Paleovirology

Holy crap.

Do you guys remember how Per Ahlberg got his big break? He sifted through the fossil collection at the London Natural History Museum, found friggen tetrapod?

Someone just did the same thing with HIV-1.

Michael Worobey dug through prehistoric (1960s hehe) tissue samples hunting for early HIV-1 sequences.

Now by ’tissue samples’ I dont mean nicely labeled bits of tissue, organized and cataloged in bright fluorescent boxes, in perfect little cryovials, stored at -80 C.

I mean dude dug through chunks of flesh soaked in formaldehyde and embedded in wax, and have been sitting at room temperature for, um, *looks at watch* 48 years, looking for HIV sequences… and he found some.

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

I repeat: Holy crap.

If youve read ERV for a while, youre probably aware of the fact that HIV is not just ‘HIV’. There is HIV-1 (the one causing a mess) and HIV-2 (causes a smaller, less deadly mess). HIV-1 is split into Group M, N, and O– representing 3 different crossover events from chimpanzees to humans. Group M is the ‘bad’ one, and is further divided into subtypes– A, B, C, D, etc. Each of those subtypes has distinctive features, which are the result of decades of evolution within humans (ie, differences in Subtype B vs C Vpu sequence and function).

The oldest HIV-1 sequence weve found was fished out of a 1959 blood sample. This sequence is closely related to Subtype D HIV-1.

Worobey found this new sequence in a lymph node biopsy from 1960. It is more closely related to Subtype A HIV-1.

This means that by 1960, HIV-1 Group M had been in the human population long enough to evolve into distinguishable subtypes.

Previous estimates placed the initial introduction of HIV-1 into humans between 1915 and 1941, probably at ~1931.

Using new evolutionary models with this new sequence, that date has been pushed back a bit– 1902-1921, no later than 1933.

While this information is undeniably cool, you might be wondering why this kind of paleovirology matters. Why does it matter what the virus looked like 50 years ago? Its not like we can just bop on back to 1902 and vaccinate everyone against a less diverse HIV-1. A fellow at the Pasteur Institute had a nice analogy for our logic:

Collecting information about old strains of HIV — even those that disappeared over time — can help researchers learn how successful strains broke through, says Wain-Hobson. “For every star in Hollywood there are fifty starlets,” he says. “We would love to know what it was that caused this strain to move out of starlet phase and to the big time.”

Im not sure if you need a subscription to read these (your local library probably does if you do), but I strongly encourage you all to read the PR article and the Sciency PR article accompanying this paper!

Comments

  1. #1 Optimus Primate
    October 2, 2008

    Fascinating.

  2. #2 minimalist
    October 2, 2008

    Hi Abbie,

    Your link contains proxy stuff from your university.

    A more generally applicable link is here.

    Thanks for calling attention to this article. I tend to skim over titles of stuff that doesn’t match my severely limited area of expertise. :)

  3. #3 Blaidd Drwg
    October 2, 2008

    But…But…

    I thought HIV/AIDS was invented by the illuminati back in the 1970′s to wipe out the blackfolks…

  4. #4 Sili
    October 2, 2008

    Just saw this on the BBC site earlier. They (obviously?) focused on the changing demographics of the time, but there was a nice mention of the divergance of strains too.

    http://news.bbc.co.uk/2/hi/health/7646255.stm

    Link in case I’m wrong and you wanna slather some “UR DOIN IT RONG” on them.

    Thank you for the summary. How does one go about analysing – and obtaining such old samples? (Sorry, don’t have access to Nature. And might there be other old stuff lurking in the archives somewhere?

  5. #5 Stacy S.
    October 2, 2008

    That’s very cool! So now what?!!

  6. #6 Ranson
    October 2, 2008

    I saw news on this elsewhere and rushed right over to see what Abbie would have to say. I wasn’t disappointed.

  7. #7 Eric Saveau
    October 2, 2008

    But…But… I thought HIV/AIDS was invented by the illuminati back in the 1970′s to wipe out the blackfolks…

    Oh, brother; there was a nasty thread over on Pharyngula yesterday where myself and several others got into a ruckus with a raving psychotic who, it turns out, has claimed precisely that -

    http://scienceblogs.com/pharyngula/2008/09/poll_you_must_choose_between_j.php

    This “John Best” fellow is a shambling toxic zombie of crazyscarystupidconspiracyfucknut.

  8. #8 windy
    October 2, 2008

    How does one go about analysing – and obtaining such old samples?

    “how do you extract RNA from half a century old paraffinated samples?”
    “Very carefully” :)

    Looks like they have a paper in PloS ONE about the isolation methods.

  9. #9 Confused
    October 3, 2008

    I was in a seminar when someone described similar work examining H1N1 from military pathology samples from the Spanish Flu epidemic… in 1918!

    Those samples may have been better kept, although I think most of them were wax embedded too.

    It mind blowing.

  10. #10 Paul Lundgren
    October 3, 2008

    So what will Peter Deusberg have to say about this one? Probably something inane (I know, I’m a big bettor).

  11. #11 Boomy
    October 3, 2008

    Very cool. Makes you wonder what other viral DNA is waiting to be discovered in old tissue samples stored around the world.

  12. #12 Eric Saveau
    October 3, 2008

    So what will Peter Deusberg have to say about this one?

    Or, more importantly… Savely Saava and Lenny Horowitz?

    ]}:-D

  13. #13 themadlolscientist, FCD
    October 4, 2008

    This news is getting around. It was mentioned on Neatorama today too – it’s good to see it getting out to the general audience so quickly.

  14. #14 Sili
    October 4, 2008

    Thank you, Windy.

    I guess I’ll have to put in an effort then.

    Duesberg? “Well, duh. Those ebol Schwarze were obviously popping poppers and having teh ghey sex until they were liberated by the compassionate colonialists.”

  15. #15 Kathy
    October 6, 2008

    Wow.

    We were just covering the fossil record in my Evolution class on Thursday, and got to hear that one of my favorite professors on campus (Dr. Ken Stedman, at Portland State) is now working on figuring out a way to identify viruses in the fossil record.

    It’s all so very, very cool. Words fail me.

  16. #16 Laurent
    October 7, 2008

    Hum… I wouldn’t be so categorical about the state of the samples. Even solute DNA at room temperature for a while (i.e. years) may not be degraded to the point it is useless: you may still be able to amplify it without much trouble (the key point is that it should not have been open too many times, since it increases the chances of contamination). As another example specimens in herbaria are perfectly valuable to extract quality DNA even if they stayed over a century in (sometimes fairly) bad conservation conditions (though not in animal collection where formol was used -this is the exception). This was also done from momified tissues (conserved for over millenia). Don’t be too pessimistic about samples, this is just sort of a modern hoaxy truth from the “clean bench era”; you would be amazed just how well conservation makes its own way above the -80°C treshold.

  17. #17 Laurent
    October 7, 2008

    Oops… Sorry, I over intrepreted your “holy crap”. Apologies!

  18. #18 windy
    October 7, 2008

    Oops… Sorry, I over intrepreted your “holy crap”. Apologies!

    Also, this was RNA, not DNA, so it’s still a bit more challenging than extracting DNA from museum samples…

  19. #19 Tom
    October 8, 2008

    Nucleic survival over long times – sure it can survive, in some conditions. Frankly what is one of the most interesting findings here is that these samples were fixed in Bouin’s solution. For those not in the know, this is formaldehyde plus picric acid. With a pH at approx 1. Now that is not, in theory, good for any nucleic acids. So the fact that there was survival is mind blowing. Its great news for anyone who wants to go trawling for old genetic material from fixed tissues.

  20. #20 Laurent
    October 8, 2008

    Well, sure these are further striking features for sample conservation, and I don’t know what the conserved tissues were neither, but I see two points (I would gladly be argued about, given I’m by no way a virologist and moreover I did not dig into the paper itself):

    - @ comment #18: retroviruses are also under a DNA form part of their life-cycle, so this is not only about hunting back old RNAs…
    - @ comment #19 (I acknowledge the point may be in contradiction with the first part above): these conditions indeed make DNA ‘resurrection’ quite striking, but I wouldn’t be so surprised by viral capsidian resistance to these conditions (but I may be utterly wrong about it, this is only a remark based on the astonishing long term survival of unrelated viruses outside their hosts). Do we know whether the sample investigated could have contained viruses in such stage?

    Further comments are welcome! :-) (I need an education on viruses)

  21. #21 windy
    October 8, 2008

    Laurent:

    @ comment #18: retroviruses are also under a DNA form part of their life-cycle, so this is not only about hunting back old RNAs…

    In this study, they used the RNA, though. I assume that finding virus RNA is considered more conclusive.

    Tom:

    …the fact that there was survival is mind blowing. Its great news for anyone who wants to go trawling for old genetic material from fixed tissues.

    Yes it is – the methodology article I linked to makes the point that a lot of the degradation in formalin fixed samples happens during extraction. The survival under so acidic conditions is still weird, though – maybe the formalin protected the nucleic acids? :)

    “our data also indicate that this success comes at a serious cost – predictably our results reveal that the application of heat and/or alkali in this way rapidly degrades the total RNA within the sample to sub-detectable levels (Figure 2). In light of the instability of DNA and RNA in both hot and alkali conditions, this is not surprising, but it does suggest that a trade-off is occurring in the extracted DNA between cross-link reversal and DNA degradation, and that a careful balance is required to ensure that PCR amplifiable DNA remains after treatment.”

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