Juan writes:

Dear Alan, Dickson, Kathy, Rich and Vincent (alphabetical order),

Thanks once again for an entertaining episode of TWiV, and also for choosing plant viruses as one of the main topics of the show.

The digression about flowers was indeed funny, and being a plant virologist, I fully align with Dickson’s side for obvious reasons. Among others, flowers can serve to diagnose virus infection of plants.

To refresh Vincent’s memory, I want to mention a link from his own Blog (http://www.virology.ws/2012/03/14/tulips-broken-by-viruses/), dealing with Tulip breaking virus. The nice patterns in these flowers are diagnostics of the presence of potyviruses, and they can be found in many old paintings from Dutch masters. Even the name “Rembrandt tulip breaking virus” was once proposed for a potyvirus species (http://www.ncbi.nlm.nih.gov/pubmed/8492092), although it was not accepted formally by the ICTV.

For Spanish-speaking listeners, there is a nice divulgative article by Jesus Navas-Castillo (available at http://es.scribd.com/doc/93830364/2010-VIROLOGIA-burbuja-tulipanes), which reproduces with permission from Museo del Prado (Madrid) a beautiful painting by Jan Brueghel “el viejo”.

Best regards,

Juanjo Lopez-Moya
(CRAG, Centre for Research in Agricultural Genomics, Barcelona, Spain)

PS1. Meteo-info: Gorgeous springtime weather in Barcelona, mostly clear skies, 20 ºC (68 ºF), humidity 67%. A bit late for tulips and cherry blossoms, though.

PS2. When searching for links to this e-mail, I realized the Potyvirus entry in Viralzone (http://viralzone.expasy.org/viralzone/all_by_species/48.html) needs to be updated. It is incorrectly mentioned there that the extra p3N-PIPO gene product “is expressed by a -1 ribosomal frameshift” (sic). However, recently it was shown that frameshift gene products in potyviruses derive from a mechanism of polymerase slippage (http://www.ncbi.nlm.nih.gov/pubmed/25878117), which reminds of the transcriptional editing as described in Ebola virus. I apologize for the self-reference, but I wonder if this might qualify for a TWiV bump?

Ramon writes:

I think this clarifies CSF glucose level meaning in CNS infections

“CNS infections may alter glucose transport across the blood–CSF barrier, resulting in a low CSF glucose level, termed hypoglycorrhachia. Further reduction in CSF glucose levels may result from glucose consumption by WBCs and organisms. Reduction of CSF glucose relative to blood glucose is characteristic of meningitis caused by bacteria, mycobacteria, or fungi (69,70). The CSF glucose level is usually normal during viral infections, but low CSF glucose levels are occasionally observed in meningoencephalitis caused by mumps, enteroviruses, lymphocytic choriomeningitis, herpes simplex, and herpes zoster viruses (25,71)”

“25. Jaijakul S, Arias CA, Hossain M, et al. Toscana meningoencephalitis: a comparison to other viral central nervous system infections. J Clin Virol. 2012;55(3):204–208”
“69. Swartz MN, Dodge PR. Bacterial meningitis—a review of selected aspects 1. General clinical features, special problems, and unusual meningeal reactions mimicking bacterial meningitis. N Engl J Med. 1965;272: 779–787.
“70. Ellner JJ, Bennett JE. Chronic meningitis. Medicine. 1976;55:341–369.”
“71. Hasbun R. The acute aseptic meningitis. Cur Infect Dis Rep. 2000;2(4): 345–351”

Quoted from “Infections of the Central Nervous System. 4 ed” Scheld, W. Michael et al. Lippincott Williams & Wilkins, 2014-04-21

Internal Medicine Dept Chief
Hospital Can Misses
Ibiza (Islas Baleares)
España (Spain)

PS: I wonder if a Physician’s point of view could be a good complement to your excellent explanation on viral basic science

Lee/John writes:

Dear TWiVumvirate,

Listening to TWiV #334, I had to laugh to hear about Dr. Racaniello’s lack of interest in cherry blossoms. I am a big fan of them, and when I am not buried under a mile of experiments, I like to go to the cherry grove in west Central Park to read, or just quietly enjoy the grove.

No doubt more than a few listeners are writing in to call Dr. Racaniello a curmudgeon (as some of you did, as well), but I think Dr. Despommier had it right: Dr. Racaniello would rather look at plaques! And what isn’t beautiful about a good plaque assay?

But the discussion of Pinot Noir and virology in the episode made me realize that perhaps there’s a virology story in cherry blossoms as well.

Google brought me to two viruses of cherry trees: Prunus necrotic ringspot virus (PSNRV) and cherry leaf roll virus (CLRV). These are both Group IV viruses, possessing single-stranded +sense RNA genomes, and so I think this would be of particular interest to Dr. Racaniello.

According to Wikipedia, which I should confirm but haven’t the time, coinfection of cherry trees with these two viruses leads to rapid decline of the tree. Interestingly, both of these viruses are segmented viruses, with PSNRV having three genomic and one subgenomic segment, and CLRV having two genomic segments. These segments, for both viruses, are packaged into separate virus particles, which must coinfect cells in the host.

I find these situations, where a virus spreads itself across multiple particle types, especially interesting, because it relies on luck for the virus to get all of its genome parts into a cell! It is almost as though these viruses’ infections are a cooperative project of three separate, attenuated viruses (or two in the case of CLRV).

Because both viruses have this multi-particle system, I find it interesting that coinfection with both viruses can cause a more severe pathology. I know nothing about the current state of research on these, whether the severity of disease is simply an effect of stress to the host or some factor of superinfection, but it seems like there’s a lot to cherry trees that is of potential TWiV interest–beyond just the blossoms.

Anyway, perhaps this will make cherry blossoms more interesting to Dr. Racaniello, perhaps not–but having been inspired to learn this stuff by TWiV 334, I thought I’d write in and share another example of the fact our planet is just lousy with viruses. They’re everywhere.


John Skylar (Lee)

Claudia writes:

Hi Vincent,

I am so moved by your response to the patient/advocate input regarding TWiV podcast 329, and grateful for your continued commitment to the ME/CFS conversation via TWiV, but I have to say that I am also a little embarrassed. My letter in response to TWiV 329 was written with much less eloquence than Jennie’s and obviously contains more emotional bias and a harsher tone toward the hosts, to whom I incorrectly referred as guests in my letter.

Because this patient population has been ignored and mistreated for so long by government agencies as well as the medical community, media and society at large, it is all too easy to allow feelings of anger and resentment to sneak into our more pure efforts of advocacy, and I apologize for having fallen into this trap. I hope you and the other hosts are able to receive the many scientific messages and personal experiences contained in my letter in spite of the colorful descriptors I used about Dickson’s and Alan’s comments on podcast 329.

Having said that, I will leave it to your discretion whether or not to read my previous note and attachment, but I would hope that if they are read it is because they add some value to this conversation. I am again attaching my previous full letter for your convenience, but after fact-checking it with Jennie I decided to make a slight change in my report of the worldwide prevalence. The number in my original document (17 million) reflects an extrapolation based on the US numbers and that includes mostly undiagnosed people, so I left it at millions. The change can be seen by reviewing all markup in the document.

BTW, The ME/CFS paper linked below just came out yesterday, but is behind a pay wall, which you can probably access and perhaps discuss on this week’s TWiV. The first author is again Mady Hornig, and in this small study she again demonstrates cytokine abnormalities, this time in the CSF of ME/CFS subjects compared to those with M.S. and no disease, supporting the prior plasma immune signatures in her other recent study.

Here is the abstract:

Thank you again,

Justin writes:

Dear TWIV hosts,

I love the show, and really appreciate what you guys are doing. I have been tempted to write in on a number of topics, but have restrained myself because you get so many emails.

My ears do perk up whenever the topic of careers for recent PhD’s and post-docs is under discussion. It is true that career options for scientists have become more limited, and the market is more saturated than it has been in the past. Being a PhD student myself, this is something I often think about.

Despite the challenging career outlook, working on a PhD has been by far the most rewarding experience of my life. I get to work with amazing people, and think about amazing things every day. If someone out there is wondering if it is worth it, from my perspective it certainly is… even in the current economic climate. At the end of the day, there are plenty of scientific problems out there to solve, and it shouldn’t be too hard for well trained and motivated people to find a niche.

So yeah, I can’t really complain. However, the topic of training too many PhD students keeps coming up so I thought I would drop an idea. One solution could be an NIH and NSF mandate to start paying PhD students and post-docs more. If you were paying students and post-docs twice as much, you would only be able to hire half as many, and the quality of the students recruited would probably improve. Why not use some of that NIH money to sweeten the pot for potential grad students rather than building another building or hiring another administrator? You need quality not quantity after all, and you generally get what you pay for.

There is huge pressure on my generation to achieve personal financial stability, thus you are potentially losing some of the best scientific minds to medical schools, Wall Street, and other more financially attractive paths. Imagine if the person who would have figured out a universal flu vaccine has just been recruited to a consulting firm. Nothing against those kinds of jobs, but that would be a very inefficient use of talent in the bigger scheme of things. It is mostly the idealistic goof balls like myself that are going into science, and given the circumstances I can’t blame others for choosing a different route. The blood, sweat, and tears of PhD students and post-docs are what keep a large part of the scientific progress in this country moving. Pay them well, scientific quality will improve, and job saturation will go down. Figuring out how to do this from an administrative or political perspective isn’t trivial, but it seems like an idea that should be seriously considered. I’d love to hear your thoughts.

The weather in Salt Lake City is a sunny 69° Fahrenheit. Again, thanks for the show and keep up the good work.



P.S. I have a listener pick for anyone out there interested in bacteriophage. The book: Molecular Biology of Bacterial Viruses, by Gunther S. Stent is an oldie but certainly a goodie. It was recommended to me by one of my committee members when I first started as a PhD student. It covers a lot of the “old school” bacteriophage experiments that are still very relevant and useful to think about. Every time I read this book it gets the gears in my head turning. It is a bit heavy, but crucial reading if you happen to be interested in phage.

Jennifer writes:

Greetings denizens of TWIV! Currently sunny and around 65 F here in Silicon Valley, though we thankfully had a bit of rain this morning for the first time in awhile. I am currently an undergrad at San Jose State university daydreaming about studying viruses in graduate school and trying to learn as much as possible. I just finished listening to twiv 326 about the soluble HIV antigens being used to protect against infection (I know, I am late), and I remember someone commented on how this wouldn’t be an effective treatment for HIV because it can’t eliminate the reservoirs. While this is true on its own, couldn’t it be combined with other therapies such as HDAC inhibitors to activate the virus? As the virus is activated the immune system can eliminate those cells that are infected and the soluble antigen would prevent the viruses from infecting new cells and potentially forming new reservoirs. Eventually the remaining reservoirs would be eliminated and no new ones would form. Though several studies have show that these re-activated reservoirs are only poorly eliminated by CD8 cells in patients anyways, so that would have to be addressed as well. I guess what it comes down to is whether this new method is more or less effective than HAART at preventing virus from infecting new cells. What are your thoughts? I think it’s a really exciting possibility for treatment in any case and may resolve the many issues with vaccines that currently plague the field. I really hope it pans out in further trials.

Keep fighting the good fight, I love the show! Thanks!

Anthony writes:

CDC — Influenza A(H7N9) Virus Transmission between Finches and Poultry


Jeremy C. Jones, Stephanie Sonnberg, Richard J. Webby, and Robert G. Webster
Author affiliations: St. Jude Children’s Research Hospital, Memphis,
Tennessee, USA

# # #

This is particularly bad news because the wild form of the model
animal used in this research, Lonchura striata, is widely found in the
Chinese Prayer Bird trade. Many are transported around China without
documentation. The birds are purchased for release as part of
cultural ceremonies.



Steve writes:

Don’t know if you follow reports from our UK FSA. If not these new reports may be of interest. I haven’t had time to read them yet myself, but the release says:

“Professor Sarah O’Brien, Chair of the ACMSF, said: ‘Until recently it has been difficult to assess accurately the impact of foodborne viruses on public health. However, significant advances in our ability to detect viruses in food, coupled with up- to-date estimates of the burden of illness, highlighted in the ACMSF’s latest update, show us that viruses are very important, preventable causes of foodborne illness.’

All the best,

Steve Hawkins,

Two reports on viruses in the food chain published today | food.gov.uk – http://www.food.gov.uk/sites/default/files/csa-report-issue-one-foodborne-viruses.pdf

Piet writes:

Dear Vincent, Dick and Alan,

I have recently discovered your podcast by randomly strolling the web and have found it to be an inspirational experience, I am only at episode 53 at the moment, so lots to listen to still. I currently live near Cape Town in South Africa and listen to the podcast during my 1h30 drive to work and found that I enjoy traffic more and more now.

I am a finance math major, that has found my way into computational biology and currently work for a bio tech company in Cape Town. I will soon be traveling to the states to start my PhD at ORNL in the fall.

Your podcast has inspired me to focus my research more into studying viruses from a bioinformatics point of view. I will also be working on plant microbe interactions and bacteriophages.

Just wanted to say thanks for the very entertaining, humorous and intellectually stimulating show. I also found this news article online that I believe might be of interest to other listeners, given the recent Ebola pandemic.


Kind Regards,

Gary writes:

Hi gang,

I was just listening again to twiv 147 with just Alan and Rich. And I have listened to many others where you talk about GMO’s and how there is nothing wrong or you are undecided about them.

While I am a huge supporter of science and in general do not have any problems with most things, I do have a problem with GMO’s. First no one can tell me that it is safe for me to eat pesticides that were somehow baked into crops. If the pesticide is not able to be drunk or eaten in any other form, why would it suddenly be ok to eat it just because it was somehow engineered into a plant?

Common sense tells you that is not safe. I am 100% comfortable with the idea of GMO’s that add vitamins, or minerals. I am thinking about the rice that adds vitamin A maybe? Can’t remember exactly which it adds.

I do not trust big ag, but that is me. I understand that you guys may trust them, though I honestly do not know why. I am not a big fan of drug companies, but that is mostly because of business reasons. Why would drug company A make a vaccine that stops someone from getting HIV, when they make billions on treatments for said virus? Just wondering.

I do love the show because it makes me think about these things. I am now more willing to listen to drug companies! While I have never been against vaccines, you reasoned arguments in favor of them are always useful when talking to anti-vaxxers.

I realize that this has bounced around a lot, but I have not written before and had many of these thoughts trying to get out! 🙂

Love the show and have worked my way through the back catalog once and going through again to make certain that I understand fully.


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