Virus gifts

17 December 2014

Looking to give a virus-themed gift to someone this year? Here are some suggestions. As expected Ebola virus dominated. Where are the EV-D68 items?

An Ebola Texas shirt from VineFreshTees:

Ebola Texas

Virus tree ornaments made of wood at BuenoMarket:

tree viruses

Viral mugs at Thefty:

viral mug

Artologica always has fabulous microbe art, including this swine flu watercolor:

swine flu

A favorite last year, Screenology, also has an Ebola virus T shirt:

Ebola virus t shirt

Another favorite from last year, Trilobite Glassworks, went the Ebola virus route with this dish; there is also a brooch:

Ebola dish

For wrapping your gifts, try The Wrap Up Project, where you will find blue, red, or green paper covered with viruses. Proceeds go to St. Mungo’s which provides assistance for homeless people in the United Kingdom.

virus wrap

This is just a small selection of what is out there – check out my Microbe art page for much more. Making beautiful art depicting viruses, bacteria, and other life forms is a great way to make everyone aware of the beauty of science. Please support these very special artists.

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The American Society for Virology was founded in 1981 to promote the exchange of information and stimulate discussion and collaboration among scientists active in all aspects of virology. These goals are achieved in part by organizing an annual meeting that brings together virologists from diverse fields to discuss their work.

As the current President of the American Society for Virology it is my honor to select the speakers for the morning symposia at the annual meeting. Below are the sessions that I have organized and the speakers that I have selected. Note the titles of the different sessions: Listeners of the science show This Week in Virology should recognize them! In addition to the plenary sessions there are hundreds of other talks, poster sessions, and much more.

The 2015 annual meeting of ASV will be held at Western University in London, Ontario, Canada. It should be a terrific meeting. All virologists are encouraged to attend; registration is now open. I hope to see you there next summer!

Saturday 7/11
Keynote Address – Joan Steitz, Yale University

Sunday 7/12
An inordinate fondness for viruses
Curtis Suttle, University of British Columbia
Christian Drosten, University of Bonn
XJ Meng, Virginia Tech
Steve Wilhelm, University of Tennessee

Monday 7/13
The kind that make you sick
Kanta Subbarao, NIAID, NIH
Theodora Hatziannou, Aaron Diamond AIDS Research Institute
Chioma Okeoma, University of Iowa
Heinz Feldmann, NIAID, NIH

Tuesday 7/14
Bucket of bolts
Britt Glaunsinger, University of California, Berkeley
Paula Traktman, Medical College of Wisconsin
Ileana Cristea, Princeton University
Leslie Parent, Penn State
James (Zhijian) Chen, UT Southwestern Medical Center

Wednesday 7/15
Virocentricity
Eugene Koonin, NCBI, NIH
Mart Krupovic, Institut Pasteur
Kenneth Stedman, Portland State University
Susana Lopez Charreton, UNAM, Cuernavaca
Karen Mossman, McMaster University

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On episode #315 of the science show This Week in Virology, Vincent, Alan, Rich and Kathy discuss the association of a virus with sea star melting disease, and the finding of a phycodnavirus in the oropharynx of humans with altered cognitive functions.

You can find TWiV #315 at www.twiv.tv.

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influenza virusHuman influenza viruses replicate almost exclusively in the respiratory tract, yet infected individuals may also have gastrointestinal symptoms such as vomiting and diarrhea. In mice, intestinal injury occurs in the absence of viral replication, and is a consequence of viral depletion of the gut microbiota.

Intranasal inoculation of mice with the PR8 strain of influenza virus leads to injury of both the lung and the intestinal tract, the latter accompanied by mild diarrhea. While influenza virus clearly replicates in the lung of infected mice, no replication was observed in the intestinal tract. Therefore injury of the gut takes place in the absence of viral replication.

Replication of influenza virus in the lung of mice was associated with alteration in the populations of bacteria in the intestine. The numbers of segmented filamentous bacteria (SFB) and Lactobacillus/Lactococcus decreased, while numbers of Enterobacteriaceae increased, including E. coli. Depletion of gut bacteria by antibiotic treatment had no effect on virus-induced lung injury, but protected the intestine from damage. Transferring Enterobacteriaceae from virus-infected mice to uninfected animals lead to intestinal injury, as did inoculating mice intragastrically with E. coli.

To understand why influenza virus infection in the lung can alter the gut microbiota, the authors examined immune cells in the gut. They found that Mice lacking the cytokine IL-17A, which is produced by Th17 helper T cells, did not develop intestinal injury after influenza virus infection. However these animals did develop lung injury.

Th17 cells are a type of helper T cells (others include Th1 and Th2 helper T cells) that are important for microbial defenses at epithelial barriers. They achieve this function in part by producing cytokines, including IL-17A. Th17 cells appear to play a role in intestinal injury caused by influenza virus infection of the lung. The number of Th17 cells in the intestine of mice increased after influenza virus infection, but not in the liver or kidney. In addition, giving mice antibody to IL-17A reduced intestinal injury.

There is a relationship between the intestinal microbiome and Th17 cells. In mice treated with antibiotics, there was no increase in the number of Th17 cells in the intestine following influenza virus infection. When gut bacteria from influenza virus-infected mice were transferred into uninfected animals, IL-17A levels increased. This effect was not observed if recipient animals were treated with antibiotics.

A key question is how influenza virus infection in the lung affects the gut microbiota. The chemokine CCL25, produced by intestinal epithelial cells, attracts lymphocytes from the lung to the gut. Production of CCL25 in the intestine increased in influenza virus infected mice, and treating mice with an antibody to this cytokine reduced intestinal injury and blocked the changes in the gut microbiome.

The helper T lymphocytes that are recruited to the intestine by the CCL25 chemokine produce the chemokine receptor called CCR9. These CCR9 positive Th cells increased in number in the lung and intestine of influenza virus infected mice. When helper T cells from virus infected mice were transferred into uninfected animals, they homed to the lung; after virus infection, they were also found in the intestine.

How do CCR9 positive Th cells from the lung influence the gut microbiota? The culprit appears to be interferon gamma, produced by the lung derived Th cells. In mice lacking interferon gamma, virus infection leads to reduced intestinal injury and normal levels of IL-17A. The lung derived CCR9 positive Th cells are responsible for increased numbers of Th17 cells in the gut through the cytokine IL-15.

These results show that influenza virus infection of the lung leads to production of CCR9 positive Th cells, which migrate to the gut. These cells produce interferon gamma, which alters the gut microbiome. Numbers of Th17 cells in the gut increase, leading to intestinal injury. The altered gut microbiome also stimulates IL-15 production which in turn increases Th17 cell numbers.

It has been proposed that all mucosal surfaces are linked by a common, interconnected mucosal immune system. The results presented in this study are consistent with communication between the lung and gut mucosa. Other examples of a common mucosal immune system include the prevention of asthma in mice by the bacterium Helicobacter pylori in the stomach, and vaginal protection against herpes simplex virus type 2 infection conferred by intransal immunization.

Do these results explain the gastrointestinal symptoms that may accompany influenza in humans? The answer is not clear, because influenza PR8 infection of mice is a highly artificial model of infection. It should be possible to sample human intestinal contents and determine if alterations observed in mice in the gut microbiome, Th17 cells, and interferon gamma production are also observed during influenza infection of the lung.

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CaribouRecovering viral genomes from ancient specimens can provide information about viral evolution, but not many old nucleic acids have been identified. A study of 700 year old caribou feces reveals that viruses can be protected for long periods of time – under the right conditions.

The oldest virus recovered so far is the giant Pithovirus sibericum, which was isolated from 30,000 year old Siberian permafrost. Other attempts have yielded fragments of viral genomes. It was possible to reconstruct the 1918 influenza virus from small RNAs recovered from formalin fixed and frozen human tissues. However this feat was not achieved for viral RNA in 140,000 year old Greenland ice cores, 900 year old North African barley grains, or 7,000 year old Black Sea Sediments.

Caribou feces have been frozen for the past 5,000 years in ice patches in the Selwyn Mountains of the Canadian Northwest territories. To determine if viruses could be recovered from this material, the frozen feces were thawed, resuspended in buffer, filtered, and treated with nucleases to destroy any nucleic acids not contained within a viral capsid. Sequence analysis of the remaining nucleic acids revealed two different viruses.

Ancient caribou feces associated virus (aCFV) has a single stranded, circular DNA genome distantly related to plant-infecting geminiviruses and gemycircularviruses. The entire 2.2 kb genome of aCFV was amplified from the caribou feces specimen. This reconstructed viral DNA replicated upon introduction into tobacco plant leaves.

Sequences of an RNA virus distantly related to picornaviruses of insects (such as Drosophila C virus) were also identified in the caribou feces. These viral genomes exceed 7.4 kb, but it was only possible to recover a 1.8 kb fragment of this virus, ancient Northwest Territories cripavirus (aNCV).

Neither virus was isolated from contemporary Caribou feces collected from an animal living in the same region. The authors also went to great pains to demonstrate that the two 700 year old viral genomes were not contaminants. The isolation was repeated in a different laboratory, and was not to be a consequence of contamination from any laboratory reagent or apparatus used for purification of nucleic acids.

It is not likely that aCFV or aNCV infected a caribou 700 years ago. The viruses were probably acquired when a caribou ingested plant material infected with the plant virus; perhaps insects harboring aNCV were also present on these plants. The exact hosts for both viruses are unknown.

The fact that two relatively large fragments of viral DNA and RNA were identified suggests that intact capsids were present in the caribou feces. Their preservation is probably a consequence of the low temperature of the arctic ice, and the stable icosahedral capsids characteristic of members of geminiviruses, gemycircularviruses, and cripaviruses.

We already know that viruses have been around for a long time, more than hundreds of millions of years, so what is the value of this work? Studying ancient viruses can provide insight into viral diversity and evolution. However, the value of two viral genome sequences is limited, and additional work should be done to acquire additional specimens spanning a long period of time. Similar sampling of other environments would also be desirable, but it is unlikely that large fragments of viral genomes can be recovered from specimens that are not frozen. And as the ice caps melt away, we will lose our ability to decode this important viral record.

Image credit

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On episode #314 of the science show This Week in Virology, Vincent travels to Albert Einstein College of Medicine where he speaks with Kartik, Ganjam, and Margaret about their work on Ebolavirus entry, a tumor suppressor that binds the HIV-1 integrase, and the entry of togaviruses and flaviviruses into cells.

You can find TWiV #314 at www.twiv.tv.

On episode #313 of the science show This Week in Virology, Vincent, Alan, and Rich discuss how norovirus, an enteric virus, can replace the functions of the gut microbiome.

You can find TWiV #313 at www.twiv.tv.

antibodies bound to Ebola virus GPZMapp, a mixture of three antibodies against Ebola virus, became a household name after it was used to treat two Americans who were infected while working in Liberia. The structure of these antibodies bound to the Ebola virus glycoprotein suggest how they inhibit infection and ways to improve ZMapp.

The three monoclonal antibodies that comprise ZMapp (called c13C6, c2G4, and c4G7) were produced by immunizing mice with a recombinant vesicular stomatitis virus in which the glycoprotein was replaced with that from Ebola virus. Antibodies that bound the viral glycoprotein and protected mice from infection were identified, and three were made to resemble human antibodies and produced in tobacco plants. Ecco Zmapp!

Embedded in the membrane of the filamentous Ebola virus particle are many copies of the Filovirusglycoprotein, seen as club-shaped spikes in the image to the right (image credit: ViralZone). The viral glycoprotein is essential for entry of the virus into cells. The antibodies in ZMapp are directed against the viral glycoprotein.

To determine how the antibodies bind the virus particle, they were individually mixed with purified Ebola virus glycoprotein, and the structures were determined by electron microscopy and image reconstruction. The results, shown in the illustration, indicate precisely where each antibody binds to the Ebola virus glycoprotein. The individual antibodies colored red (c2G4), yellow (c4G7), and purple (c13C6) are bound to a single Ebola virus glycoprotein in white, with the viral membrane below (Image credit).

The structures reveal that c13C6 (purple) binds at the tip of the viral glycoprotein, perpendicular to the plane of the viral membrane. The other two antibodies (red, yellow) bind at the base of the viral glycoprotein. Their binding sites overlap but are not identical (the Ebola virus glycoprotein is a trimer, and in the image, the yellow and red antibodies are shown binding to different subunits for clarity). Two other antibodies that block Ebola virus infection also bind at the base of the glycoprotein.

Antibody c13C6, which binds to the tip of the viral glycoprotein, does not neutralize viral infectivity. Nevertheless, it can protect animals from Ebola virus infection. This observation suggests that the c13C6 antibody may work in concert with complement, a collection of serum proteins, to block virus infection. It is not known why c13C6 antibody is non-neutralizing, but one possibility is that it binds to a part of the viral glycoprotein that is removed by an endosomal protease, cathepsin, before receptor binding in late endosomes.

Antibodies c2G4 and c4G7, which bind to the membrane-proximal part of the viral glycoprotein, neutralize viral infectivity. How they do so is not known, but one possibility is that they prevent structural changes of the viral protein that are essential for the fusion with the endosomal membrane, a process that delivers the viral nucleic acid into the cell cytoplasm.

These studies reveal two general areas of the Ebola virus glycoprotein that are important targets for antibodies that protect animals from Ebola virus infection. Those directed at the base of the glycoprotein neutralize infectivity while those that bind the tip do not. This information can now be used to isolate additional antibodies that bind either site. These can be used in animal protection studies to design mixtures that are even more potent than ZMapp.

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TWiV 312: She sells B cells

23 November 2014

On episode #312 of the science show This Week in Virology, the TWiVbolans discuss the finding that human noroviruses, major causes of gastroenteritis, can for the first time be propagated in B cell cultures, with the help of enteric bacteria.

You can find TWiV #312 at www.twiv.tv.

A virus that melts sea stars

17 November 2014

Sun flower sea starSea stars are lovely marine invertebrates with a round central body connected to multiple radiating legs (photo credit). In the past year millions of sea stars in the west coast waters of North America have melted into piles of slime and ossicles. Sea star associated densovirus might be the cause of this lethal disease.

Sea star wasting disease (SSWD) is characterized by lesions, limb curling and deflation, and death as the animals rapidly degrade or ‘melt’. The current outbreak began in June 2013 and has killed sea stars from Baja California, Mexico, to Southern Alaska. SSWD might be the biggest marine wildlife epizootic ever observed.

Evidence that SSWD is caused by a virus came from experiments in which extracts of diseased sea stars were passed through a filter with pore sizes small enough to allow passage of viruses but not bacteria or other microbes. When injected into healthy sea stars, these filtrates induced sea star wasting disease. Extracts of diseased sea stars collected in Vancouver, CA contained 25 nanometer virus particles, as determined by electron microscopy.

Nucleic acid sequencing was to identify the viral agent of SSWD. Virus particles were purified from diseased animals, and both DNA and RNA was extracted. Analysis of the nucleotide sequences revealed the presence of giant DNA viruses such as mimiviruses and phycodnaviruses (link to algal virus paper), and among RNA viruses, retroviruses, dicistroviruses, and parvoviruses. With few exceptions, all samples containing parvoviruses were from symptomatic asteroids, and so the authors decided to pursue the study of this virus.

Analysis of the DNA sequence data revealed the presence of a densovirus (a parvovirus) related to viruses found in Hawaiian sea urchins. The authors called this virus sea star-associated densovirus, SSaDV. Like other members of the parvovirus family, these are small (25 nm diameter), naked icosahedral viruses with a ~6 kb single stranded DNA genome. When sea stars were infected in the laboratory with filtrates from diseased animals, virus loads, determined by PCR, increased with time together with disease progression. Field surveys revealed that the virus was more abundant in diseased than in healthy sea stars. The virus was found in marine sediments, plankton, and sea urchins. Viral nucleic acid was also found in sea stars preserved in museums since 1942.

While retrovirus sequences were found in sea star tissues, the authors believe that such ‘Retroviral annotations are likely spurious because they were detected in DNA libraries (and have RNA as nucleic acids).’ The detection of retrovirus sequences in sea stars is not at all spurious! DNA copies of retrovirus genomes are produced during infection and integrated into the host genome, explaining why these sequences were detected in DNA libraries. Their absence in RNA libraries means that virus particles are not produced, as is the case in many other organisms that contain endogenous retroviruses.

The evidence that SSaDV causes sea star wasting disease is strong but not yet complete. The crucial experiment that remains to be done is to isolate infectious virus in cell culture, inoculate it into sea stars, and show that it causes wasting disease.

While the authors’ work reveals that sea star wasting disease virus has been present on the North American Pacific Coast for over 70 years, the disease is not always observed. The current outbreak has been ongoing since just June 2013. Perhaps other environmental conditions have lead to the increased susceptibility of sea stars to disease. It is important to determine if a human activity is involved in precipitating the disease, so that we can prevent future loss of sea stars. The authors suggest one possibility, that increased populations of adult sea stars in small bays and inlets have produced increased virus levels which lead to more infections. It will also be important to determine if the virus has undergone any changes in transmissibility or virulence.

Sea star associated densovirus was also found in non-asteroids, including ophiuroids (brittle stars and basket stars) and echinoids (sea urchins and sand dollars). We need to know the host range of this virus, how it is transmitted, and whether it can cause disease in other species. A troubling scenario is that the recent amplification of the virus in sea stars could lead to infection, and perhaps death of, many other marine species.

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