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 

Highlights

Summary

Significance

Abstract

The global coronavirus disease 2019 (COVID-19) pandemic is currently ongoing. It is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A high proportion of COVID-19 patients exhibit gastrointestinal manifestations such as diarrhea, nausea, or vomiting. Moreover, the respiratory and gastrointestinal tracts are the primary habitats of human microbiota and targets for SARS-CoV-2 infection as they express angiotensin-converting enzyme-2 (ACE2) and transmembrane protease serine 2 (TMPRSS2) at high levels. There is accumulating evidence that the microbiota are significantly altered in patients with COVID-19 and post-acute COVID-19 syndrome (PACS). Microbiota are powerful immunomodulatory factors in various human diseases, such as diabetes, obesity, cancers, ulcerative colitis, Crohn’s disease, and certain viral infections.

In the present review, we explore the associations between host microbiota and COVID-19 in terms of their clinical relevance. Microbiota-derived metabolites or components are the main mediators of microbiota-host interactions that influence host immunity. Hence, we discuss the potential mechanisms by which microbiota-derived metabolites or components modulate the host immune responses to SARS-CoV-2 infection. Finally, we review and discuss a variety of possible microbiota-based prophylaxes and therapies for COVID-19 and PACS, including fecal microbiota transplantation (FMT), probiotics, prebiotics, microbiota-derived metabolites, and engineered symbiotic bacteria. This treatment strategy could modulate host microbiota and mitigate virus-induced inflammation.

Published in Signal Transduction and Targeted Therapy (April 29, 2022):

https://doi.org/10.1038/s41392-022-00986-0 

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......

A recent publication by a Stanford scientist, Bali Pukendran, reviews how the microbiome may play a key role in vaccines efficacy.

Multiples examples have highlighted the role of the microbiota. Earlier studies have evaluated the role of the microbiota small animal models in which  depletion of their microbiota by antibiotics or the testing with germ-free animals resulted in reduced vaccine efficacies. Other studies in human have helped understand how the microbiome influences vaccine's responses by monitoring the vaccine's  signature. The use of  artificial intelligence has been used to predict immune responses.

Immunization with influenza vaccines led to the discovery of potential  links with the microbiota.  The inactivated influenza vaccine induces expression of Toll-like-receptor 5 (TLR5), a key protein recognizing  bacterial components and triggering an innate immune response. Mice deficient in tlr5 induce poor anti-influenza antibody  responses upon vaccination. Similar results have been observed with an adjuvant-free polio vaccine, but not with vaccines containing adjuvants, suggesting that the microbiota may act as an endogenous adjuvant, and may play an even more important role when the individuals have no pre-existing immunity against the pathogen the are immunized against.

Several studies have revealed that in addition to specific gene signatures, antibiotics also lead to significant changes in the blood metabolome, including changes in bile acids that have been shown to modulate inflammatory responses in humans. Furthermore, age may increase gut permeability, exacerbating the effects of the bacterial metabolome and perhaps playing a role in the limited  vaccine efficacy observed in elderly patients.

These findings highlights the importance of avoiding antibiotic use during vaccination, especially in children, where pre-existing responses may be limited. They also highlight the importance to stratify patients in vaccine trials by their microbiomes and bacterial metabolomes, to better elucidate which patients better response to future experimental vaccines.

Published in Science (29 November , 2019):

https://doi.org/10.1126/science.aau6975

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....

Researchers from Karolinska Institutet in Sweden have discovered that the gut microbiome can influence how well people respond to mRNA COVID vaccines. The study, published in the journal npj Biofilms and Microbiomes, suggests that certain bacteria in the gut can enhance the immune response to the vaccine, whereas other bacteria may weaken it. The gut microbiome is the collection of microorganisms that live in our digestive tract. It plays an important role in many aspects of our health, such as digestion, metabolism, and immunity. The researchers wanted to find out if the gut microbiome also affects the response to mRNA COVID vaccines. To do this, the researchers collected stool samples from 68 people living with HIV and 75 healthy individuals before their first mRNA COVID vaccine dose. The researchers analysed the microbiome composition using a technique called 16S rRNA sequencing, which identifies the types and relative abundance of bacteria in the samples. They also measured the levels of antibodies and immune cells that were produced after the vaccination.

The results showed that the initial makeup of the gut microbiome could predict the immune response to the vaccine in both groups. They found that a less diverse gut microbiome was associated with a stronger vaccine response, marked by higher levels of spike protein antibodies and spike specific CD4 T-cells. These are key components of the immune system that help to neutralize the virus and prevent severe infection. The researchers also identified specific bacteria that were linked with better or worse vaccine responses. For example, they found that Lactobacillus, Bacteroides, and Lachnospira were associated with higher antibody and immune cell levels, while Cloacibacillus was associated with lower antibody levels. They also found that Bifidobacterium and Faecalibacterium were microbial markers of individuals with higher antibody levels.

According to the researchers, the study highlights the significant role of the gut microbiome in the effectiveness of mRNA COVID vaccines. The findings could lead to developing microbiota-focused treatments to enhance vaccine responses, especially in groups that may have weaker responses, such as the elderly or immunocompromised individuals. The potential strategies could include changing the diet or taking probiotics to improve the gut microbiome and immunity, the researchers suggest. The study was conducted in collaboration with the Karolinska University Hospital, and SciLifeLab National Genomics Infrastructure in Stockholm, Sweden. The research was funded by Region Stockholm, the Swedish Research Council, and Physicians Against AIDS.

Cited study published in NPJ Biofilms and Microbiomes (Dec. 20, 2023):

https://doi.org/10.1038/s41522-023-00461-w 

Scientists have uncovered a possible explanation for one of COVID-19's most vexing legacies: the stubborn neurological symptoms of long COVID, such as brain fog, memory loss and fatigue. The first clue emerged when researchers scoured the blood of long COVID patients: It was serotonin – specifically, a lack of the neurotransmitter circulating in the body — that grabbed their attention. Their analysis revealed that having low levels of that chemical predicted whether or not someone was suffering from persistent symptoms following an infection. Next, the team of researchers at the University of Pennsylvania carefully recreated the chain of events that might be depleting serotonin and causing downstream consequences that could line up with some of the symptoms characteristic of long COVID.

Their findings, published in the journal Cell, point to an intriguing hypothesis that winds its way from the gut up through the vagus nerve and ultimately into the brain. "Basically, we can explain some of the neurocognitive manifestations of long COVID through this pathway that leads to serotonin reduction," says Christoph Thaiss, a senior author on the study and an assistant professor of microbiology at the University of Pennsylvania. The work has made an impression on those studying long COVID, a condition that still has no validated treatment or widely accepted biomarker that doctors can use to diagnose the condition. The study weaves together several prominent lines of evidence on the potential drivers of the condition — the ongoing presence of viral material, blood clotting and chronic inflammation — and offers up possible targets for clinical trials that can test treatments in humans. "I'm impressed by the study," says Dr. Michelle Monje, a professor of neurology at Stanford University. "I think they did a beautiful job showing the causality of these changes." Given that much of the work was done on mice, the implications for long COVID patients still need to be fully explored in future studies, but the results tell a "very nice linear story," says Akiko Iwasaki, an immunologist at Yale University. "Everyone who's engaged in this research should now be thinking about this serotonin pathway," says Iwasaki.

So what exactly did they find?

Tracing the cause of brain fog

With serotonin on their minds, the researchers tried to start from the very beginning of the disease process, primarily using experiments on mice to trace its course. Their hunch was that "viral persistence" — a major suspect in long COVID — could underlie the depletion of serotonin. Multiple studies show that well after the initial illness passes, some long COVID patients may have a lingering infection in certain parts of the body, sometimes called a "viral reservoir," which could be driving some of their symptoms. Maayan Levy, a senior author, says they looked for evidence of viral persistence by checking the stool of their long COVID subjects for genetic material from the virus. "In about 30% of patients, we could find viral RNA in their gastrointestinal tract, so we took this and tried to model it in mice," says Levy, an assistant professor of microbiology at the University of Pennsylvania. Those experiments revealed that a chronic viral infection (they used lymphocytic choriomeningitis virus as a stand-in for SARS-CoV-2) also led to reductions in serotonin and that the body's own immune response seemed to be the culprit. This led to further experiments focused on a cytokine, called type 1 interferon, revealing that this signaling protein was driving inflammation and interfering with serotonin levels in the bloodstream in several ways. The gut produces 90% of serotonin in the body. The amino acid tryptophan is critical to this task — it's a precursor to serotonin and gets absorbed in the gastrointestinal tract from the food we eat. Except, this inflammatory response in the gut actually impaired the absorption of tryptophan. "If there's less tryptophan, there's less serotonin production," says Thaiss. On top of that, these cytokines also lead to clotting of blood platelets — which store serotonin — further reducing the amount of serotonin in circulation.

The brain connection

Here, the detective work moved away from the gut to the vagus nerve, which essentially acts like the brain's monitoring system of the body and connects to the gastrointestinal tract and many other organs. Levy says they found this reduction in serotonin impairs communication between the vagus nerve and the brain, which then reduces some activity in a region of the brain known as the hippocampus. What's promising, though, is that the cognitive symptoms the Penn researchers documented in mice could be reversed. "We can make the animals remember perfectly again by just reactivating their vagus nerve or by restoring their serotonin signaling," says Thaiss, referring to a cognitive behavioral test they performed on their mouse models of long COVID. "Whether the exact same thing is true in individuals with long COVID is something we don't know." Because much of this work was done on mice, there are limitations to what conclusions can be drawn about humans. Levy points out that their data can't prove a viral reservoir is causing these events in humans and that a lack of good mouse models of long COVID still hampers research. "To make any recommendations for patients, we need to perform a large clinical trial that is well-controlled," she says, "The obvious next step would be for us to to try an intervention that will increase serotonin levels or stimulate the vagus nerve in other ways or [to] supplement tryptophan." In their experiment, they gave the mice a generic form of Prozac — a class of medication known as an SSRI that's typically prescribed for depression and increases circulating serotonin in the brain.

Untangling the complex causes of long COVID

The research offers new insights into how immune problems outside of the nervous system can have far-reaching consequences on the brain and other functions in the aftermath of COVID-19, says Stanford's Monje. "It's not the whole puzzle — and it's not meant to be the whole puzzle — but it's a really important aspect of it," she says. Indeed, scientists don't expect to find a single mechanism that, once unearthed, will resolve all these problems. "There are many ways that COVID can influence the nervous system that are not mutually exclusive," says Monje. "Any individual might be suffering from some combination of those." For example, her lab has found that, in mice, a mild COVID-19 infection in the lungs sets off an inflammatory cascade that impairs neuron production in the hippocampus. The long COVID "brain fog" syndrome encompasses a constellation of symptoms, everything from problems with memory and attention to speed of information processing to executive function and fatigue. Monje says research on the effects of COVID-19 have revealed neurobiological changes elsewhere in the brain, too. "It's broader than just the hippocampus, but certainly the hippocampus has been implicated." As with all long COVID research, the challenge is figuring out how these findings fit into our ever-changing understanding of the disease. "Long COVID is a heterogeneous disorder. There are many different manifestations," says Dr. Saurabh Mehandru, a professor of medicine at Mount Sinai in New York. "It's novel, exciting data. I would consider this as important but initial findings which have to be further studied." Mehandru says "it makes sense the tryptophan-serotonin pathway is being affected" given that SARS-CoV-2 utilizes the ACE-2 receptor, which is widely expressed on the surface of the small intestines. "It's expressed there because it plays a role in absorption of amino acids" like tryptophan, he says. But he says there are still many open questions about this business of viral persistence in the gut of long COVID patients.

Because these cells renew every three to five days, "for anything to be persistently active in this layer, it would by definition imply there's some level of replication," he says. It's not clear, however, exactly what's replicating. Multiple studies have found evidence of genetic material and viral proteins in different tissues. Yet, no one has actually cultured the virus from intestinal tissue, which is admittedly difficult to do, he says. "These are active and important scientific areas of interest." While it's possible a chronic viral infection in the gut could be driving these symptoms in some patients, as the Penn study suggests, Yale's Iwasaki says the neurocognitive dysfunction in long COVID can be "downstream of many different things, including circulating inflammatory factors and autoantibodies." "Even though the dots are very well connected with animal models and patient samples, whether this is happening in patients and what proportion might be suffering from this particular pathology, that still requires future studies," says Iwasaki, whose research has found that low levels of the stress hormone cortisol are also associated with long COVID symptoms. Ultimately, this research may not explain all the neurological symptoms that surround long COVID — and that's okay, says Monje. "It's not that we have to put all the pieces of the puzzle together to begin to make meaningful therapeutic changes," she says. "I think it's worth further pursuing."

Research published in Cell (October 16, 2023):

https://doi.org/10.1016/j.cell.2023.09.013

In what outside experts called the most rigorous and comprehensive survey of bacteria in human tumor samples, scientists have discovered distinct populations of microbes living inside different types of tumors: In other words, breast and brain and pancreatic tumors have their own characteristic microbiomes.

Recent research has revealed an intriguing relationship between microbes and cancer, including how bacteria in the gut can affect the way immunotherapies like checkpoint inhibitors or even standard chemotherapy work to shrink tumors. Now the new paper suggests the bacterial communities within tumors could be exploited to devise a new form of targeted therapies, in the same way we now develop drugs based on the molecular features of a tumor...

Original Research Published in Science ( May 29, 2020):

https://doi.org/10.1126/science.aay9189

Microbes living in the rectum could make a difference to the effectiveness of experimental HIV vaccines, according to researchers at the University of California, Davis. The work is published Dec. 11 in the journal mSphere. Evidence from human and animal studies with other vaccines suggests that Lactobacillus supplements can boost production of antibodies, while treatment with antibiotics can hamper beneficial immune responses, said Smita Iyer, assistant professor at the UC Davis Center for Immunology and Infectious Diseases and School of Veterinary Medicine. Iyer, graduate student Sonny Elizaldi and colleagues wanted to know if microbes living in the rectum and vagina — sites of HIV transmission — interacted with an experimental HIV vaccine similar to the HVTN 111 vaccine currently in early stage clinical trials in humans. HVTN 111 includes two doses of HIV DNA snippets and a final boost with an HIV protein, all given through the skin. A vaccine that produces antibodies at the mucosal membranes where infection takes place is thought to be important in preventing HIV infection, Iyer said. The team studied vaginal and rectal microbes from rhesus macaques before and after they were vaccinated. They found that vaginal microbes did not show much difference before and after vaccination. However, rectal microbes did show changes, with Bacteroidetes-type bacteria, especially Prevotella, decreasing after vaccination. 

Lactobacillus bacteria and better immune response

The common gut bacteria Lactobacillus and Clostridia did not change with vaccination, but the amounts of these microbes in the rectum did correlate with the immune response. Animals with high levels of either Lactobacillus or Clostridia made more antibodies to the HIV proteins gp120 and gp140, the researchers found. Prevotella bacteria showed the opposite pattern: High levels of Prevotella were correlated with weaker immune responses. It’s not clear what the mechanism could be for some bacteria to boost local immune responses in a specific site in the body, Iyer said. However, targeting these bacteria could be important to get the best possible performance out of vaccines that do not induce a particularly strong immune response, as is the case with HIV. The microbiome could also be an important but overlooked factor to consider when evaluating vaccines in humans or animals, she said. 

Published in mSphere (December 11, 2019):

https://doi.org/10.1128/mSphere.00824-19

The highly contagious norovirus causes diarrhea and vomiting and is notorious for spreading rapidly through densely populated spaces, such as cruise ships, nursing homes, schools and day care centers. Each year, it is responsible for some 200,000 deaths, mostly in the developing world. There are no treatments for this intestinal virus, often incorrectly referred to as stomach flu. Now, a new study led by scientists at Washington University School of Medicine in St. Louis has shown that gut microbes can tamp down or boost the severity of norovirus infection based on where along the intestine the virus takes hold.  The study, published Nov. 25 in the journal Nature Microbiology, suggests new routes to possible therapies for norovirus infection. Collaborators included researchers at the University of Florida, the University of Michigan and Yale University Medical School.

"There are currently no treatments for norovirus, which is very easily spread through fecal-oral transmission," said co-senior author Megan T. Baldridge, MD, Ph.D., an assistant professor of medicine at Washington University. "Norovirus is especially dangerous in young children, older adults and people with compromised immune systems. We are trying to understand how the gut microbes interact with norovirus in an effort to pursue new therapeutic strategies." In these mouse studies, the researchers found that normal gut bacteria boosted the severity of viral infection in the lower small intestine, which is in line with past work in the field. But simultaneously, normal gut bacteria blocked or inhibited viral infection in the upper small intestine. In other words, gut microbes can have totally opposite effects on norovirus infection depending on the infection's location along the length of the gut. "These results were a huge surprise to us," Baldridge said. "We showed that different parts of the intestine can show dramatically different responses to this type of infection. Our research reveals that we can't view the gut as a homogeneous tube that responds to infection in a uniform way."

Baldridge and her colleagues found that the difference in response was driven by bile acids, which are mainly known for their roles in digestion. "Bile acids are powerfully regulated by bacteria all along the gut," Baldridge said. "But there had not been a realization that these bile acids could prime the gut to mount an immune response against intestinal viruses." In the new study, the researchers showed that bile acids in the upper small intestine—but not the lower—stimulated the immune system to respond to the infection. The researchers determined that bile acids in that region of the gut triggered a molecule called interferon III—one of the body's key antiviral defenses in the intestine—to become activated. Baldridge noted that this complexity of interactions between gut microbes and bile acids could explain some of the variability seen in norovirus infections. Some people become extremely ill with this virus; others develop no symptoms at all. "The different ways people respond to viral infections could be related to their individual gut microbial community," Baldridge said. "The severity of an infection could be tied to where exactly along the gut you get an infection, and that might be controlled by your individual microbiome. Subtle differences along the intestine could end up having dramatic effects on how the gut perceives the virus and responds to it."...

Published in Nature Microbiology (25 November 2019):

https://nature.com/articles/s41564-019-0602-7