Marian writes:

The question arose as to why RNA viruses, rather than DNA viruses, have such an abundance of mechanisms to increase the number of translated proteins. the largest known RNA viruses are coronaviruses at about 30 kb. this upper size limit is thought to be due to the error catastrophe. Presumably larger size would have a level of mutation not compatible with replication. therefore RNA viruses must maximize their coding capacity in a limited genomic space. thus an abundance of translation mechanisms.

minor point:

I believe it was stated that picornaviruses and flaviviruses have polyproteins. many other RNA viruses, such as coronaviruses, caliciviruses, alphaviruses and retroviruses, have polyproteins.

Sebastian writes:

Dear TWIV team,

Thanks for last week’s (06/06/2013 Episode#236) most enjoyable podcast. Towards the end you guys discussed a paper sent in by a listener (Schaller et al “Mere Visual Perception of Other People’s Disease Symptoms Facilitates a More Aggressive Immune Response”) and commented on the strangeness of the study. Just wanted to say that Dr. Dove was correct in asserting that psychology and immunity have a very intricate relationship which is described in the oft ignored field of psychoneuroimmunology (PNI). I have come to understand that outside of the select few psychologists who choose to study this interesting intersect of immunity and psychology, the work is virtually ignored by biomedical scientists; whether through ignorance of the field or poorly directed disdain at a “soft-science”, i.e. psychology. What a shame. It was a revelation to me when I first learned about this subject in undergrad to discover how the HPA-axis, glucocorticoid levels, and general psychological health influenced everything from recovery time in sick patients to the success of flu-vaccines. From what I can gather, some of the first data to emerge suggesting that stress and behavioral states influence immune behavior can be traced back to Harry Harlow’s infamous isolation experiments, where serum IgG and IgM titers in monkeys in response to immune challenges varied depending on time spent in isolation. Of course, more sophisticated (and humane) studies have been done since then, and for those who are interested I would suggest PubMed-ing “Maier Watkins” for some excellent work by the current stars of PNI. Please keep the great podcasts.



Hongju Wu Laboratory

Tulane University School of Medicine-Graduate Program in Biomedical Sciences

Eric writes:


I’m sure you get plenty of fanboy-isms already, so very briefly: love the podcast, longtime listener, first time emailer, etc.

On your most recent podcast, you reviewed two papers about the efficacy of AAV Vectors carrying human anti-influenza antibodies as vaccines. You and your contributors characterized Adeno Associated Virus vectors as integrating in a site-specific manner to a human locus (AAVS1) on chromosome 19, and identified such integration events as the primary mechanism of stable expression of vector payloads. Now, don’t quote me on any of this since I’ve only spent about nine months in the field of AAV gene therapy, but I’d like to suggest a correction: the primary mechanism of persistent gene expression likely does not involve any integration event.

Although tissue culture studies have demonstrated that AAV viral vectors integrate into human chromosome 19 at the AAVS1 locus in a highly specific manner, such integration events are largely considered to be in-vitro artifacts. Since the findings of Schnepp et al. 2005, the view is that (in vivo) AAV Genomes are maintained primarily as extrachromosomal concatamers which form as a result of interactions between inverted terminal repeats (ITRs) which flank the viral genomes.

One of the papers you mentioned use IM injection as the route of delivery of the vector. In the case of mouse muscle, it was found that the overwhelming majority of vector DNA within cells (>99.5%) is extrachromosomal (Schnepp et al., 2003). The rates of integration into other murine tissues (notably liver) have been demonstrated to be higher, but to the best of my (admittedly still very underdeveloped) knowledge, the rates of integration into various human tissues have not yet been compared.

Keep up the excellent work! Your podcast is part of the reason why I’m continuing to pursue a career in science!


Research Assistant

Vandenberghe Lab

Schepens Eye Research Institute

Harvard Medical School

Tim writes:

Hey Twivers,

I am wondering whether you think that broadly protective stalk-specific antibody delivery via AAV vectors could be a viable strategy for protection against influenza in the long run. Presumably, the reason that the stalk is highly conserved is because the host organism is typically unable to mount an immune response against the stalk epitope(s) – therefore there is very little selection pressure for variation in the stalk portion of HA. That’s not to say that variation of the stalk is impossible from the perspective of the virus, just that new antigenic variants wouldn’t be expected to dominate unless they also conferred some type of functional advantage. If a gene therapy technique were developed that allowed the “immunized” populations to target this region however, would we not expect to see different stalk variants arising soon after? Would the result be new influenza strains that needed to be classified based on three antigenic determinants instead of two (e.g. H7N9S1 – “S” for “stalk”)? If this were the case, I’m not sure we could keep up with variations in the “S” epitopes as they arose given the extremely laborious nature of isolating, identifying, and sub-cloning the genes for newly protective stalk-specific antibodies into AAV vectors – a whole different ballgame compared to shuffling a few influenza genes into a vaccine strain of virus for traditional immunization. Logistically, it seems to me that the future of utilizing these antibodies will depend on whether we can “convince” people’s own immune system to preferentially mount a response to these epitopes by delivering something more easily developed in response to newly emerging strains. Love to hear your take on this – thanks!

– Tim

PS I am writing this as a p.s. to the email I just sent about AAV vectors providing a selection pressure for novel “S” variants of influenza – as is often the case, writing down my question lead me to a partial answer, and another question. I am wondering what is known about the frequency/importance of transmission of influenza from humans back into pigs? Would an applied selection pressure in humans have any bearing on the ecology of influenza and the emergence of new variants? If not, a broad-spectrum “vaccine” like the AAV vectors could be useful against seasonal flu, or at the very least a good safety measure against a potential pandemic strain from birds or pigs that could be mass-produced before even knowing the HA/neuraminidase profile of the threatening strain.


Joseph writes:

Greetings TWiV Drs.,

First, let me start by saying thank you for a tremendous podcast; it’s one of the things in viral world that I hope is never eradicated. I became a TWiV listener last summer as I was preparing to teach a virology course at Lehigh University in the fall. Needless to say I was hooked immediately and tried my best to convert many of the students in the class to regular listeners. I hope it worked!

I wanted to write in about the Yang et al. paper discussed on the latest episode of TWiV to share my interpretation of the results. I have a special interest in this field- I did my Ph.D. with Ike Eisenlohr at Thomas Jefferson University where a major focus of the lab is antigen processing and presentation during influenza virus infections. I always try to read everything that I come across about influenza immune responses. I agree with Dr. Spindler that an analysis of HA/NA on the virion would be an important experiment to do- otherwise we are left to assume that a decrease in HA or NA synthesis automatically means a decrease on the virion surface which may or may not be true. But my initial thought (in agreement with what was briefly discussed on the podcast) is that the cross protection observed in these studies is a direct result of the adaptive immune response, specifically a CD4 driven response. The synthesis of internal genes was not affected in these mutant strains and degradation of these proteins most likely resulted in the presentation of conserved epitopes on MHC II (and probably MHC-I) molecules and subsequent activation of CD4- and CD8 T cells. Since a subset of these epitopes are conserved among influenza viruses, the cross protection observed is probably the result of a memory response to these epitopes. As you well know, this explanation forms part of the foundation for the rationale behind a T cell based universal influenza vaccine. In fact there was a paper published in Nature Med in Jan 2012 dealing with this in human subjects ( Hopefully, analysis of the adaptive immune response is followed up in this model.

Re: PR8 not being a great model. We know that PR8 infection of mice is a “finicky” thing. Morbidity/mortality and immune responses against influenza depend on many factors: inoculation route, inoculation amount, how the virus is grown (eggs vs. mouse passage vs. cell culture), mouse strain etc. Even the most “appropriate” route of inoculation (IN) is subject to many variables- inoculation amount (confusing and non-standard approaches; I’ve heard uL should be determined by mouse weight but I know it usually isn’t), where the infection is established in the airway (how far down did the droplet go), any amount of inoculum not inhaled by the mouse etc. There are now better ways being used to infect mice, for example, aerosolization chambers using sub-lethal doses of influenza. Despite these downfalls, we have learned many valuable things about antigen processing and presentation using this virus (and other influenza viruses too!)

If I may offer a pick of the week: The Science magazine issue on science education (“Grand Challenges in Science Education” April 19, 2013; volume 340). This is a free (with website registration) issue of Science containing many reviews on how to reform and improve science education for everyone, from teachers to non-scientists. I highly recommend the series even if I’m not sure I agree with all of the suggestions in the reviews.



Postdoctoral Fellow

Immunotope Inc

Connor writes:

Hey Vincent and the rest of the TWiV crew – thought you and your listeners might like to have a look at this new movie that is coming out, called Antiviral (link here: It appears to be a disturbing thought experiment on the future of our often celebrity-obsessed culture, but with a viral twist. Good to note that this film is a little less scientifically accurate than Contagion!!

All the best,


Kristi writes:

Hey there TWIV gang,

Nevada Weather Update: This week we have had completely bipolar weather. Monday it was snowing, Wednesday it was 70F and beautiful, and today it is rainy and gloomy.

I am currently finishing up my Bachelor’s and Master’s Degree in Biotechnology at the University of Nevada, Reno. I heard about TWIV, TWIP, TWIM in February while I was interviewing for PhD programs, and I have been hooked ever since! It was definitely surreal hearing Vincent talk about Elke Muhlberger and The Needle, right after interviewing with her at BU. Even though I was extremely excited about the Needle opening, I was completely wowed by Madison and will be starting in the Cellular and Molecular Pathology program at UW-Madison this Fall. Go Badgers!

So, I just finished episode 224 and I was extremely interested in the pick about the patient getting an organ transplant from a donor who died of the Rabies virus. And, I wanted to share that ABC decided to take that news story and turn it into a very intriguing episode of Body of Proof: Season 3, Episode 7 – Skin and Bones. It can be easily found on Hulu. The main character delves into many of the issues of why they weren’t able to screen the donor for this virus. Maybe you guys can watch the episode and see if ABC actually got it right. (Don’t worry, there’s no overlapping story lines with this episode.) Like, they said that they were unable to screen for it because the virus is in the nerves, not the blood. (But, in the show the real reason it wasn’t discovered was because of this organ harvester serial killer… well, that’s all I’ll say. I don’t want to ruin it.)

Also, I wanted to tell Vincent that I heard his 5 minute interview with studio 360 as well! I very much enjoyed it.

And, I definitely was cracking up with the threat that you and Dickson would be quitting TWIP, and I have decided to add my plea to the many others. PLEASE, please don’t stop TWIP. My school doesn’t offer parasitology, so I consider TWIP as my course on the subject. I love it because I learn a ton, but I’m not expected to take any exams on the material.

Finally, thanks for the website on all the pens. Just like Vincent, I have a thing with pens.

Cris writes:

Dear TWIVeroos,

Greetings from the end of the World (Dunedin, NZ).

20 degrees and cloudy. Climate change at its best!

On March 26th, researchers reported to have discovered the cause of the deadly Devil Facial Tumor Disease (DFTD), a disease that has annihilated 80% of the population of Tasmanian Devils in only 16 years and has the potential to drive this species to extinction. Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5103-8.

It turns out that DFTV cells lose their ability to express cell surface MHC molecules due to down-regulation of genes associated with antigen presentation. The down-regulation of those genes, in turn, seems to be due to epigenetic changes.

Why these epigenetic changes occur is still unclear, but the researchers point out that it’s possible to restore the expression of MHC on the surface of the affected cells by using a recombinant version of the devil IFN-gamma.

The researchers go on proposing that MHC-positive or epigenetically modified DFTV cells treated with, for instance, a deacetylation inhibitor such as Trichostatin, may provide a vaccine against the disease

“What does that have to do with viruses?”, you may ask. Well, poxviruses, such as Orf virus (ORFV) have been used in veterinary research for many years as an effective immunomodulating agent. ORFV infection leads to the accumulation of cells associated with innate response, as well as the release of INF-gamma, amongst other immunomodulating factors.

ORFV has been successfully used as an immunomodulating agent to treat many animals, such as dogs, cats, mouse, rats, guinea-pigs, horses, pigs, rabbits. Even the immune system of humans respond to it. Eur J Clin Microbiol Infect Dis. 2013 Apr;32(4):451-60.

I hope researchers look at a more feasible and economic alternatives to treat DFTV and test whether inactivated poxviruses can be used to save the devil.

What do you think, Rich?


PS: I only singled out Rich Condit, as he is the expert in poxviruses, but, I would also love to hear what Vincent, Kathy, Alan and Dick think of it as well.

PPS: Why did Vincent stop calling Dickson, Dick?

As always, love the show!

Cris Felipe-Alves, PhD

Post-Doctoral Fellow

Virus Research Unit

Microbiology & Immunology Dept

University of Otago

PPPS: Me again. I realized I left one important piece of info out of my last email.

Before the issue of whether ORFV can infect/enter Tasmanian Devil cells I must clarify one thing: It’s true that ORFV has never been tested against Tasmanian Devil. We just don’t know. However, what has been tested out there?

My idea is merely focused on whether ORFV can be tested as a potential candidate to boost levels of INF-gamma in devils. Hope that helps.


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