
We know the city where HIV first emerged - Perados
http://www.bbc.com/earth/story/20151119-we-know-the-city-where-hiv-first-infected-a-human
======
nonbel
Simian AIDS was discovered after human AIDS. How do they know the jump didn't
occur in reverse?

Here is the first report of simian AIDS: "Examination of the species-specific
annual mortality rates of macaques at the center during the previous 4 yr
showed a significant increase in deaths in 1980 and 1981"
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393899/](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393899/)

Also, it is convenient they do not share the mcmc traces. Based on these
settings I bet they were ugly:

>"For each data set, at least 3 MCMC chains of 250 million steps were
computed. Parameters and trees were sampled every 50,000th step. Samples were
combined with LogCombiner (77) and between 10 to 30% of each MCMC chain was
discarded as burn-in. MCMC mixing was diagnosed using visual trace inspection
and calculation of effective sample sizes in Tracer (77). We report the
posterior mean and 95% Bayesian credible intervals for evolutionary
parameters."

[http://dx.doi.org/10.1126/science.1256739](http://dx.doi.org/10.1126/science.1256739)

Another thing, they write:

"Our estimated location of pandemic origin explains the observation that
Kinshasa exhibits more contemporary HIV-1 genetic diversity than anywhere
else"

This is totally circular. As shown in their figure S2, they used genetic
diversity in a region as an indication of earlier presence.

~~~
lloydde
My limited understanding is that once discovered scientists found the families
of simian viruses that demonstrated evolutionary and divergence that cannot be
explained in going the other way or the timeframe of human hiv.

See
[http://news.nationalgeographic.com/news/2006/05/060525-aids-...](http://news.nationalgeographic.com/news/2006/05/060525-aids-
chimps.html)
[http://www.ncbi.nlm.nih.gov/m/pubmed/8026477/#](http://www.ncbi.nlm.nih.gov/m/pubmed/8026477/#)

There is a video documentary that I watched in the last couple years that I
was really hoping to find again and link to.

~~~
nonbel
Thanks. I wonder if this analysis will be reproducible though (they don't
mention any parameters...):

>"Phylogenetic analysis Phylogenetic relationships were estimated from
comparisons of predicted protein sequences. Sequences were aligned using
CLUSTAL (Higgins and Sharp, 1988, 1989). Evolutionary distances between all
pairs of sequences were computed using Kimura's empirical method (Kimura,
1983; eqn. 4.8) to estimate the number of superimposed amino acid
replacements; sites at which there was a gap in any sequence in the alignment
were excluded from all comparisons. Phylogenetic relationships were estimated
from these distances by the neighbor-joining method (Saitou and Nei, 1987).
The reliability of branching orders was estimated by the bootstrap approach
(Felsenstein, 1985). These methods were implemented using CLUSTAL V (Higgins
et al., 1992).

Nucleotide accession numbers All sequences were submitted to GenBank and are
available under accession numbers U03994-U04018."

It looks like those sequences are a mixture of the various proteins (env, pol,
etc) so it would take some time to figure out which is which. I don't feel it
like right now. It seems like getting the sequences from genbank and then
aligning using default params with clustalw would be closest to their method.
If someone wants to do it:
[http://www.ncbi.nlm.nih.gov/genbank/](http://www.ncbi.nlm.nih.gov/genbank/)
[http://www.genome.jp/tools/clustalw/](http://www.genome.jp/tools/clustalw/)

------
achille
There's an excellent Radiolab Podcast that covers the same study, I'd highly
recommend listening to it:

* [http://www.radiolab.org/story/169879-patient-zero/](http://www.radiolab.org/story/169879-patient-zero/)

~~~
anton_gogolev
There's also an updated version which briefly covers recent Ebola outbreak:
[http://www.radiolab.org/story/patient-zero-
updated/](http://www.radiolab.org/story/patient-zero-updated/)

~~~
univalent
Thanks! I didn't know about the updated one. The original is one of my
favorite episodes.

~~~
douglasisshiny
Same here, although the description of chimps hunting was a bit disturbing.

------
nikatwork
It's a morbid irony that HIV emerged from "Leopoldville" considering the other
atrocities unleashed on Africa by Leopold II.

~~~
splouk
[https://en.wikipedia.org/wiki/Leopold_II_of_Belgium](https://en.wikipedia.org/wiki/Leopold_II_of_Belgium)

If anyone else is curious like I was.

~~~
adevine
Wow, on the order of 10 million dead - half the population. That's Hitler-
level genocide right there.

~~~
nikatwork
Workers who were short of the quotas might have their hands severed. Leopold
II is a forgotten monster. Arguably it birthed the international human rights
movement.

------
theseatoms
tl;dr, Kinshasa, Democratic Republic of the Congo (then known as Leopoldville)

~~~
fwn
There's actually more content in the article. It's far from click-bait.

After reading it I think that the exact city is the least interesting fact
they have to offer.

~~~
kedean
Click-bait titles dont' mean the article is crap. It's a good article with a
clickbait title, plain as that. Clickbait is when some information is left out
of the title in an obvious way such that readers will click in pursuit of that
piece of information, rather than clicking it in pursuit of expanding on the
headline.

------
olegious
The book "The history of AIDS" was a fascinating and accessible read on the
subject of the spread of HIV, from it's origins to today.

~~~
masklinn
Definitely, highly recommended book. Learned of it from Quammen's
"Spillover"[0] (a great — if somewhat terrifying — book in its own right)
mentioning it as a source in the AIDS chapter and it was a fantastic read.
Note that Quammen released his own AIDS-history book this hear, "The Chimp and
the River"[1] (haven't read it yet though I intend to).

Direct link to Jacques Pépin's "The Origin of AIDS" on amazon:
[http://www.amazon.com/dp/0521186374](http://www.amazon.com/dp/0521186374)

[0]
[http://www.amazon.com/dp/0393346617/](http://www.amazon.com/dp/0393346617/)

[1]
[http://www.amazon.com/dp/0393350843/](http://www.amazon.com/dp/0393350843/)

------
simonebrunozzi
Is HN becoming "spammy"? In this case, would it hurt to include the name of
the city in the title?

------
AnAfrican
It's not really clear to me:

Are they saying that the jump happened in a large metropolis ?

Or that Kinshasa was the first large city in which HIV became an epidemic ?

~~~
WalterSear
The first large city.

------
hawkice
Belgian control of the Congo was rife with pretty extreme abuse -- the
obvious, often horrifying consequences of conquest. But the influx of
ambitious businesspeople and capital which they claim started the wider
outbreak of HIV, is a curious case. Often people will hand-wring about vague
cultural factors, but this seems like one of the most concrete major
international disasters caused by rapid gentrification and international
investment.

In many ways, whether you support e.g. more direct foreign investment areas in
India and China or not, I'd prefer the conversations about costs to be as well
formulated as this (I also suspect free trade and foreign investment in China
and India has done a lot more good than HIV has done bad, even if you just
count lives saved).

~~~
caoilte
_rapid gentrification_ of __Congo __

whuhh???

Just 'caus it had a CIA sponsored coup, doesn't mean things got any better.

~~~
fabulist
This would be the first time I've seen someone suggest gentrification makes
things better.

------
random778
Kinshasa, the capital of the Democratic Republic of Congo.

------
jackgavigan
tl;dr - Kinshasa.

