second-most common DNA virus in human lung and mouth specimens. The new virus family has been given the name Redondoviridae—from the Spanish word “redondo”, which means round.

The team’s studies found elevated levels of redondovirus DNA in lung specimens from critically ill patients in intensive care units, and also in mouth samples from patients with untreated gum disease. Viral levels in the gum disease patients declined after they received treatment for their periodontitis. Research leads Frederic D. Bushman, PhD, chair of the department of microbiology, and Ronald G. Collman, MD, a professor of pulmonary, allergy and critical care, and colleagues report on their discoveries in Cell Host Microbe. 

A large proportion of redondovirus-positive samples were from studies that had included patients with periodontal disease, and the team found that redondovirus DNA levels were higher in individuals with gum disease prior to treatment, and then fell after treatment. “Thus, we conclude that redondoviruses are associated with periodontitis in multiple studies and that levels are reduced with effective treatment,” they wrote. “The role of redondoviruses in periodontitis warrants further study.” Interestingly, direct qPCR analysis of lung samples from 60 healthy adults and 69 critically ill individuals indicated that although redondoviruses were present in healthy people, viral levels were also elevated in the critically ill patients.

“Here, we introduce Redondoviridae, a family of small, circular DNA viruses discovered in metagenomic sequence data, which is found selectively in human lung and oro-pharyngeal samples,” the scientists commented. “Of the DNA viruses we surveyed in 20 human virome datasets, redondoviruses were the second most abundant, exceeded only by anelloviruses.

The findings were published in May 19 in the journal Cell Host Microbe: 

https://doi.org/10.1016/j.chom.2019.04.001

Mammalian cells outpace bacteriophages in the microbial food chain by devouring phages to fuel their growth. The human gut is a bustling highway for a highly diverse microbial community, including an abundance of bacteriophages that modulate the gut microbiome. It’s a phage-infect-bacteria world, and while bacteriophages cannot infect mammalian cells, their paths still intersect. Mammalian cells can engulf phages within the gut. Researchers have observed that different bacteriophages induce opposing reactions such as anti- or proinflammatory responses in mammalian cells. However, it is unclear how bacteriophages interact with cells and modulate these cellular and immune responses. Jeremy Barr, a bacteriophage biologist at Monash University, and his team set out to clarify whether or not phages activate inflammatory pathways. Their findings, published in PLOS Biology, demonstrated that mammalian cells engulfed bacteriophages to fuel cellular growth without inducing inflammation....

Blood transfusion safety is an essential element of public health. Current blood screening strategies rely on targeted techniques that could miss unknown or unexpected pathogens. Recent studies have demonstrated the presence of a viral community (virobiota/virome) in the blood of healthy individuals. Here, we characterized the blood virome in patients frequently exposed to blood transfusion by using Illumina metagenomic sequencing. The virome of these patients was compared to viruses present in healthy blood donors. A total number of 155 beta-thalassemia, 149 hemodialysis, and 100 healthy blood donors were pooled with five samples per pool.

Members of the Anelloviridae and Flaviviridae family were most frequently observed. Interestingly, samples of healthy blood donors harbored traces of potentially pathogenic viruses, including adeno-, rota-, and Merkel cell polyomavirus. Viruses of the Anelloviridae family were most abundant in the blood of hemodialysis patients and displayed a higher anellovirus richness. Pegiviruses (Flaviviridae) were only observed in patient populations. An overall trend of higher eukaryotic read abundance in both patient groups was observed. This might be associated with increased exposure through blood transfusion. Overall, the findings in this study demonstrated the presence of various viruses in the blood of Iranian multiple-transfused patients and healthy blood donors.

Published in Viruses (June 23, 2023):

https://doi.org/10.3390/v15071425 

Scientists who study glacier ice have found viruses nearly 15,000 years old in two ice samples taken from the Tibetan Plateau in China. Most of those viruses, which survived because they had remained frozen, are unlike any viruses that have been cataloged to date. The findings, published today in the journal Microbiome, could help scientist understand how viruses have evolved over centuries. For this study, the scientists also created a new, ultra-clean method of analyzing microbes and viruses in ice without contaminating it.  “These glaciers were formed gradually, and along with dust and gases, many, many viruses were also deposited in that ice,” said Zhi-Ping Zhong, lead author of the study and a researcher at The Ohio State University Byrd Polar and Climate Research Center who also focuses on microbiology. “The glaciers in western China are not well-studied, and our goal is to use this information to reflect past environments. And viruses are a part of those environments.” The researchers analyzed ice cores taken in 2015 from the Guliya ice cap in western China. The cores are collected at high altitudes – the summit of Guliya, where this ice originated, is 22,000 feet above sea level. The ice cores contain layers of ice that accumulate year after year, trapping whatever was in the atmosphere around them at the time each layer froze. Those layers create a timeline of sorts, which scientists have used to understand more about climate change, microbes, viruses and gases throughout history. Researchers determined that the ice was nearly 15,000 years old using a combination of traditional and new, novel techniques to date this ice core. When they analyzed the ice, they found genetic codes for 33 viruses. Four of those viruses have already been identified by the scientific community. But at least 28 of them are novel. About half of them seemed to have survived at the time they were frozen not in spite of the ice, but because of it.

“These are viruses that would have thrived in extreme environments,” said Matthew Sullivan, co-author of the study, professor of microbiology at Ohio State and director of Ohio State’s Center of Microbiome Science. “These viruses have signatures of genes that help them infect cells in cold environments – just surreal genetic signatures for how a virus is able to survive in extreme conditions. These are not easy signatures to pull out, and the method that Zhi-Ping developed to decontaminate the cores and to study microbes and viruses in ice could help us search for these genetic sequences in other extreme icy environments – Mars, for example, the moon, or closer to home in Earth’s Atacama Desert.”  Viruses do not share a common, universal gene, so naming a new virus – and attempting to figure out where it fits into the landscape of known viruses – involves multiple steps. To compare unidentified viruses with known viruses, scientists compare gene sets. Gene sets from known viruses are cataloged in scientific databases. Those database comparisons showed that four of the viruses in the Guliya ice cap cores had previously been identified and were from virus families that typically infect bacteria. The researchers found the viruses in concentrations much lower than have been found to exist in oceans or soil. The researchers’ analysis showed that the viruses likely originated with soil or plants, not with animals or humans, based on both the environment and the databases of known viruses.

The study of viruses in glaciers is relatively new: Just two previous studies have identified viruses in ancient glacier ice. But it is an area of science that is becoming more important as the climate changes, said Lonnie Thompson, senior author of the study, distinguished university professor of earth sciences at Ohio State and senior research scientist at the Byrd Center. “We know very little about viruses and microbes in these extreme environments, and what is actually there,” Thompson said. “The documentation and understanding of that is extremely important: How do bacteria and viruses respond to climate change? What happens when we go from an ice age to a warm period like we’re in now?” This study was an interdisciplinary effort between Ohio State’s Byrd Center and its Center for Microbiome Science. The 2015 Guliya ice cores were collected and analyzed as part of a collaborative program between the Byrd Polar and Climate Research Center and the Institute of Tibetan Plateau Research of the Chinese Academy of Sciences, funded by the U.S. National Science Foundation and the Chinese Academy of Sciences. Funding also came from the Gordon and Betty Moore Foundation and the U.S. Department of Energy.

Published in Microbiome (July 20, 2021):

https://doi.org/10.1186/s40168-021-01106-w

Ring Therapeutics, a Flagship Pioneering spinout, launched Thursday with ambitious plans to expand the universe of vectors available for gene therapy. Gene therapy, treatments intended to treat disease by inserting a gene instead of using drugs or surgery, has had a banner year, with the second ever such therapy approved this year in the US. Ring want to use its research into viruses that exist in the human body without apparent negative effects to provide more and better options to fuel the rise of gene therapy treatments. For the past two years, Flagship Pioneering partner and Ring’s founding CEO Avak Kahvejian says the company has been exploring the human commensal virome—basically, a group of viruses that exist within humans without negative effects—for its potential to address limitations of the vectors currently used.

The sector relies heavily on adeno-associated viruses (AAVs), which naturally infect humans but aren’t known to cause disease, to deliver the DNA. Previous exposure, however, can spark an immune response. “A lot of the workhouses in gene therapy have either been pathogenic viruses or viruses that have been taken from other species or viruses that are highly immunogenic, or all of the above,”  Kahvejian tells Xconomy. “That leads to a certain number of limitations, despite the successes and advances we’ve made to date.” A number of issues stymie widespread use of AAVs, Kahvejian says, including the fact that 10 percent to 20 percent of people have at one time or another been infected with such a virus, thereby building up an immune response to it. Another concern is where such gene therapies end up, because viruses tend to gravitate toward certain types of tissues, and to go elsewhere, require special tweaking.

The Cambridge, MA-based startup believes the viruses it has found are unlikely to cause an immune response or prove pathogenic, given their ubiquity in the body. Like extrachromosomal DNA—a new discovery at least one company is exploring for its potential as a target in cancer treatments—the viral sequencing Ring is studying are circular pieces of DNA that exist outside the 23 chromosomes of the human genome. Ring says it has found thousands of these viruses that coexist with our immune system. It aims to use those to develop vectors that can facilitate gene replacement throughout the body—multiple times, if necessary. While gene therapy is thought of as a one-time fix, cell turnover means whatever the “fix” engendered by the inserted gene could falter over time, necessitating a re-up.

Press Release (Dec. 19, 2019)  available here:

https://www.prnewswire.com/news-releases/flagship-unveils-newest-pioneering-platform-ring-therapeutics-300976832.html

Comparing a living cell to a virus is a bit like comparing the Sistine Chapel to a backyard dog house. Lacking the intricate machinery of living cells, viruses represent biology stripped down to an extreme level. They are the true minimalists of the biological world. Nevertheless, the field of virology is brimming with unanswered questions about these architecturally simple, yet mysterious entities. In new research, Arvind Varsani, a molecular virologist at Arizona State University, joins a prestigious international team to explore a particular class of viruses, ferreting out genetic fragments revealing the complexities of viral evolution.

The new study examines the evolutionary dynamics of circular Rep-encoding single-stranded (CRESS) DNA viruses. The findings show that this broad class of single-stranded DNA viruses, which infect all three cellular domains of life, have acquired their genetic components through complex evolutionary processes not traceable to a single ancestral event. Rather, viruses are obsessive borrowers, appropriating genetic material from many sources, including bacterial, archaeal and eukaryotic cells as well as circular parasitic replicons, known as plasmids, and other mobile genetic elements, such as transposons. When a group of mobile elements—like CRESS DNA viruses— arise from more than a single common evolutionary ancestor or ancestral group, they are known as polyphyletic. The phenomenon is common in the viral world.

Such explorations also hold the potential to shed new light on the origins of earth's earliest life, and resolve the question of how cell-based life came to co-exist with the planet's staggering array of viruses (dubbed the virome). "Over the last decade we have been discovering viruses in various ecosystems using metagenomic approaches and as a result populating the CRESS DNA virus databases," Varsani says. "This has paved the way for a global analysis for CRESS DNA viruses yielding insights into the origin of these and other related viruses." "It is remarkable to see all these evolutionary connections between viruses and non-viral selfish replicons, which once were considered to be unrelated," Krupovic says. The results reveal three distinct evolutionary events contributing to the genetic composition of CRESS-DNA viruses. An intriguing kinship appears to exist between CRESS-DNA viruses and rolling circle plasmids found in bacteria, archaea and some eukaryotes.  "As a result, the general mechanisms of virus evolution as well as the global organization of the vast viral world start to unravel."

Published July 31 2019 in Nature Communications:

https://doi.org/10.1038/s41467-019-11433-0