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TWiV 60: Making viral RNA

29 November 2009 by Vincent Racaniello

TWiV_AA_200Hosts: Vincent Racaniello and Dickson Despommier

Vincent and Dick continue Virology 101 with a discussion of how RNA viruses produce mRNA and replicate their genomes.

[powerpress url=”http://traffic.libsyn.com/twiv/TWiV060.mp3″]

Click the arrow above to play, or right-click to download TWiV #60 (51 MB .mp3, 71 minutes)

Subscribe to TWiV in iTunes, by the RSS feed, or by email

Links for this episode:

  • Diagrams of viral RNA synthesis
  • Animations of influenza virus and HIV-1 replication
  • Video for this episode – see below

Weekly Science Picks
Dick The Double Helix by James D. Watson
Vincent
Worms and Germs Blog

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also send articles that you would like us to discuss to delicious and tag them with to:twivpodcast.

Below is a video of TWiV 60, which highlights the diagrams I referred to during the podcast.

Get the Flash Player to see this video.

Download TWiV 60 video. These videos are slightly larger (800 x 512) than the flash version shown above

186 MB .mov video file

584 MB .wmv video file

Filed Under: This Week in Virology Tagged With: genome, genome replication, influenza, mRNA, nucleic acid, poliovirus, polymerase, rabies, replication, RNA polymerase, rna synthesis, rotavirus, viral, virology, virus

TWiV 49: Viral genomes

13 September 2009 by Vincent Racaniello

twiv-200Hosts: Vincent Racaniello and Dick Despommier

On episode 49 of the podcast ‘This Week in Virology”, Vincent and Dick continue Virology 101 with a discussion of the seven different types of viral genomes, and how to use the pathway to mRNA to understand viral replication.

[powerpress url=”http://traffic.libsyn.com/twiv/TWiV049.mp3″]

Click the arrow above to play, or right-click to download TWiV #49 (45 MB .mp3, 62 minutes)

Subscribe to TWiV in iTunes, by the RSS feed, or by email

Links for this episode:
Dick talks about hookworm on Radio Lab
Dick’s video page at BigThink
The seven types of viral genome
Animation of HIV replication (thanks axiomatically atypical!)
Changes in transcript abundance relating to colony collapse disorder in honey bee (thanks Judi!)

Weekly Science Picks
Dick Discovery Channel: Planet Green
Vincent Influenza videos at BigThink: one, two, three, four, five, six

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also send articles that you would like us to discuss to delicious and tagging them with to:twivpodcast.

Filed Under: This Week in Virology Tagged With: colony collapse, david baltimore, DNA, genome, H1N1, HIV, hookworm, influenza, pandemic, RNA, swine flu, viral, virology, virus

How viruses are classified

7 August 2009 by Vincent Racaniello

virosphere-2005For the first 60 years of virus discovery, there was no system for classifying viruses. Consequently viruses were named haphazardly, a practice that continues today.

Vertebrate viruses may be named according to the associated diseases (poliovirus, rabies), the type of disease caused (murine leukemia virus), or the sites in the body affected or from which the virus was first isolated (rhinovirus, adenovirus). Some viruses are named for where they were first isolated (Sendai virus, Coxsackievirus), for the scientists who discovered them (Epstein-Barr virus), or for the way people imagined they were contracted (dengue = ‘evil spirit’; influenza = ‘influence’ of bad air).

By the early 1960s, new viruses were being discovered and studied by electron microscopy. As particles of different sizes, shapes, and composition were identified, it became clear that a systematic nomenclature was needed. Lwoff, Horne, and Tournier suggested a comprehensive scheme for classifying all viruses in 1962. Their proposal used the classical Linnaean hierarchical system of phylum, class, order, family, genus and species. The complete scheme was not adopted, but animal viruses were soon classified by family, genus, and species.

An important part of the scheme proposed by Lwoff and colleagues is that viruses are grouped according to their properties, not the cells they infect. The nucleic acid genome was also recognized as a primary criterion for classification. Four characteristics were to be used for the classification of all viruses:

  1. Nature of the nucleic acid in the virion
  2. Symmetry of the protein shell
  3. Presence or absence of a lipid membrane
  4. Dimensions of the virion and capsid

Other characteristics which were subsequently added include the type of disease caused, and which animals and tissues are infected. With the development of nucleic acid sequencing technologies in the 1970s, genomics has played an increasingly important role in taxonomy. Today new viruses are assigned to families based on the nucleic acid sequence of their genome.

The International Committee on the Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. A complete catalog of known viruses is maintained by the ICTV at ICTVdb. Although the ICTV nomenclature is used to classify animals viruses, plant virologists do not place their viruses into families and genera, but use group names derived from the prototype virus.

Because the viral genome carries the blueprint for producing new viruses, virologists consider it the most important characteristic for classification. Next we’ll discuss the Baltimore classification, an alternative scheme based on the viral genome.

Lwoff, A., Horne, R., & Tournier, P. (1962). A system of viruses. Cold Spring Harb Symp Quant Biol., 27, 51-55

Buchen-Osmond, C. (2003). The universal virus database ICTVdB Computing in Science & Engineering, 5 (3), 16-25 DOI: 10.1109/MCISE.2003.1196303

Filed Under: Basic virology, Information Tagged With: capsid, classification, genome, ICTV, ICTVdb, nucleic acid, viral, virology, virus

TWiV 32: Influenza in silico

17 May 2009 by Vincent Racaniello

twiv-200On episode #32 of the podcast “This Week in Virology”, Vincent, Alan, and Raul Rabadan converse about polio survivors in iron lungs, bocavirus, structure of mimivirus, and genome sequence analysis of influenza H1N1 viruses.

[powerpress url=”http://traffic.libsyn.com/twiv/TWiV032.mp3″]

Click the arrow above to play, or right-click to download TWiV #32 or subscribe in iTunes or by email.

Filed Under: Information Tagged With: bioinformatics, bocavirus, genome, H1N1, influenza, iron lung, mimivirus, pandemic, podcast, poliovirus, sequence, swine flu, TWiV, viral, virology, virus

Is an effective treatment for the common cold at hand?

16 February 2009 by Vincent Racaniello

2289334120_c27ed36206_mThe sequence of all known rhinovirus genomes reported in Science last week is an important advance for the field. Analyses of the sequences have revealed new relationships among the viruses, evidence for recombination, a new viral species, and conserved regions of the genome. These findings will be extremely valuable for those studying the biology, pathogenesis, and epidemiology of the common cold. But the press has over reacted to this work –  it was reported on the front page of the New York Times with the headline “Cure for the Common Cold? Not Yet, but Possible”.  Does the work deserve such fanfare?

The Times quoted Stephen Liggett, an asthma expert, as saying “We are now quite certain that we see the Achilles’ heel, and that a very effective treatment for the common cold is at hand.” He was apparently referring to the observation that a sequence within the 5′-noncoding region of the viral genome is highly conserved among the 99 rhinovirus sequences, in comparison with other regions of the viral RNA. He suggested that all 99 rhinovirus serotypes would therefore be susceptible to the same drug. But what kind of drug, and what function would it inhibit? The very 5′-end of the genome of enteroviruses and rhinoviruses binds viral and cellular proteins, and these interactions are essential for viral replication. So it might be possible to identify small molecules that block these protein-RNA interactions. But such drugs are very difficult to identify. Furthermore, if such a drug were identified, its efficacy would have to be tested against all rhinovirus serotypes. Therefore it is not clear that knowing that this sequence of the genome is conserved helps to identify drug targets and more readily than did the observations made years ago about the importance of RNA-protein interactions in this region. Clearly, many years of research are needed before such drugs are developed – not consistent with Dr. Liggett’s a treatment is ‘at hand’.

An even more crucial aspect of the problem was omitted from the Times article. Even if an antiviral drug could be identified that blocks essential RNA-protein interactions, it probably would not be useful in treating the common cold. As we discussed last week, rhinoviruses cause acute infections - characterized by rapid onset of disease, a relatively brief period of symptoms, and resolution within days. Most are complete by the time the patient feels ill, and the virus has already spread to another host. Antiviral therapy  must be given early in infection to be effective. There is little hope of treating most acute viral infections with antiviral drugs until rapid diagnostic tests are become available.

To be fair, some of the scientists quoted in the Times article were more realistic about the possibilities for rhinovirus treatments. One antiviral drug expert noted that it costs about $700 million to bring a drug to market. Because most rhinovirus infections are benign, who would pay for such an expensive drug, and would the Food and Drug Administration ever approve it? Ann Palmenberg, the lead author on the study, was even more realistic, admitting that a rhinovirus vaccine would not likely be made.

I cannot see how this new study identified a new or better target for therapeutic intervention. So why get the public excited by running a front page headline in the New York Times? It’s great to keep the public informed about scientific progress – but the press should not cry wolf. If this advance does not soon lead to a treatment for the common cold, the public will shake their heads and lose a bit more trust in science.

I’m not blaming the scientists for this over reaction to their study. I am sure that the journal Science engaged in strong pre-publication promotion: more publicity is better for their advertising revenues. And the newspapers are equally at fault: they should speak to a broader range of scientists to obtain a more balanced view. I particularly blame the author of the Times article, Nicholas Wade, for not sufficiently researching his article.

Perhaps Dr. Liggett and his colleagues would benefit from the lessons of history – specifically, the history of poliomyelitis and its conquest. On March 9, 1911, three years after the isolation of poliovirus, The Rockefeller Institute issued a press release, saying that it believed “that its search for a cure for infantile paralysis is about to be rewarded. Within six months, according to Dr. Simon Flexner, definite announcement of a specific remedy may be expected.” They quoted Dr. Flexner:  “We have already discovered how to prevent the disease, and the achievement of a cure, I may conservatively say, is not now far distant.” Dr. Flexner’s imminent ‘cure’ was a failure, and a successful poliovirus vaccine required another 44 years of research. Last week’s Times article seemed to have a similar overdose of hubris.

A. C. Palmenberg, D. Spiro, R. Kuzmickas, S. Wang, A. Djikeng, J. A. Rathe, C. M. Fraser-Liggett, S. B. Liggett (2009). Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveals Structure and Evolution Science DOI: 10.1126/science.1165557

Filed Under: Information Tagged With: common cold, genome, poliovirus, rhinovirus

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