TWiV 246: Pandora, pandemics, and privacy

On episode #246 of the science show This Week in Virology, Vincent, Alan, Rich, and Kathy discuss the huge Pandoravirus, virologists planning H7N9 gain of function experiments, and limited access to the HeLa cell genome sequence.

You can find TWiV #246 at

We recorded this episode of TWiV as a Google hangout on air. Consequently the audio is not the same quality as you might be used to. But the tradeoff is that you can see each of us on video.


TWiM 5: Mercury-methylating Desulfovibrio and antimicrobial nanoparticles

desulfovibrio biofilmHosts: Vincent Racaniello, Cliff Mintz, Michael Schmidt, and Ronald Atlas.

Vincent, Cliff, Michael and Ron discuss the genome sequqnce of a mercury-methylating bacterium and the antimicrobial effects of nanoparticles.

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Click the arrow above to play, or right click to download TWiM #5 (52.5 MB .mp3, 76 minutes).

Subscribe to TWiM (free) on iTunesZune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Image of Biofilm of Desulfovibrio desulfuricans by PNNL – Pacific Northwest National Laboratory via flickr

Links for this episode:

Send your microbiology questions and comments (email or mp3 file) to, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at and tag them with twim.

TWiV 32: Influenza in silico

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.

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

Nucleotide sequences of influenza A/Mexico/2009 (H1N1) viruses available

Here at virology blog we have been speculating for a week why sequences of the Mexican influenza virus isolates have not been available. Today we received a comment from Dr. Ruben Donis, who we quoted in a previous post. Dr. Donis wrote:

Thank you for the nice vignette about the ScienceInsider interview. I would like to point out that full genome sequences of Mexican viruses have been available in the public domain at the GISAID database since April 24, 2009. Sequences were posted in the public domain as soon as they were completed and curated. The availability of sequences at GISAID was also posted at the WHO website (pdf)

I thank Dr. Donis for clarifying this situation. Clearly I and many readers of virology blog had missed the original WHO statement, and unfortunately we took the lack of sequence information as a sign of greed or evil intent. My apologies to all who were offended.

GISAID is the Global Initiative on Sharing Influenza Data, established in 2006 to help sharing data on influenza virus:

Several countries and international agencies have recently taken steps to improve sharing of influenza data following the initiative of leading veterinary virologists in the field of avian influenza. However, the current level of collection and sharing of data is inadequate given the magnitude of the threat. We propose to expand and complement existing efforts with the creation of a global consortium – the Global Initiative on Sharing Avian Influenza Data (GISAID) – that would foster international sharing of avian influenza isolates and data.

Registration is required for access to the site.

Structure of influenza virus

influenza-virion3In this week’s discussion of swine flu A/Mexico/09 (H1N1), we have considered many aspects of influenza virus biology that might not be familiar to some readers of virology blog. I thought it might be useful to explain how the virus multiplies, how it infects us, and how we combat infection. Today we’ll start with the basic structure of influenza virus, illustrated above.

The influenza virion (as the infectious particle is called) is roughly spherical. It is an enveloped virus – that is, the outer layer is a lipid membrane which is taken from the host cell in which the virus multiplies. Inserted into the lipid membrane are ‘spikes’, which are proteins – actually glycoproteins, because they consist of protein linked to sugars – known as HA (hemagglutinin) and NA (neuraminidase). These are the proteins that determine the subtype of influenza virus (A/H1N1, for example). We’ll discuss later how the HA and NA are given subtype numbers. The HA and NA are important in the immune response against the virus; antibodies (proteins made by us to combat infection) against these spikes may protect against infection. The NA protein is the target of the antiviral drugs Relenza and Tamiflu. Also embedded in the lipid membrane is the M2 protein, which is the target of the antiviral adamantanes – amantadine and rimantadine.

Beneath the lipid membrane is a viral protein called M1, or matrix protein. This protein, which forms a shell, gives strength and rigidity to the lipid envelope. Within the interior of the virion are the viral RNAs – 8 of them for influenza A viruses. These are the genetic material of the virus; they code for one or two proteins. Each RNA segment, as they are called, consists of RNA joined with several proteins shown in the diagram: B1, PB2, PA, NP. These RNA segments are the genes of influenza virus. The interior of the virion also contains another protein called NEP.

This week, when we discussed the nucleotide sequence of swine influenza RNAs, we were referring to these RNA molecules. Tomorrow I’ll show you how each RNA codes for protein. This way it will be easier to understand the meaning of the swine flu virus sequences that were released this week.

Let me know if this type of explanation is useful, and if you would like me to continue.