We know the city where HIV first emerged
1–10 of 48 posts
Re: We know the city where HIV first emerged
#2tl;dr, Kinshasa, Democratic Republic of the Congo (then known as Leopoldville)
Re: We know the city where HIV first emerged
#3Belgian 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).
Re: We know the city where HIV first emerged
#4Simian 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/
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
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.
Re: We know the city where HIV first emerged
#5There's an excellent Radiolab Podcast that covers the same study, I'd highly recommend listening to it:
Re: We know the city where HIV first emerged
#6The 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.
Re: We know the city where HIV first emerged
#7Simian 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/ Also, it is convenient they do not share the mcmc traces. Base…
> Simian AIDS was discovered after human AIDS. How do they know the jump didn't occur in reverse?
I'm not sure we (that is, humans) realized that SIV was a thing until HIV prompted us to look in those places. It's the classic example of not knowing what to look for until you've found it.
Re: We know the city where HIV first emerged
#8Simian 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/ Also, it is convenient they do not share the mcmc traces. Base…
Thanks for the article link!
>"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.
It seems like they also used phylogenetic history. Diversity alone is not a sufficient to identify origination.
>A very high genetic diversity of HIV-1 has been reported, not only in Kinshasa and the north and south of the DRC (12, 13, 31, 32), but also in Brazzaville in the RC and, to a lesser extent, in the Mayombe area of RC near Pointe-Noire, all of which have been suggested as potential source locations of the pandemic (22, 33, 34). We therefore performed phylogeographic analyses of viruses collected in both the DRC and RC (table S1) and compared sequence sampling locations with phylogenetic history to formally test hypotheses concerning the location of ancestral viral lineages (30). Our analyses robustly place the spatial origin of the HIV-1 group M pandemic in Kinshasa [posterior probability (PP) = 0.99]
They could have used "consistent with" rather than "explains", though that may be a bit pedantic and debatable and we wouldn't be in the sorry state of science education/trust if all researchers would communicate like Neil deGrasse Tyson.
Re: We know the city where HIV first emerged
#9Simian 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/ Also, it is convenient they do not share the mcmc traces. Base…
> Simian AIDS was discovered after human AIDS. How do they know the jump didn't occur in reverse? I'm not sure we (that is, humans) realized that SIV was a thing until HIV prompted us to look in those places. It's the classic example of not knowing what to look for until you've found it.
I agree, the time of discovery proves nothing. But I asked how they can tell either way since there is no data from earlier. However, I would think captive animals were monitored more closely for strange diseases than people in rural mid-1900s Africa.
Re: We know the city where HIV first emerged
#10Earlier quoted context omitted.
> Simian AIDS was discovered after human AIDS. How do they know the jump didn't occur in reverse? I'm not sure we (that is, humans) realized that SIV was a thing until HIV prompted us to look in those places. It's the classic example of not knowing what to look for until you've found it.
I agree, the time of discovery proves nothing. But I asked how they can tell either way since there is no data from earlier. However, I would think captive animals were monitored more closely for strange diseases than people in rural mid-1900s Africa.
You'd probably be wrong about that. Even today in most of these places, a captive animal that dies is just 'sick' and disposed of. Or often sold off as food if the death symptoms aren't obviously apparent, as would be the case with HIV. There is no functioning FDA in central africa.