
Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966 - mmoez
https://www.livescience.com/oldest-hiv-genome.html
======
ImaCake
People might be interested in why this useful. Much like with Covid today,
scientists are interested in understanding when the disease first appeared.
Because that gives us clues about where it came from and how quickly it is
changing now. You can estimate this based on changes in the sequence of the
genome. Changes (mutations) will appear in the genome at a predictable rate
("mutation rate"), and is measured as mutations per generation.

For HIV, there are plenty of estimates for the mutation rate based off a
mixture of statistical bioinformatics and knowledge of genetics. But they are
all inferences because we don't have many sequences from before 1988. This
relatively ancient genome allows scientists to see how good their estimates
are by looking at a genome that will have -20 years worth of mutations. Turns
out the estimates are really good. I would then draw the link back to Covid
where the mutation rate is estimated in the same way. So it's a good bet that
the date estimated for Covid's emergence is pretty close to the mark.

You can see the paper here[0]. I think the actual paper would make a better
link on HN, but I guess the press release is useful for those without a
molecular biology background.

0\.
[https://www.pnas.org/content/early/2020/05/18/1913682117](https://www.pnas.org/content/early/2020/05/18/1913682117)

~~~
acqq
It's also relevant to demonstrate now that this virus too hasn't been made in
the lab. The "lab origin" is a claim that some like to spread on every
outbreak, even in spite of the fact that virologists know that nature produces
the viruses very easily and there are no facts supporting anything else this
time too.

From the abstract:

"Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to
a time period around the turn of the 20th century (1881 to 1918)."

At that time humanity didn't even know what the virus really is -- they just
knew that something in some _liquid_ transmits some illness. The most advanced
lab at that time could only get that liquid using the filters.

~~~
rewoi
The question is not really "was this particular one man made?", but "is it
possible?" It is pretty obvious 1970ties technology was not advanced enough to
pull this stunt. But times change.

~~~
trhway
the "gain-of-function" experiments - ie. increasing the deadliness and
transmissibility of a virus - doesn't seem to require any meaningful
technology, at least not the way it was done in the Wuhan labs to the
coronavirus[1]. Such "improved" virus wouldn't look like a "lab made". In
theory similar gain-of-function experiments could have resulted in the human
transmissible HIV back then.

[1][https://www.newsweek.com/dr-fauci-backed-controversial-
wuhan...](https://www.newsweek.com/dr-fauci-backed-controversial-wuhan-lab-
millions-us-dollars-risky-coronavirus-research-1500741)

~~~
DiogenesKynikos
Those gain-of-function experiments were done at the University of North
Carolina.

But we know for certain that SARS-CoV-2 was not created through gain-of-
function experiments. It doesn't use any of the standard viral backbones used
in such experiments, it has a receptor binding domain that computational
chemistry algorithms would not have predicted to work (meaning that nature
"invented" it, not scientists), and the virus contains seemingly random
differences throughout its genome from all known viruses - that would not be
the case for a lab-created virus.

The boring answer is the correct one: this virus evolved in nature, and then
spilled over into the human population late last year.

~~~
scottlocklin
Your statement contradicted itself in several places: a "gain of function"
virus would contain random differences, and would look indistinguishable from
something "created by nature." Effectively that's how nature makes more
virulent viruses; the more virulent examples reproduce more effectively. Just
like that's how nature/bakeries makes yeast that works better on flour. No
genetic engineering involved.

I don't think there is any evidence of this, despite the usual suspects
(neocon types on our side, and militarists on the Chinese side) ginning up the
case for an "escape from lab" casus belli, but let's get the facts straight.

~~~
DiogenesKynikos
> a "gain of function" virus would contain random differences, and would look
> indistinguishable from something "created by nature."

No, a chimeric virus created in a gain-of-function experiment would look
extremely similar to known viruses, because these chimeras are created by
combining elements of known viruses. It would not be 4% different from the
closest known natural virus. Accumulating thousands of mutations throughout
the entire genome takes decades of evolution. In the wild, that means
thousands of generations of hosts.

A virus created in a gain-of-function experiment would also use a well-known
backbone. It would not be based on some virus that nobody had ever heard of.

~~~
scottlocklin
Yeah dude that could never happen. Except it already did:

[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797993/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797993/)

[https://norkinvirology.wordpress.com/2015/12/04/genetically-...](https://norkinvirology.wordpress.com/2015/12/04/genetically-
modified-emerging-viruses-debate-over-gain-of-function-research/)

[https://www.pnas.org/content/113/11/3048](https://www.pnas.org/content/113/11/3048)

I don't know what your purpose is in regurgitating verifiable but admittedly
realistic-sounding bullshit on hacker news, but virtually every statement you
have made here is obvious bullshit.

I don't even particularly believe the "possibly released from a lab" meme, and
am generally against the shadowy dipshits that push it. But you're not helping
here.

~~~
DiogenesKynikos
What happened?

Are you saying that a chimeric virus created in a lab was found to have
thousands of seemingly random mutations throughout its genome?

Or are you claiming that a chimeric virus was created using a backbone that
nobody had ever heard of?

Be specific, because it's impossible to respond if you vaguely call what I'm
saying BS.

------
masklinn
> Those fragments were also from different subtypes of HIV, Gryseels said,
> which shows that the virus had been circulating for some time in humans
> before the 1950s.

That was already pretty much a certainty from the already known fragmentary
genomes (also mostly from the DRC), as well as the phylogenetic analysis of
known strains, groups and subtypes.

~~~
koheripbal
Was this restricted to Africa?

~~~
masklinn
Looks so. The virus seems to have "brewed" in the Congo basin for a few
decades, _possibly_ amplified by the vaccination campaigns of the early 20th
century (as they'd be using the same glass syringes and steel needles for
dozens of patients).

If it got out before the second half of the 20th century it apparently didn't
manage to gain enough of a foothold to go pandemic[0]. Though the long
incubation rate and somewhat mixed symptoms also make it somewhat uncertain.

[0] as may have been the case for Robert Rayford who looks to have been
something of a terminal case rather than vector or victim of a more widespread
infection

~~~
Engineering-MD
I’m skepticism that vaccinations would have increased it much tbh. A needle
stick from a patient with HIV has a 1/300 chance of transmitting HIV, so it
would probably have had a very limited impact. Needle sharing amongst IVDUs is
higher risk due to the repeated exposure to the small risk.

------
joyj2nd
TLDR: The "news" is not the age of the samples, there are older ones, but that
the virus genome is still intact and allows for a more accurate estimation of
mutation rates and origins of HIV.

"There are older fragments of HIV out there, one from 1959 and one from 1960,
also from DRC. But those pieces aren't as complete, and thus can't offer as
much information about the virus' mutations. "

------
gjkood
If you have time I would recommend two movies that touches deeply upon this
topic. They are 'Philadelphia'[1] which garnered a 'Best Actor' Oscar for Tom
Hanks and 'And the band played on'[2] starring Mathew Modine.

'Philadelphia' a fictional movie that touches on the social stigma associated
with HIV and 'And the band played on' captures the politics of why it was
ignored by Reagan and his supporters for so long and the sad politics and
scientific infighting in the chase for a cure.

Both are incredible movies.

[1]
[https://www.imdb.com/title/tt0107818/?ref_=nv_sr_srsg_3](https://www.imdb.com/title/tt0107818/?ref_=nv_sr_srsg_3)

[2]
[https://www.imdb.com/title/tt0106273/?ref_=fn_al_tt_1](https://www.imdb.com/title/tt0106273/?ref_=fn_al_tt_1)

~~~
jdm2212
Both are really incredible movies, and I'd also highly recommend them. "How To
Survive A Plague" is pretty great too (it even features everyone's favorite
NIH official, Anthony Fauci!).

One thing worth being aware of with "And The Band Played On": it's quite old,
and science advanced a lot after the book it's based on was written, so it's
sometimes factually inaccurate (Gaetan Dugas didn't personally cause the
pandemic, and the incubation period is longer than they thought then). It's
_not_ a work of history or a documentary, but it makes for fascinating viewing
precisely because it was made so close to the events that the story it tells
is not neat and polished with the benefit of decades of hindsight and
narrative shaping. It's chaotic and emotional and raw and authentic and,
inevitably, sometimes wrong about stuff that wasn't known then.

~~~
overkill28
The Gaetan Dugas thing seems to dominate every discussion about And The Band
Plays on which is too bad because the book is like 600 pages long, tracks
dozens of real life individuals, has tons of incredible primary source
material, and gives a very touching, grounded, contemporary look at AIDS in
the early 80s.

And out of the small portion of the book that talks about Dugas, I never got
the impression that Schilts was trying the blame him for causing the pandemic,
but rather that he was using him as a real life example of the type of man
that existed in that era, who flew around the country having sex with
thousands (yes thousands) of other men, whose behavior doubtlessly and
unknowingly sped the spread of AIDS.

~~~
jdm2212
Most people have only seen the film, I think (I only read half the book).
Gaetan Dugas is much more prominently featured in the film, which pretty
strongly implies he was a key factor in the wide spread of HIV.

------
djaque
I didn't understand the AIDS epidemic until I listened to a podcast [1] where
they interviewed a gay survivor. I can't imagine my friends dying off one by
one around me from an unknown specter. The government pretending you didn't
exist and ignoring you because it was a "gay problem". Society demonizing you.

He said that even after it was understood that AIDS was not transmissible by
touch, morgues would refuse to accept the bodies of gay men. When people knew
they were at the end of the rope, they would ask their friends to throw their
ashes over the fence into the white house lawn. That way as their final act,
they could tell the government that their active silence was literally killing
people and that even if they considered them others, they wouldn't be ignored.

It's heartbreaking, but I'd recommend anyone to listen to the interview if you
don't know much about that period in history.

[1] [https://www.stitcher.com/podcast/shame-on-
you/e/66787240](https://www.stitcher.com/podcast/shame-on-you/e/66787240)

~~~
klmadfejno
The white house lawn comment sounds powerful. But I don't see any evidence it
actually happened. Right?

~~~
redis_mlc
I followed the AIDS crisis in the newspaper from Day One, starting with one-
inch long columns about "mysterious purple lesions called Kaposi's sarcoma" to
shrines with hundreds of photos occupying whole sections.

The similarity with corona in 2020 is that so little was known, but for years,
not months. The difference was that AIDS was 100% fatal until drugs were
developed, and AIDS killed a generation of young adults rather than older
people.

(There were interviews with a handful of men who were immune to the AIDS
virus, but had to endure all of their friends and partners dying, and had to
deal with inheriting a lot of possessions that reminded them of dead people.)

Almost all hemophiliacs in North America used pooled blood products from
thousands of donors, so just about all of them died. (There's a Canadian film
on Youtube that covers this.)

~~~
fortran77
Isaac Asimov was so embarrassed to have contracted AIDS from a blood
transfusion that it wasn't mentioned 'til after his death.

~~~
djaque
I had no idea that he died of AIDS and that was in the 90s. It's terrifying
how recent it was that he would have received public backlash for contracting
a disease during a surgery.

~~~
foldr
I feel like you're leaving homophobia out of the equation. Asimov was ashamed,
and there would have been a backlash, because society associated AIDS with gay
men. If people had really believed that he'd got it through surgery, there
wouldn't have been a bad reaction.

------
at_a_remove
I remember how _little_ was known in the beginning, when it was called GRID.
For a while it was theorized in the media that semen hitting the bloodstream
was causing the immune system to freak out; my friends, who had just started
puberty, asked me (as the designated science nerd) what I thought of that, as
they had somewhat random scenarios of nocturnal emissions striking road rash
from skateboarding. I thought it unlikely, given what I knew of history.

We had very little idea of what constituted "transmissible" and what did not
for a period of time, and so while our parents had "free love" and The Pill,
with the biggest risk being herpes, at least a section of my generation got
"sex = death" internalized on top of all of the other apocalyptic gloom.

Of course, even what would be transmissible was subject to propaganda: on one
side, you had people arguing for any gay sex being a risk, but on the other
side, some activists _insisted_ that heterosexual intercourse was exactly and
precisely as risky as homosexual (male) intercourse. Quite a lot of
misinformation floating around.

~~~
koheripbal
There are still a lot people spreading the misinformation that hetero sex is
as risky as anal sex, because they have some odd agenda to push.

~~~
NelsonMinar
You understand heterosexual people have anal sex too, right? It's become quite
trendy.

~~~
at_a_remove
Everyone here knows precisely what was being discussed. Me, the writer, you.
Why quibble?

------
interestica
"When AIDS was funny"
[https://youtu.be/yAzDn7tE1lU](https://youtu.be/yAzDn7tE1lU)

It shows the challenges of the press to have serious conversations about the
disease with the Reagan administration.

~~~
Fezzik
Is it that much different than how _everyone_ jokes about HSV1 today? It is
still a (ridiculous and stupid) running punchline on SNL. Obviously it is a
far less dire virus (as far as we know, today) but, we as a species
(generally) compared to our individual potential, are absolute idiots and
almost always take the easy intellectual route (humor and bullshit) when faced
with uncommon information.

The video really seems like par for the course and not surprising in the
slightest...

~~~
umanwizard
“far less dire” is an understatement. HSV-1 causes only cosmetic effects in
the vast majority of cases.

~~~
Fezzik
That is... not exactly true: [https://www.npr.org/sections/health-
shots/2018/06/21/6219083...](https://www.npr.org/sections/health-
shots/2018/06/21/621908340/researchers-find-herpes-viruses-in-brains-marked-
by-alzheimers-disease)

I was not trying to diminish the atrocity that is how the AIDS epidemic was
handled, I was only trying to illuminate that people (and the super-majority
of our lawmakers) are immature and uninformed when talking about all
infectious diseases.

Edit: just look at our President’s response to Covid... it is bumbling and
moronic.

~~~
MiroF
So what, this tentative research that shows _no_ causal link whatsoever
between HSV-1 and alzheimers is the same as the 32 million killed by AIDS
globally?

No. It isn't. Stop trivializing HIV. I don't know what you're getting out of
it, but it comes across as incredibly tone deaf.

~~~
Fezzik
I truly was not trying to offend or trivialize anything: my only point, as
best as I can distill it, is that people react irrationally and
inappropriately to infectious diseases. And we need to work on that. This is
not at all unique to HIV/AIDS, even though people suffering from AIDS have
born the brunt of the actual suffering. If we can’t have open, rational
discussions about HSV, how can we do the same with HIV?

Edit: grammar

~~~
MiroF
I understand the point you were trying to get across. Many STIs have
substantial stigma around them and it makes it harder to fight them.

I just want to caution you that making these forms of equivalences is a common
tactic to derail and discount the impact of HIV or the experience of
populations disproportionately harmed, in the same way that people derail
discussions about the disproportionate killing of black people by police with
statements like "why focus on black people? nobody should be killed by
police."

I believe that you were not intending to do so, but I also hope that you
understand and can be cognizant of that dynamic.

~~~
Fezzik
MiroF - I (could not initially) reply to your comment directly, but that was a
perfect analogy to make your point. I can definitely see how my first comment
could be taken that way, and that was not at all my intention. As with many
things, I gotta work on my contextual phrasing and presentation!

------
bluetwo
Semi-related: Thinking about this era I wondered how long it look for AIDS to
kill 100,000 Americans. The answer is about 5 years. CoViD did it in 5 months.

~~~
sn41
It's disturbing that we are being told to learn to live with the virus when
there is such a high risk of contraction.

~~~
ekianjo
High risk but most infected have close to no symptoms which is nothing like
AIDS which used to be a death sentence.

~~~
ImaCake
But even a tiny mortality rate is catastrophic when talking about city and
country sized populations. The lockdowns happened for a reason, because this
disease overwhelms public health.

~~~
TheOtherHobbes
And if enough people start dying the disease overwhelms public _everything._

In the UK, some schools are refusing to reopen and some people are refusing to
return to work in spite of government orders.

~~~
ImaCake
Indeed, mass panic is an under appreciated risk in the discourse in some
countries. We may have the misfortune of discovering just what that looks like
in the coming months.

------
ddingus
[https://youtu.be/0KthBMpST7Q](https://youtu.be/0KthBMpST7Q)

A 90's film telling the story of how AIDS was ignored.

