Fossil hunting-- Digging up extinct viruses in reptilian genomes


Did someone declare this week 'cool ERV research week.' or something?? Yet another awesome ERV paper came out:

Distribution of Endogenous Retroviruses in Crocodilians.

The title is pretty non-sexy, but what they found... AAAAH!

Okay, Jaratlerdsiri and company set out to look at ERVs in the order crocodilians. Crocodilians include the families of alligatoridae, crocodylidae, and gavialidae. Nobodys done it. So why not?

Armed with PCR primers for pol, Jaratlerdsiri went digging. Heres what they found:
CERV-1: This group of ERVs werent found in gators or gharials. All of the ones they found were super similar between species, if not identical. Closely related to gammaretroviruses, like lots of ERVs found in other species.

CERV-2: Found in all families. But they appear to be genetically distinct (ie- probably independent insertions). But heres the deal: these sequences arent related to any retrovirus alive today. Nothing. Not even close. Non-rooted tree? CERV-2 are out in BFE:
So CERV-2 isnt just a different species of lentivirus or betaretrovirus, or whatever. CERV-2 must be the fossilized remnants of an extinct genus of retrovirus! We know its a retrovirus, because these guys primers was for the RT region of ERVs. And this genus was 'robust' enough to endogenize itself in independent lineages of crocodilians... but it still died off. Like, totally. HOW?? WHY?? AHHHH!



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Why is it more likely that CERV-2 represents an extinct genus rather than one yet undiscovered in the wild?

.. and the diagram looks like a Giant Human Brain with a low-slung and preternaturally large cerebellum. Like zombies might have.

But yeah, that is cool.

I don't have access to the paper, and I can't tell from the non-rooted tree, but one reason to suspect this is the age of the ERV, using a molyclock.

Did someone declare this week 'cool ERV research week.' or something??

Didn't get the memo, eh. Maybe they have your email addres wrong.

Does this have something to do with the Texas and Oklahoma legislatures? I don't understand this stuff; it hadn't been invented when I was in college.

Optimus Primate - Yeah me too - then I figured out I was wrong, becasue like Uncle Glenny - this stuff hadn't been invented when I was in college. But that's ok cuz drinking and girls were...

Abby, what feeds do you read for your article updates? You always find the coolest stuff and I'm becoming dangerously reliant on you for updates in my own field!

That being said, what primer pair are they using (can't access this article until I'm back at work)? Even though pol is such a conserved region, it's still amazing to me that these primers work given how 'conserved' is such a relative term even amongst HIV subtypes.

By Katherine (not verified) on 21 Jul 2009 #permalink

Cain-- That is possible! We have blinders-- we only see viruses that cause disease. But if there is an alive CERV-2 out there. its so different from what we know exists........ eeeeeeeeeeeEEEEEEEEE!!!!!! **explodes with excitement**

Katherine-- I get my info from a very exclusive list-serve: I put 'endogenous retroviruses' as one of my tabs on Google News :P hehehe! Like, how you can have 'World' or 'Local' tabs? Mostly its just press releases, and vary rarely gets new articles, but sometimes cool ones roll along!

I dont have the article right in front of me now-- I know they used nested primers, so these results might be pretty conservative.

Hi Abby, I don't have access to this journal. Just out of curiosity was Tomistoma amongst the sampled crocodilians? It would be very interesting to know if it had CERV 1 given the debate over wether it is a crocodylid or the gavial sister taxon.

OK, I've left this a couple days to see if the answer comes to me but it hasn't... LOLspeak translation fail... what does BFE stand for? (ie. please translate into old fart) doesn't have it... Maybe urban dictionary?

OK, urban dictionary had it... but that's pretty derived! Not nearly as obvious as GTFO or WTF or LOL. Oh well,.. kids these days!

Hey Abbie, if you're getting close to defending, there's an open tenure-track faculty position in Microbiology at a certain college in PA.

Ya interested? ;)

By minimalist (not verified) on 23 Jul 2009 #permalink