I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
Before I start talking about endogenous retroviruses, there is one thing I need to make clear about exogenous retroviruses first, for anyone who deals with pseudoscientists.
When dealing with Creationists/Deniers on the topic of virology, almost immediately you will be confronted with a form of 'viruses are magic'. For instance, Professional HIV Denier Rebecca 'Blondie' Culshaw is just certain that HIV-1 is really a harmless ERV (see points 1-17), and Creationists routinely pull 'scientific facts' about ERVs out of thin air.
So I really cant stress this one point enough:
Okay, you all know that a retroviruses are viruses that go 'backwards', genetically. Instead of going DNA-->RNA-->Protein, they go RNA-->DNA-->RNA-->Protein. While its easy to lump all 'retroviruses' into a homogeneous group, its important to remember that retroviruses are actually an extremely diverse family.There are currently seven types of retroviruses, with their own defining genes (simple? complex? lots of bells and whistles?), methods of virus assembly (cytoplasm? cell surface? trafficked through the ER?), viral structure (cone? cylinder? sphere? spikes? sugars?), desired host cells (dividing cells? terminally differentiated?), etc.To say 'HIV-1 is the same as Rouse Sarcoma Virus is the same as Mouse Mammary Tumor Virus. Theyre all retroviruses!' is as silly as saying 'Humans are the same as blue whales are the same as fruit bats. Theyre all mammals!'
But what all of these guys have in common is their need for the genes gag, pol, and env (which I will be discussing more at a later date), genes we can sometimes find hanging out in our DNA as endogenous retroviruses:
- Alpharetroviruses-- Can be ERVs
- Betaretrviruses-- Most ERVs
- Gammaretroviruses-- Can be ERVs
- Deltaretroviruses-- No ERVs
- Epsilonviruses-- No ERVs
- Lentiviruses-- We have found *one* lentiviral ERV
- Spumaviruses-- Can be ERVs, but the endogenous versions are only distantly related to current-day, exogenous spumaviruses
If your pseudoscientist friend says something that sounds like magic-- "Well maybe HIV-1 is an ERV that got a functional envelope gene from influenza cause you had the flu and were huffing poppers!"-- Dont stand for it. Say "Retroviruses are not magic. Show me the evidence for that claim."
And, if you want to learn more about retroviruses (I mean beyond Wikipedia, but not quit 'IM GONNA GO BUY A TEXTBOOK!'), Cold Spring Harbor has a book on retroviruses online, for free!! Its 'advanced' reading, but if this topic interests you, you can get through it. Or if you get stuck, leave me a Q in the comments or drop me an email :P
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Comments
Abbie, I just want to thank you for this post. Not because I understand a word of it, because I don't. But because it's obvious there are still smart, optimistic, devoted, and determined people in the world who will strive to make a difference. Thank you.
Posted by: Paul Lundgren | May 12, 2008 9:38 PM
NOOOOOOOOOOOOOOOOO!!!!
NOOOOOOOOOOOOOOOOOOOOOO!!! Dont say that!!!
If you dont understand something, ask a Q!!! Because if YOU have a Q, that means someone else probably has the same question, which means I need more practice talking about this stuff cause EVERYONE can get this stuff!!!
Ask questions!
Posted by: ERV | May 12, 2008 9:49 PM
Ah dammit, now I have another book to read. And this one is free too so it is even harder to resist. I should just avoid all the interesting blogs. I'd get so much more done that way.
Posted by: Joshua Zelinsky | May 12, 2008 10:13 PM
Sorry, this isn't strictly related to this post, but it's something I was wondering about and couldn't find the answer to: This video by cdk007 says (at 5:45) that there are 16 ERVs in common between humans and chimpanzees and then goes on to clarify (at 6:45) that those are "K class retroviruses" and that there are ~98,000 ERVs total in the human genome.
My question is, what is a K class retrovirus, and why are there so few (16 in common with our closest related species) of them compared to other types of ERVs?
Posted by: Jason Creighton | May 12, 2008 11:34 PM
"To say 'HIV-1 is the same as Rouse Sarcoma Virus is the same as Mouse Mammary Tumor Virus. Theyre all retroviruses!' is as silly as saying 'Humans are the same as blue whales are the same as fruit bats. Theyre all mammals!'"
I have to admit I don't know a ton about retrovirus phylogeny, but given my ignorance couldn't it be more accurate to say that it's like pointing out that bees, chickens, and coral all have pointy protrusions, so they're all the same? I ask this because if these defining characteristics of retroviruses do not correlate with a single monophyletic group (outside going back really, really ridiculously far), couldn't they be an analagous character rather than homologous?
Of course, this is based entirely on my speculation and ignorance, so I'd appreciate any correction!
Posted by: Shirakawasuna | May 13, 2008 12:36 AM
Which of the seven is HIV, out of curiosity?
Posted by: Confused | May 13, 2008 5:00 AM
IIRC HIV is a lentivirus, which means "Kills you reeeeal slow."
Posted by: Stephen Wells | May 13, 2008 6:46 AM
HIV is a lentivirus.
See http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fs_retro.htm#Genus16
Posted by: Joshua Zelinsky | May 13, 2008 2:14 PM
@ #4
Thats a neat video! They got a little confused, but not much-- When he/she said 'K class of retroviruses', they meant the HERV-K family of endogenous retroviruses!
When scientists started hunting for families of ERVs in Humans (HERVs), they started at the beginning of the alphabet, and moved down: HERV-A, HERV-B, HERV-C, etc.
HERV-Ks turned out to be a neat family, because they happen to be the 'youngest', thus most intact, thus most capable of forming viral particles. Because theyre so young, its possible that HERV-K 1 is found in humans only, while HERV-K 2 is found in both humans and chimpanzees, meaning following the HERV-K family insertion pattern is a great way to tease out primate phylogenies :)
Posted by: ERV | May 13, 2008 9:16 PM
PS-- Search for 'HERV-K chimpanzee' for lots of cool info
Posted by: ERV | May 13, 2008 9:19 PM
Umm, Do retroviruses have any clinical relevance whatsoever?
Top ten killers in USA per CDC:
Heart disease: 652,091
Cancer: 559,312
Stroke: 143,579
Chronic lower respiratory diseases: 130,933
Accidents: 117,809
Diabetes: 75,119
Alzheimer's disease: 71,599
Influenza/Pneumonia: 63,001
Nephritis, nephrotic syndrome, and nephrosis: 43,901
Septicemia: 34,136
Do you see any retroviruses on this list? Do you now understand why you toil away at 10 bucks/hour? Your work has not an iota of relevance to the real world.
Posted by: Fleming | May 14, 2008 12:11 AM
Do you see any retroviruses on this list?
uhh
Posted by: aporeticus | May 14, 2008 2:02 AM
Wow. My work also doesn't help alleviate any of the killers on Fleming's list. I guess my job also has not an iota of relevance to the real world.
Posted by: Brian | May 14, 2008 6:22 AM
Posted by: Rrr | May 14, 2008 9:33 AM
This is a really stupid comment in a number of ways.
To begin with ERV is a graduate student. Graduate students get paid a bare survival wage, in part because they aren't yet worth a lot, and in part because most of their benefit is in the training they receive. And it doesn't matter whether they are working on some obscure protein that nobody knows what it does or on heart disease. Graduate students at an institution generally all get paid pretty much the same (barely enough to survive).
It is also an example of the "bigger problem" fallacy: "You shouldn't be worrying about X, because Y is a much bigger problem!" This is a really, really stupid way to think. Taking this reasoning to its logical conclusion, there is one "biggest problem," and nobody should work on anything else until it is solved. In reality, scientific requires diversity, just like an ecosystem. Throwing all of your effort at the "biggest problem" doesn't necessarily get it solved any faster; at any given time, there are only so many good ideas and approaches, so you get to a point of duplication of effort and diminishing returns.
Moreover, in basic research, it is sometimes not the direct attack that yields the solution to a problem. Very often, it comes from something discovered by some other guy who was working on some obscure question that nobody thought was very important.
Finally, research needs to be dedicated not merely to the present, but to the future. The fact is that we really don't understand viruses very well, and viral infections are really hard to treat, because viruses have only a few proteins of their own, and mostly hijack the cell's apparatus. HIV was a big wakeup call. We were very, very lucky that HIV is so difficult to catch that you pretty much have to have sex or share blood to get it. The next virus to come down the pike might not be so well-behaved. But HIV got us worrying about viruses, so now if we run into a really nasty one, maybe we'll be prepared.
Posted by: trrll | May 14, 2008 11:56 AM
=lightbulb suddenly switches on= Yeah, now I get it!
(Bet you couldn't tell that biology isn't my usual stomping ground, huh? No, really!)
Thanks for the clearest, most concise explanation I've ever seen regarding retroviruses. I had a vague idea what they're about, but the name "retrovirus" still conjures up the weird idea of a virus that somehow infects you before you're exposed to it. Never mind that I know full well that [1] no such thing exists and [2] the very idea is ridiculous.
Maybe I've been warped by reading too much Asimov in my younger daze.......
Posted by: themadlolscientist | May 14, 2008 12:58 PM
Nice note Abbie.
Your troll, #11 here, is, well, typical for that species. Like most, it goes ahead and uses the results of science that would never have existed if he had his way. It's true that some important things were found by people who were trying to find them. So it can keep the smallpox vaccine and the steam engine.
On the other hand, it has to give up penecillin and anything that uses electricity, among many other things. Alexander Fleming was not trying to find antibiotics when he discovered penecillin. And electricity spent over 2 centuries as a highly abstract bit of science (starting from, let's say, Oersted in the 1600s and up to mid-1800s).
Also have to give up anything that uses radio waves (granted that's already eliminated by the fact the troll can't use electricity) as their existence was a theoretical prediction out of Maxwell's equations, themselves developed for no particular application. Just trying to understand the universe.
Posted by: penguindreams | May 14, 2008 5:57 PM