What isn't true? Once in our history doesn't mean once as in a single host.
There are four major groups of HIV, HIV1 (likely to have originated in a strain of SIV commonly infecting chimpanzees and gorillas) O and M and HIV2 (likely to have originated in a strain of SIV commonly infecting mangabeys) A and B, it's not cleared how many times it independently jumped, what is clear that this was more or less a single temporal event in modern history (cavemen didn't had to worry about HIV or aids, neither did the Romans, and even the bushmen in africa only have been recently infected) and the jump happened between the late 19th and early to mid 20th centuries.
SIV doesn't jump species all the time, there are plenty of SIV strains that haven't done so even tho humans were and are in contact with primates that are infected by those strains all the time.
Other immuno suppressing viruses also haven't made the jump from other species to humans.
If you eradicate HIV today with a push of a button there is no guarantee that SIV will make a jump again and turn into HIV, and there is little to no evidence that HIV jumped back to primates or has yet to infect another species.
There is also no conclusive evidence that the four groups of HIV happened to jump species on 4 distinct occasions, could have been 4, could have been 2 could have been 1 could have been 400.
Heck if HIV1C somehow originated in South America and then was introduced to the human population in Africa half of our models can be thrown down the toilet.
What we do know is that this happened 80-140 years ago, why did a virus that infected primates for 50,000 to 2000000 years suddenly jumped species all of a sudden despite the fact that there was just as much if not more cross species interaction during human history is a better question, in fact if it indeed jumped multiple times all within a pretty small time window that would only raise more questions than give any answer.
>"What we do know is that this happened 80-140 years ago, why did a virus that infected primates for 50,000 to 2000000 years suddenly jumped species all of a sudden despite the fact that there was just as much if not more cross species interaction during human history is a better question"
Simian AIDS was discovered after human AIDS though:
"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/
I don't see how people really know whether the problem originated in humans and spread to apes or vice versa. If anything you would expect such issues to be detected in highly monitored animals kept in well controlled research facilities first...
Human HIV was discovered probably 5 decades if not more after it jumped.
We know it didn't originate in humans, because we can estimate how old SIV and HIV are based on their genetic material and other factors.
And we also know how old SIV at least is because we've tested primates on isolated islands and found that they are also infected, so if you find SIV infected primates on an island that was isolated from mainland Africa 30,000 years ago and it's preset within 100% of the primate population you know it's at least that old.
Another thing you can do is look at the DNA of the host and see if any viral DNA has been embedded within it, depending on where it is you can also estimate a timeline based on known processes and mutation rates.
There is very little to no doubt that HIV originated from SIV, the question is why now.
And yes we've discovered SIV later because AIDS happened then we found that it's a virus and not because they are gay, so people started looking at it's source and discovered SIV, FIV, EIAV and others.
You also need to understand that viruses are very hard to find, it's not like you just look at blood samples and see them, there are also not that many generic tests that can simply detect if a virus is present or not, it takes years to decades to isolate, classify and then develop methods to identify a virus and it's not like in the 1980's you could just order a full genome to be sequenced at will.
>"And yes we've discovered SIV later because AIDS happened then we found that it's a virus and not because they are gay, so people started looking at it's source and discovered SIV, FIV, EIAV and others."
This doesn't really fit with the narrative in the paper I linked. They give this reason: "It was the impression of workers at the New England Regional Primate Research Center that there had been an increase in the number of deaths in its macaque colony."
The paper you linked is from 1983 before any genetic and even epidemiological studies were conducted, AIDS was clinically observed in the US in 1980 or 1981, it wasn't even called AIDS until 1982, and HIV was only identified in 1983.
So what's exactly the surprise in the fact that an article from 35 years ago that was written at the dawn of HIV and AIDS research doesn't exactly fit with our modern understandings of the disease?
Given that the research animals are much more heavily monitored it is surprising that the simian analogue only showed up in that environment after the human version became a big deal.
As quoted earlier, they say the study was initiated because they noticed the animals dying more often than usual. You don't need genetic/epidemiological data to notice something like that. I do not understand what relevance that should have.
In 1983 AIDS wasn't still a big deal, no all primates have SIV strains, some primates never develop AIDS, we know some species for primates can effectively suppress SIV permanently, while some do develop immunodeficiency syndromes, heck it's even possible that the species or sub group of primates in the research was introduce to SIV from another species because of humans (mostly because the research does states that they have had 14 different species locked in their research center), it is however not possible for HIV to be the origin of the virus since we now have genetic models of the disease.
When that research was conducted we didn't even knew what was causing AIDS as neither SIV nor HIV have been identified yet.
Also research animals die all the time in great numbers, if it's a research laboratory then they'll probably die or be put to death way before they'll develop AIDS, if it's a conservation then they die to natural causes all the time, it's more likely that no one bothered to think why primates die to various infectious diseases more frequently than they should beforehand and then when AIDS research began to be published some one made a connection and looked into it.
It's not like in 1983 or prior to that we commonly had 100's of primates locked in for a multi decade research in a state of the art habitat which was constantly monitored, they were either lab rats that lived a very short life or at best simply tracked for conservation purposes on a reservation.
In fact after reading the research fully, it looks to me like they've unintentionally introduced SIV to Asian Macaca Cyclopis from an African species M. Mulatta (commonly known as a rhesus monkey) since SIV is not commonly present in Asia it's no real wonder why an Asian primate species would be considerably more affected as African species would be more or completely immune to AIDS while being SIV carriers.
If anything this paper proves that African primates coexisted with SIV for a long enough time to develop an immunity or high tolerance to the virus while species from other regions that did not have SIV strains did not.
And you can chuck this again to the fact that in 1983 no one knew that AIDS was caused by HIV, SIV, FIV and other similar viruses.
>"Also research animals die all the time in great numbers, if it's a research laboratory then they'll probably die or be put to death way before they'll develop AIDS"
Yes, yet (relatively) soon after human AIDs is discovered people start noticing an increase in macaque deaths in their labs. This was later attributed to a similar cause. I think that is an important aspect of the timeline to keep in mind, that is all on that point. The rest hinges on other evidence which we are discussing in parallel here.
In a species that was never exposed to SIV before, what is actually surprising here?
I really don't understand why you are even attempting to quite wrongly interpret the results of a study before HIV or SIV were even discovered that actually disproves your assertion.
>"we've tested primates on isolated islands and found that they are also infected, so if you find SIV infected primates on an island that was isolated from mainland Africa 30,000 years ago and it's preset within 100% of the primate population you know it's at least that old."
This sounds familiar, do you remember the ref? From what I remember the degree of "isolation" was questionable.
It's important to note that even if the location is not isolated it doesn't matter, and we do have proof that it is, what we look at is the molecular clock of the virus basically it's molecular structure based on the mutation rate of each virus.
When you calculate the drift between different strains you can estimate the age, more isolated populations help since they tend to have less types of infections, while it's not common to find a primate with multiple strains on the mainland primates in the deep jungles of south america and on isolated islands off the coast of africa usually only have a single strain due to their relative isolation from other primate populations.
Not much more time for me to read into this today but I see that the molecular clock estimate is based on the "isolation" estimate. So these are not independent measures:
"Crucially, he knew from geological records that the island separated from continental Africa around 12,000 years ago. Assuming that the strains had had at least 12,000 years to evolve apart, he determined that the mutation rate of SIV is much slower than originally thought."
I find it difficult to believe that for 10k years a plausible scenario is that nothing happened like eg:
A) someone was hunting monkeys from more populated areas and traveled to "isolated" islands/regions to get more.
B) monkey on a branch gets thrown out to sea and floats to the island.
The molecular clock isn't dependant only on the isolation estimate, it comes from in vitro studies of a given virus and each of it's offshoots combined with our understanding of it's replication rates in a host.
Again it doesn't need to have a perfect isolation, and the fact that the island is home to completely different strains which are unique to that island and can be genetically studied for drift and mutation rates does show that there was sufficient isolation to prevent transmission between the mainland and the islands.
All isolation is relative, N. Korea is isolated it doesn't mean that nothing gets in or out, same thing here a monkey on a branch might be thrown out to the ocean but it doesn't mean it will become a transmission vector.
Strain X exists only on Island Y while strain M N and O exist only on Mainland Z but not vice versa is enough proof for isolation for the studies to be valid.
>"The molecular clock isn't dependant only on the isolation estimate"
Sure, not only, but according to your source it is dependent on the assumption the island was "isolated" for 10k years. We would have to look at the model to tell what effects relaxing this assumption and definition may have.
The molecular clock doesn't care when the island was isolated or for how long, it's used as a benchmark tool to differentiate the relative time period between 2 genetic sequences which share a common ancestor, it never gives you a date it can tell you that it took 4 times the time to arrive to state X from state Z than it took from state Y.
We know that the island is isolated sufficiently because of the unique SIV strains, we also know that the populations of the animals were isolated because there are no signs of cross-breeding.
There have also been countless studies to determine the age and the source of the tMRCA between HIV and SIV, and SIV is the source for every genetic study, even those that do not rely on using molecular phylogenetics to ascertain the time scale.
SIV and other primate lentiviruses are old, they are asymptomatic in the vast majority of their natural hosts which suggest coevolution which resulted effectively in cohabitation.
Most of the current work is done in regards to tMRC identification to build an accurate timeframe to understand why did HIV1 jumped from chimps to humans and HIV2 jumped from mangabeys.
We are also studying the divergence of different strains of SIV between different species of primates to better understand the virus, all of these studies find completely different time scale than what you are proposing, in fact other than conspiracy theories that were already disproven no science actually backs up any of your assertions.
Overall even if we take the studies that point to a completely different pathology and estimate the age of SIV at 100's or a few 1000's of years old, the divergence of the different strains still means it came first, spread across the primate population of africa, and then jumped to humans.
>"The molecular clock doesn't care when the island was isolated or for how long"
The rest of what you wrote is interesting (or will be once I get some sources for your claims), but you start out with this one that blatantly disagrees with what was written in your own source. In your source it says that molecular clock depends on the assumption the island was isolated for 12,000 years.
It would be great if you could:
1) Focus on that one point to clear up why you disagree with your own source, do this without writing about anything else. I am stuck on that issue right now.
2) Bring some links when referring to evidence, so I can tell what has made you believe the things you say. I am getting the sense you are well informed but not quite skeptical enough (perhaps current grad student?). The devil is in the details, as I have seen with the "isolated" island and molecular clock interdependence.
You might have to eradicate a number of species.