Judi writes:

too late for halloween, but …

3 vampires walk into a bar. The first 2 ask for blood, the third asks for serum.

Bartender says  “let me get this straight;  2 bloods and a blood light”

(everyone groans)

Judi, san Diego

81F/27C and sunny , no wind  – and this is the last day of October!​

David writes:

Follow up to episode 361, where a couple of incorrect paleontological statements were made.

There are no known marine dinosaurs. Mosasaurs are reptiles but not dinosaurs, as are other marine reptiles such as plesiosaurs, ichthyosaurs, and turtles. Also mentioned were pterosaurs – they are also non-dino reptiles. There have been some semi-aquatic dinosaurs, but none that lived predominantly in the ocean.

However, there have been rare cases of land based dinosaurs found in marine deposits. The theory is that they were entangled in plant mats that floated out to sea during a storm. The bones then fall to the bottom of the ocean after the ‘meat’ of the dinosaur and the mat decays away.  I don’t know if that is the case of the Japanese dinosaurs.

One of the topics discussed on several TWiV episodes combines two of my interests – Paleovirology. Please continue including such discussions in future episodes along with viral evolution. From my online research, the oldest viruses from endogenous retroviruses in present day insects is about 300 million years ago (about the time reptiles began, but before dinosaurs). Maybe one day we will be able to answer the question, Did T. Rex get the flu?

It is a nice 75F (25C) in Austin.

David from Austin

Neva writes:


Hi Twiv gang,

WOW. The idea that the methods in this article can identify all and every virus in a sample is really terrific. Really? What a leap forward in diagnostics and discovery!


Can something like this work for  microbes or parasites in all their diversities?

Sounds very cool! I bet you have gotten many notes about this and hope you can explain a bit with your usual verve.


in Buda where it is 91F and partly cloudy at 6:30 this evening.

Marcia writes:

Hi there TWIV people!

I came across this article today, and since it’s about testing for viruses I immediately thought of TWIV.


I would love to know more about how this works, and maybe how it was developed.



in Salem, Massachusetts

Dusan writes:

Dear TWIV team,

We would like to make a few comments regarding episode 351 and the follow-ups in which you discussed attenuation of a dengue virus by synthetic attenuated virus engineering (SAVE).

As you discussed, SAVE has been successfully employed for attenuation of several RNA viruses, but it has never been tested on large double-stranded DNA viruses.

We wanted to know whether SAVE could also be used to attenuate DNA viruses. So, we recoded several genes of Gallid herpesvirus 2, aka Marek’s disease virus (MDV), an oncogenic herpesvirus of chickens. We deoptimized, optimized and randomized codon pairs of several essential MDV genes. While we were able to propagate viruses with optimized or randomized genes, we failed to grow some of the mutants that contained codon pair deoptimized genes. To confirm that codon pair deoptimization was responsible for the observed “dead phenotype”, we generated additional MDV mutants that contained chimeric genes composed of different WT and codon pair deoptimized sequences. Interestingly, viruses with chimeric genes grew with characteristics that correlated with the level of codon pair deoptimization of recoded genes.

On another note: We share the overall conclusion on the issue that vertebrate viruses that contain codon pair deoptimized sequences are not attenuated because they contain increased numbers of codon pairs that are somehow unfit for efficient protein production, but because these viruses indeed contain increased numbers of CpG (and to a lower extent also UpA) dinucleotides in the recoded sequences. The most underrepresented codon pairs in vertebrates contain CpG or UpA dinucletotides at the codon pair boundary (for example, of the 100 most underrepresented codon pairs 97 codons pairs contain CpG and 3 codon pairs contain UpA at the codon pair boundary). In addition, 94% and 98% of codon pairs that contain TpA and CpG dinculeotides at the codon pair boundary are underrepresented in the human ORFeome, respectively. Logically, maximization of codon pairs with the lowest codon pair scores (codon pair deoptimization) must lead to an increase of CpG and to a lesser degree also UpA dinucleotides in the recoded sequences.

Sincere greetings from your long time listeners

Dusan Kunec and Klaus Osterrieder

Institut für Virologie, Freie Universitiät Berlin, Germany

Dusan Kunec

Zentrum für Infektionsmedizin

Institut für Virologie

Freie Universität Berlin

Robert-von-Ostertag-Str. 7-13

14163 Berlin


Jon writes:

Dear Twivsters,

Some time back there was some discussion on your show about the relative merits of the  flumist nasal vaccine vs the flu shot.  If I recall correctly, you all preferred flumist for efficacy.

(The obvious question which you didn’t address is whether getting both is better than getting only one of them.)

Unfortunately, here in sunny Hawaii the flu shot has been available for weeks, but flumist is  nowhere to be found yet.

Is it better to take the shot now and then get flumist later, to get the shot now and not get flumist, or simply forget about the shot and to wait for flumist?

One wholesaler I spoke to is not shipping flumist until mid to late september, but I don’t have any firm date on when it will be here in Hawaii.


Porter writes:

Hello Twivies!

My name is Porter and I am currently an undergraduate at Skidmore College and I thoroughly enjoyed this week’s TWIV.

My question pertains to potential uses of RNAi to treat viral infections after the infection has taken place.  This could be useful for viruses that cannot be vaccinated against or places where the vaccines could not reach the hosts before infection occurs.  An example of this is HBV (Hepatitis B) and with this example there are many ways we could conceivably target the virus using RNAi i.e. its genome and mRNA.  However, the idea of this brings up many questions one of which being whether or not the RNAi machinery is actually strong enough to destroy the viral infection at a rate which would allow the immune system to take over.  The RNAi machinery would have to overcome all of the RBPs associated with the virus and cleave the RNA to a length that nucleases would be able to degrade it effectively.

My main question is whether we can overcome this by targeting multiple sites on the viral RNA at once, thus increasing the rate of cleavage (assuming the machinery does not become saturated) and additionally target endogenous proteins that allow the virus to propagate.  Obviously we cannot target RNAPII, but using the HBV example, could we feasibly target the Bile Acid transporter which is required to transport the virus into the cell to a level that is not fatal to the host and possibly combine that with targeting the mRNA and viral genome thus lowering the viral presence to a level that allows the immune system to take over.  I hope that this idea is not too far fetched, however, I believe the consideration of this is in order.

Thank you very much,


Trudy writes:

Dear TWiVers,

I ran across this paper in Nature and thought you might find it interesting, since it is a frequently discussed topic.




Anthony writes:

The International Federation of Pharmaceutical Manufacturers & Associations did not reply to my email, but this news article claims that the Midwest Avian Influenza outbreak did not affect vaccine production:




[———- Forwarded message ———-

From: Anthony

Date: Fri, Sep 11, 2015 at 9:53 PM

Subject: Egg-Based Vaccine Production

To: info@ifpma.org]

Did the recent Avian Influenza outbreak in the US Midwest in any way hinder production of egg-based vaccines?

Thank you.

Jim writes:

Margo and I just got our seasonal flu shots. She got the senior version with two strains, but this is when we first heard about the “quad” vaccine which seemed like a better idea and is what I got.  I see online that there’s also Flublok that’s 3 strains, but two types, the A and B versions.  The nasal spray is four strains…

Seasonal Flu Shot | Seasonal Influenza (Flu) | CDC

Is this evolution of flu vaccines part of the personalization of medicine? It’s starting to be confusing. Seems to me there should be a senior version of the quad vaccine, like the trivalent vaccine.  Will we see a patch option, next, that’s available in several versions?  We’ve seen lots of signs urging us to get flu shots, but nothing that sorts out the options and reasons for selecting one over another.


Smithfield, VA

Joakim writes:


Thank you for you great shows, and I am glad to hear that you (Vincent) liked my tip about Dan Carlin’s podcast! Here in Stockholm, Sweden, fall has almost just begun with mean temperatures around 12C, however still with quite fair weather!

I think that it needs to be taken up that also young scientists can do awesome things. This year’s grand prize in the Google Science Fair goes to Olivia Hallisey (16), for her ebola detection system! Pretty cool huh? I am not informed enough to understand whether this is a new invention, however it still tells the tale of young people being interested in Science and in doing good. Just to compare with the last week price bumps in TBC and toxoplasmosis drugs, which might put some shade on the drug industry.

News: http://www.msn.com/en-us/news/technology/this-16-year-old-won-the-google-science-fair-with-a-way-to-detect-ebola/ar-AAeAOXm?li=AAa0dzB&ocid=iehp

Info: https://www.googlesciencefair.com/en/

Presentation: https://www.youtube.com/watch?v=bhdA95dcwc4

Regards, Joakim

Jessica writes:

Dear Twivologists,

I began listening not too long ago and have thoroughly enjoyed your show.  I’m not sure how many of your listeners are in “Risk Management” careers as I am, but when you mentioned that particular perspective for studies of biohazardous agent releases (during building collapse), I thought I’d let you know I am a listener from that community.  More specifically Environment, Health and Safety and even more specifically Biosafety.  Unfortunately, I have not heard of or found many studies of this type, but I did find a wish list of studies from the Department of Homeland Security which basically gives some resources for who to turn to in such an event, general testing recommendations/standards, etc.  Maybe this document will give some listeners in research ideas for grant proposals?


As someone who is involved in conducting risk assessments for research, much of which involves viruses, I’m always picking out your virologist opinions on the risk profiles of the viruses you talk about on the show. And as a promoter and practitioner of biosafety, I think the show could use the opinion of a biosafety expert from time to time.  In fact there have been many recommendations to include an MD on the show and if this is a possibility, perhaps consider an MD with expertise in Occupational Health particularly around exposure to viral vectors used in research or clinical trials?

As a member of ABSA (the American Biological Safety Association), I belong to their listserv as there’s often helpful or interesting chatter there.  It is free and you don’t need to be a member to join–may be a good location for “picks” etc.   I picked an article that came up today that combines the recent discussion topics of transmissible cancer cells and risk management.  I thought it might generate some interesting commentary from the panel.  Particularly because there have been cases in which exposure to human cancer cells generated tumors in immunocompetent individuals!



I’ll leave it at that (although I’d like to reference a question I’m still looking to answer from a previous email in regards to mycoplasma–why isn’t this being engineered as a potential “tool” for immunotherapies etc.–ideas?)

It is currently 13C, 87% Humidity, wind 14km/h and as Dr. Neil deGrasse Tyson told us last night, we’re on the verge of a “rare”  harvest, blood moon AND lunar eclipse tomorrow night!  (He actually was quite annoyed at the proclamation that this was a “rare” event).

Thank you for your awesome insight!

P.S.  Thank you Dr. Spindler for representing lady scientists on the show!!!! We need more super-cool, intelligent, scientist role-models who are females represented in our culture for many reasons and I love that you’re a panelist 🙂


Anonymous sender:


Paul writes:

From Saturday Morning Breakfast Cartoon http://www.smbc-comics.com/  on October 3, 2015


Judi writes:

Dear virus virtuosos:

Thought you’d enjoy this –  maybe a listener pick


As usual –  thanks for all you do and thanks for keeping my retired brain working…


(retired high school teacher in San Diego)

today – RAIN!!!

slight winds  7MPH,  20 C (perfect room temp!)