TWiV 194: Five postdocs in North America

On episode #194 of the science show This Week in Virology, Vincent returns to Madison, Wisconsin and meets with postdocs to discuss their science and their careers.

You can find TWiV #194 at

TWiV 185: Dead parrots and live Wildcats

On episode #185 of the science show This Week in Virology, Vincent visits with members of the Department of Microbiology and Immunology at Northwestern University School of Medicine to discuss their work on herpesviruses and parainfluenzaviruses.

You can find TWiV #185 at

TWiV 132: Virology 911

alfred sacchettiHosts: Vincent Racaniello, Rich Condit, Dickson DespommierAlan Dove, and Alfred Sacchetti

Vincent, Rich, Alan, and Dickson speak with Alfred Sacchetti, MD, Chief of Emergency Services at Our Lady of Lourdes Medical Center, about viral infections encountered in the emergency room.

Click the arrow above to play, or right-click to download TWiV #132 (48 MB .mp3, 100 minutes).

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Weekly Science Picks

Al – The Physics of Superheroes and NKT Watch
Dickson –
Fibonacci Fun by Trudi Hammel Garland and Rachel Gage
Rich – Retraction Watch
Alan – Neil deGrasse’s comments on UFOs, argument from ignorance, and scientific method (YouTube)
Microcosm by Carl Zimmer
Vincent – The intestinal microbiota and viral susceptibility

Listener Pick of the Week

Jim  – Extraordinary Measures

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TWiV 115: Color me infected

brainbow pseudorabies virusHosts: Vincent RacanielloAlan DoveRich Condit, and Marc Pelletier

On episode #115 of the podcast This Week in Virology, Vincent, Alan, Rich and Marc discuss the finding that a limited number of incoming herpesviral genomes can replicate and express in a cell, and controlling viral replication in Aedes aegypti with a Wolbachia symbiont.

Click the arrow above to play, or right-click to download TWiV #115 (84 MB .mp3, 117 minutes).

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Marc – Homebrew bioreactor (photo, movie) – culture bottle and drive, oil-free vacuum pumps
Rich –
Logitech Harmony Universal Remote
Alan – H.M.S. Challenger Reports
Vincent – Sequence of the strawberry genome and blog post by lead author

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TWiV 106: Making viral DNA II

the 5prime end problemHosts: Vincent Racaniello, Dickson Despommier, and Rich Condit

On episode #106 of the podcast This Week in Virology, Vincent, Dickson, and Rich continue Virology 101 with a second installment of their discussion of how viruses with DNA genomes replicate their genetic information.

Click the arrow above to play, or right-click to download TWiV #106 (69 MB .mp3, 95 minutes)

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  • Figures for this episode (pdf)
  • Letters read on TWiV 106
  • Video of this episode – download .mov or .wmv or view below

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Rich – Google Health
Dickson – The Neandertal genome
Vincent – Lab techniques videos (thanks, Erik!)

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Bats harbor many viral sequences

How large is the zoonotic pool – all the animal viruses that could one day infect humans? Assuming that there are 50,000 vertebrates on earth, each with 20 viruses, the number is one million – probably a vast underestimate. Determining just how many viruses exist in a variety of animal species is technically feasible, limited only by the number of hosts that can be sampled. A study of the virome of several North America bats reveals that these animals – which constitute 25% of all the known mammalian species – harbor a very large collection of viral sequences.

Advances in nucleotide sequencing technologies (deep sequencing) have made it possible in recent years to study the virome – the genomes of all viruses in a host – in human blood, diarrhea, and respiratory secretions; grapevines, and feces of horses and bats. The latter mammals are a particularly important subject because it is known that they harbor the predecessors of several important human viruses, including SARS coronavirus, ebolavirus, marburgvirus, Nipah, Hendra, and rabies viruses. Since there are about 1200 known species of bats, the potential for future human zoonoses is significant.

A multicenter group comprising virologists* and chiropterists (scientists who study bats) has examined the virome of three North American bat species: big brown bats (Eptesicus fuscus), tri-colored bats (Perimyotis subflavus), and little brown myotis (Myotis lucifugus). Deep sequencing was used to analyze fecal and oral samples from 41 bats captured on one night in Western Maryland. The results provide a comprehensive glimpse of the bat virome.

The 576,624 sequence ‘reads’ (a read is the result of a single sequence reaction, in this study ~250 nucleotides) on six pools of fecal samples revealed an amazing diversity of viral sequences (figure), with representatives of human, other mammals, insect, bacteriophage, fish, shrimp, protist, reptile, plant, avian, fungi, algae, and marine viruses. Among the interesting findings are sequences of three novel coronaviruses from big brown bats. Many coronaviruses have previously been found in bats; the results of this study provide more evidence that these mammals are likely to be sources of future human infections.

Novel viruses of plants and insects were also identified in fecal samples from all bats. This observation can be explained by the bats’ prodigious appetite for insects, which harbor both insect or plant viruses (the latter transmitted to plants by insect vectors). It seems unlikely that these viruses replicate in bats, but pass through the gastrointestinal tract into the feces.

Perhaps not surprisingly (given the diversity of bacteria that colonize mammalian intestinal tracts), sequences of novel bacteriophages were also identified in fecal samples. One appears to have high sequence identity with a bacteriophage that infects the plague bacterium Yersina pestis. Curiously, such bacteria are not known to colonies animals in the northeastern United States. A second bacteriophage infects strains of E. coli associated with human illnesses. These findings suggest that bats could be involved in the spread of human bacterial pathogens.

The main viral sequences identified in pooled oral samples were of a novel cytomegalovirus. These viruses appear to be common in bats, and have been been detected in many previous studies.

One question that arises from these findings is whether bats are unique in harboring a large collection of diverse viruses. The answer to this question awaits studies of the viromes of other wild animals.

Viral discovery by massive sequencing will no doubt identify many new viruses in a wide range of species. However, this technology cannot answer some of the more intriguing biological questions, such as which hosts support viral replication, and whether it is associated with disease. Answers to these questions will require construction of complete DNA copies of viral genomes and recovery of infectious viruses by transfection of cells in culture.

The title of this post is ‘Bats harbor many viral sequences’, not ‘many viruses’. That’s because no infectious viruses were identified – only parts of their genomes. If you wish to conclude that a certain virus infects bats, you must either isolate the virus in cell culture, or show that the entire viral genome is present in tissues or fluids.

*including Eric F. Donaldson and Matt Frieman, who spoke about this work on TWiV 90 and 65.

Donaldson EF, Haskew AN, Gates JE, Huynh J, Moore CJ, & Frieman MB (2010). Metagenomic Analysis of the Virome of three North American Bat Species: Viral Diversity Between Different Bat Species that Share a Common Habitat. Journal of virology PMID: 20926577

TWiV 84: Gators go viral

Hosts: Vincent Racaniello, Rich Condit, Dave Bloom, and Grant McFadden

On episode #84 of the podcast This Week in Virology, Vincent and Rich spoke with Dave Bloom and Grant McFadden about their work on herpesviruses and poxviruses in this episode recorded before an audience at the University of Florida, Gainesville – home of the Gators.

This episode is sponsored by Data Robotics Inc. Use the promotion code TWIVPOD to receive $75-$500 off a Drobo.

Win a free Drobo S! Contest rules here.

Click the arrow above to play, or right-click to download TWiV #84 (71 MB .mp3, 99 minutes)

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Rich Charles F. Littlewood photographs
Not so humble pie (thanks, Sophie!)
GrantThe Strangest Man by Graham Farmelo
DavidIs Parkinson’s Disease a prion disorder?

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What color is a virus?

neuronconnThe Nobel Prize in Chemistry for 2008 was awarded to Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien for the discovery and development of the green fluorescent protein, GFP. Dr. Chalfie’s contribution was to show that GFP could be used as a genetic tag by producing the protein in the transparent roundworm Caenorhabditis elegans. Who was the first to insert the gene for GFP into a viral genome?

The GFP gene was first inserted into the genome of potato virus X, a plant pathogen. One to two days after inoculation of the recombinant virus onto plants, regions of the leaves fluoresced bright green when illuminated with UV light. Animal viruses followed several years later, with insertion of the GFP gene into the genome of adenovirus. Infection with the recombinant virus lead to green fluorescence in cultured mammalian cells and in living brain slices, suggesting the possibility of using this technology to trace neuronal connections. This potential was subsequently realized when recombinant viruses that produce GFP were used to trace neuronal connections in the nervous system of living animals. Proteins like GFP that emit light of different wavelengths have been discovered in different organisms, allowing the tracking of multiple proteins in virus infected cells.

More recently, fluorescent proteins have been used to visualize single virus particles in living cells. In an early validation of the technique, the gene encoding the herpes simplex virus type 1 VP26 protein, which is located on the outer surface of the capsid, was fused with the coding sequence for GFP. The fusion protein was incorporated into intranuclear capsids and mature virions, which produced green fluorescence in infected cells. By using such viruses, entry, uncoating, replication, assembly, and exit of single virus particles can be studied in real time in living cells. For example, the movement of HIV-1 particles labeled with GFP (by fusion with the viral protein Vpr) was beautifully visualized in cells that had been injected with rhodamine-tubulin to label microtubules.

Of course, virus particles are too small to have color. I once told this to a second-grade class as I was showing them the X-ray structures of eight different picornaviruses, each of which I had colored differently. One young man raised his hand and said “Do you make them different colors just to know which is which?” Who said you can’t teach virology in elementary school!

M Chalfie, Y Tu, G Euskirchen, W. Ward, D. Prasher (1994). Green fluorescent protein as a marker for gene expression Science, 263 (5148), 802-805 DOI: 10.1126/science.8303295

David C. Baulcombe, Sean Chapman, Simon Cruz (1995). Jellyfish green fluorescent protein as a reporter for virus infections The Plant Journal, 7 (6), 1045-1053 DOI: 10.1046/j.1365-313X.1995.07061045.x

K MORIYOSHI, L RICHARDS, C AKAZAWA, D OLEARY, S NAKANISHI (1996). Labeling Neural Cells Using Adenoviral Gene Transfer of Membrane-Targeted GFP Neuron, 16 (2), 255-260 DOI: 10.1016/S0896-6273(00)80044-6

Desai P Person S (1998) Incorporation of the green fluorescent protein into the herpes simplex virus type 1 capsid. J. Virol. 72:7563-7568.

M EKSTRAND (2008). The alpha-herpesviruses: molecular pathfinders in nervous system circuits Trends in Molecular Medicine, 14 (3), 134-140 DOI: 10.1016/j.molmed.2007.12.008

D. McDonald Vodicka MA, Lucero G, Svitkina TM, Borisy GG, Emerman M, Hope TJ. (2002). Visualization of the intracellular behavior of HIV in living cells The Journal of Cell Biology, 159 (3), 441-452 DOI: 10.1083/jcb.200203150

Equine herpesvirus 9 in zoo animals

We previously discussed infection of zoo elephants with endotheliotropic elephant herpesvirus in This Week in Virology episode #7. A recent report in Emerging Infectious Diseases indicates that another herpesvirus, equine herpesvirus 9, is also infecting zoo animals. In July 2007, a polar bear in the San Diego Zoo developed encephalitis and was subsequently euthanized. Polymerase chain reaction was used to identify EHV-9 in the animal’s brain. The virus was also identified in members of a herd of Grevy’s zebras which was housed in close proximity to the polar bear.  The authors of the study speculate that the virus was transmitted from the zebras to the polar bear by fomites (contaminated objects). 

EHV-9 has been previously shown to cause encephalitis in Thomson’s gazelles and giraffes. EHV-9 and the highly related EHV-1 are endemic in horses. EHV-9 can also infect other animal species, including primates. The studies discussed here demonstrate that the host range of this virus is broader than previously known. 

With respect to virus infections, zoos appear to be a microcosm of the wild. The ability to rapidly and definitively identify the etiologic agents of viral diseases in zoos has changed how we view infection of a broad range of animal species. Studies of the kind reported here will provide a great deal of information about viral pathogenesis, tropism, and host range.

The Department of Veterinary Science at the University of Kentucky College of Agriculture has an excellent website on diseases of the horse caused by equine herpesviruses.

Emerging viruses?

The term emerging virus was coined by scientists in the 1990s to describe the agent of a new or previously unrecognized infection. The term implies that emerging viruses are new; however this assumption is incorrect. New virus infections have been emerging for thousands of years, at least since the rise of agriculture 11,000 years ago. The development of agriculture and commerce provided the large populations needed to sustain human infections such as measles and smallpox.

Viruses probably (although we do not know for sure) appeared when living cells evolved, possibly even before. They subsequently infected multicellular forms of life and then mammals, which were present on the globe before humans. Humans then acquired virus infections from animals (an infection transmitted from animals to humans is a zoonosis). At some point the number of virus genomes and virion structures became established, and for the next millions of years, viruses evolved. It is unlikely that new viruses emerge de novo; rather they evolve from existing viruses.

Some examples serve to illustrate the origins of viruses. Comparisons of genome sequences of today’s members of the herpesvirus family has lead to the suggestion that these viruses arose 180-220 milllion years ago, possibly from ancestors of similar viruses that infect oysters and fish today. Smallpox virus may have emerged after an infection of humans with a gerbil poxvirus. Measles virus may have originated from infection of humans with an ancestor of a virus that today infects cows, rinderpest virus. It has been suggested that the virus ‘jumped’ from cows to humans about 5,000 years ago, when humans first began to domesticate cattle. Measles virus then spread throughout the Middle East and was then brought to the Americas by colonization and migration, where it had lethal effects on the Native Americans.

It is safe to say that all of the human viruses that exist today originated from a zoonotic infection. In some cases, related viruses still infect animals (e.g. measles and rinderpest virus). However, often the human virus has no known counterpart in animals. An example is the human pathogen, poliovirus. The ancestral poliovirus is not known, and there are currently no hosts for the virus other than humans. However, other members of the picornavirus family, of which poliovirus is a member, infect a variety of animals, and ancient versions of these viruses may have made the jump from animals to humans.

Two simple facts ensure that new human virus infections will continue to emerge from animal hosts. The first is the ability of viruses to produce huge numbers of progeny (billions and billions!) with a high level of diversity (mutation). The second is the fact that human and non-human animal populations continue to grow and interact. Put another way, humans are always finding new ways to acquire novel virus infections!

Viral evolution is a fascinating subject. A good place to start reading about it would be Principles of Virology, volume II, chapter 10.