The Hollywooding of Science
"The Hollywooding of Science". Beatrice Hahn's latest SIV sequences from Cameroonian chimps: an alternative interpretation
Updated 5 August, 2006
If you're new to these issues, read this first.
a) The latest paper by Beatrice Hahn's team (B. F. Keele, B. H. Hahn et al: "Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1") [Reference 1] features claims that they have discovered the source of pandemic HIV-1, the "AIDS virus".
b) However, on the basis of the evidence presented, this claim is unsafe. In fact, more than that, it represents a rash over-extrapolation.
c) The reasons for rejecting Hahn's claim include the following: (i) less than 1 in 200 of the chimp troops in this part of Africa have thus far been sampled for SIV; (ii) in reality, the new chimp viruses she has found fall far short of being "dead ringers" for pandemic HIV-1, as has been claimed; (iii) there are close physical and biomedical similarities between Pan troglodytes troglodytes (Ptt) chimps and Pan troglodytes schweinfurthii (Pts) chimps, which some believe should be regrouped into a single subspecies; (iv) members of some groups of Ptt cluster genetically with Pts, and vice versa; (v) despite their claims to the contrary, Hahn and co-authors have not established that Ptt (rather than Pts) represents the reservoir of pandemic HIV-1; (vi) furthermore, the closest primate virus ancestor to pandemic HIV-1 may have existed in a chimp troop that is now extinct.
d) The true reason why it is so important to Hahn's group to establish the Pan troglodytes troglodytes subspecies of chimpanzee as the reservoir of pandemic HIV-1 is that they believe that this refutes the OPV/AIDS theory, which proposes that AIDS began as a result of chimpanzee experiments conducted in Stanleyville, Belgian Congo, in the late 1950s.
e) However, their latest findings do not disprove the OPV/AIDS theory. For a long time, there has been substantial anecdotal and circumstantial evidence that at least some Ptt chimps were present at Stanleyville and/or the nearby chimp camp at Lindi. But a recently-unearthed Belgian article from 1965 proves that the Stanleyville doctors were working with at least one Ptt chimp in early 1960, and perhaps in 1959. Co-caging and group caging were routine at the holding centres at both Lindi and Stanleyville, meaning that viruses could have spread from this Ptt (or similar animals) to other primates (Pts and bonobos) housed in these centres.
f) Furthermore, it is far easier to postulate Ptt chimps, including chimps from south-eastern Cameroon, ending up in the huge holding centres at Lindi and Stanleyville than it is to postulate a human infectee moving from Cameroon to Leopoldville, allowing AIDS to spawn there - and only there.
g) It is also worth emphasising that because of recombination between SIV strains, the origin of pandemic HIV-1 does not automatically require the involvement of the closest viral ancestor genetically. [See below for further details.]
h) There are multiple problems with the latest Hahn/Sharp scenario of how the AIDS pandemic might have started in Leopoldville (over 600 miles by river from her alleged chimpanzee "source"). By contrast, the OPV/AIDS hypothesis is inconvenienced by none of these.
i) The discovery that Ptt were used in the Stanleyville experiments has more significance for the origin of AIDS than Hahn's latest data from Cameroon. Once again, the claims by Hahn and her buddies that "the OPV theory has been laid to rest" are revealed as empty bluster.
The Major Claims (and Flaws) of the Latest Hahn Paper
The latest paper by Beatrice Hahn's group about newly-discovered simian immunodeficiency viruses (SIVs) among ten troops of wild chimpanzees from Cameroon was published on line in Science express in May 2006, and in Science itself on July 28th, 2006.
The article elicited considerable media attention, and is notable for several reasons.
- The authors report rather high SIV prevalence rates (of between 29% and 35%) among some of these populations of wild-living Pan troglodytes troglodytes (Ptt) chimps. The overall prevalence of SIV among the five troops for which they provide full numerical details is just over 13%, but is likely to be somewhat lower (approximately 10%) among all of the Ptt troops that they sampled. The SIV-prevalence of 10% to 13% in Ptt chimps is slightly lower than the SIV-prevalence of "about 20%" previously reported by the same authors from three troops of Pts chimps living near Gombe, Tanzania.
- The authors report that two of the ten chimp troops sampled (both of which came from the south-eastern corner of Cameroon) were infected with SIV strains that were genetically closer to the virus that has caused the AIDS pandemic (pandemic HIV-1, or HIV-1 Group M) than any other previously-sequenced SIVs from African primates.
- Surprisingly, the degree of genetic homology between the new chimp SIV strains and pandemic HIV-1 is not reported. All we have is the authors' rather vague claim that "inclusion of the new viruses [in phylogenetic trees] reduced the lengths of the branches marking the cross-species transmission events for all genomic regions by almost half". Since the previous closest homology between chimpanzee SIVs and pandemic HIV-1 was reported as roughly 80%, this statement would seem to suggest that the degree of homology between these latest chimp viruses and HIV-1(M) is approaching 90%. However, examination of the trees that are published at the end of the article suggests that this is incorrect, for here the degree of homology (especially for the important env, or envelope gene) appears to be considerably less than 90%.
- This discovery of a new closest ancestor to pandemic HIV-1 is undoubtedly exciting, but sadly, as so often is the case with Dr Hahn and her collaborators, the manner in which they report it involves a substantial amount of exaggeration. In February 2006, Professor Sharp gave a speech entitled "Where AIDS Came From" to the 13th Conference on Retroviruses and Opportunistic Infections at Denver, Colorado, in which he claimed that he and his colleagues had discovered "the source" of HIV-1. Similarly, journalists who have recently interviewed Professor Hahn (and who have clearly been influenced by her comments) have stated that she has found "the cradle" of pandemic HIV-1, and that the new Cameroonian chimp viruses are "dead ringers" for the human pandemic virus. All these claims are untrue. Hahn's group has definitely found the closest non-human primate relative to pandemic HIV-1 to be discovered thus far. However, on the basis of the evidence they present in Science express, they have found neither the source nor the cradle of pandemic HIV-1, nor a "dead ringer" for the human AIDS virus.
- Keele, Hahn and Co. also assert: "Given these short branch lengths, it is highly unlikely that other SIVcpz [chimp SIV] strains exist that are significantly more closely related to HIV-1 Group M…..than the viruses from [these Cameroonian chimp] communities". This is a sweeping - and almost meaningless - statement, partly because all depends on one's definition of the word "significantly", and partly because, even if someone were to find a virus that was even slightly more closely related to pandemic HIV-1, this would substantially lessen the impact and import of the present paper. In fact, it might well render the present paper redundant. It is important to note that - as Keele and Hahn themselves acknowledge - there are "vast areas of west central Africa not yet sampled" for chimp SIV - a situation that is even more true for central Africa, and in particular for the Democratic Republic of Congo (DRC, the former Belgian Congo).
- Hahn's team also claims that: "These findings establish P. t. troglodytes as the natural reservoir of HIV-1." Again, this statement is incorrect. On the basis of HIV epidemiological studies, Pan troglodytes troglodytes had already been established as the probable natural reservoir of the minor groups of HIV-1 (Group O and Group N), but it is still unclear which chimp subspecies is the natural reservoir for "pandemic HIV-1" (HIV-1 Group M). Hahn is seeking to transpose the apparently reasonable claims about reservoir made for the minor HIV-1 groups across to the major group, HIV-1 Group M, the "pandemic virus". It is both irresponsible and dangerous to make such sweeping claims for Group M, the virus that is the real focus of everyone's attention, especially when fewer than 1 in 200 wild chimpanzee troops from west central Africa (Pan troglodytes troglodytes) and central Africa (Pan troglodytes schweinfurthii) have actually been sampled.
- To give just three examples of why these claims are over-stated: (a) In 1961, a group of Pts chimps from Mambasa, eastern DRC, was reported which had notably similar blood characteristics to Ptt chimps, 800 miles (as the crow flies) to the west. A genetic link between the two groups was posited. (b) I have photos of young Pts chimps from northern DRC, chimps that were captured by Gilbert Rollais from around Ango and Bondo for use at Lindi camp, that display the "early balding" that the great American zoologist, Jonathan Kingdon, says is typical of Ptt chimps. Once again, this suggests that there might be genetic similarities between Ptt chimps and certain groups of Pts. (c) In 2001 the Swiss primatologist Pascal Gagneux published an article that featured a series of phylogenetic trees which show how the genomes of Ptt and Pts chimps are to a large extent intertwined. Because of this, Gagneux postulated that it was perhaps not legitimate to classify Ptt and Pts as two separate subspecies. Additional background: 57 of the north Congo chimps mentioned in (b) and 21 of the Mambasa chimps mentioned in (a) were among the 400 chimps used for oral polio vaccine (OPV) studies at Lindi camp. This illustrates that these, or chimps from any other part of the 200,000 square mile area that provided chimps for Lindi camp, might represent the true reservoir of pandemic HIV-1. There is also another possibility for, as Gagneux noted, the viral reservoir might have existed in a chimp troop which is now extinct.
- The Hahn team, however, seem strangely determined to "prove" that the crucial reservoir, that of pandemic HIV-1, lies as far from Stanleyville/Kisangani and Lindi camp as possible. An example: at the aforementioned Denver conference in February 2006, another of the Hahn collaborators, Fran van Heuverswyn, gave the key paper in which these new Cameroonian chimp viruses were reported. The Webcast of her speech includes some questions asked at the end, and a member of the audience points out that all the studies seem to be from Cameroon, and asks if it is hard to obtain similar samples from wild chimps in the Democratic Republic of Congo [DRC]. She responds: "In the lab of Beatrice Hahn they have analysed samples from the DRC and they were all negative." This claim is untrue, for at least one of the two currently reported chimp SIV sequences from the DRC was analysed in Hahn's lab, as well as that of Michael Worobey. Furthermore, it is known that people working in Hahn's lab, notably Brandon Keele, have been analysing large quantities of chimp samples from the DRC over the last couple of years, and given what is already known about the epidemiology of SIV in chimpanzees, it is highly unlikely that none of these samples should have been found to contain SIV. Other teams, too, obtained chimp samples from the DRC several years ago, but no SIV sequences have been reported apart from the sequence from the Parisi forest reported by Worobey and Hahn, which they then falsely claimed to have "refuted" the OPV theory. This lack of reporting of chimp sequences from the DRC (and the misrepresentation of the significance of one of the two reported sequences) is now so pronounced that it is cause for some concern. In the light of the known suppression of other data in this heated debate [see "The annexing of the Stanleyville samples" on this website], one has to ask whether data about SIV in Pts chimps could have been deliberately suppressed.
- Although Keele and Hahn's paper is rather brief, it contains several problem areas. However, as with previous papers from the Hahn team, the authors' response to flaws or snags in their arguments is to gloss over them. The other main shortcomings of the paper include the following: (a) the fact that there is a more than 500-mile distance by road, and a more than 600-mile distance by river, between their alleged cradle of pandemic HIV-1 in south-eastern Cameroon, and the place where they believe AIDS "spawned" (Leopoldville/Kinshasa); (b) the fact that for someone to travel from their "source" to their "spawning-ground" would have required crossing two national boundaries (from Cameroon to Afrique Equatoriale Francaise, AEF, and from there to the Belgian Congo); (c) the fact that there is zero evidence of early AIDS, or early infection with pandemic HIV-1 anywhere near south-eastern Cameroon, or, indeed, anywhere in the intervening area between south-eastern Cameroon and Leopoldville; and (d) the fact that many commentators (including members of the CDC retrovirus team, led by Tom Folks) believe that recombination between different immunodeficiency viruses in humans was the event that sparked the AIDS pandemic. The Hahn group has persuasively argued that chimp SIV originally arose as a result of recombination between two other primate SIVs in the body of a chimpanzee - but that has no relevance for what Folks et al. are saying. The Hahns find it extremely difficult to explain convincingly how the key recombination event or events identified by Folks might have occurred - namely at the time of, or soon after, the transfer of chimp SIV to humans. By contrast, recombination is an intrinsic part of the OPV theory, which proposes that such recombination occurred at the very beginning of the story, both in vivo and in vitro, at Lindi camp and the Laboratoire Medical de Stanleyville, respectively. Each of these issues will be examined in more detail below.
The Bushmeat Advocates Finally Announce How They Think AIDS Began
To my mind, there is one truly valuable thing about this latest article by the Hahns, and it is this. For years, Hahn and her team have kept their hypothesis of the origin of AIDS as vague as possible, which had the great merit (from their perspective) that it could not easily be refuted. But now, for the very first time, they have actually spelt out in print how they think the AIDS pandemic started.
Of course, once a hypothesis is actually on the table, then counter-arguments can be raised against it.
Because they have to weave their account into their favoured hypothesis of origin of AIDS (the bushmeat hypothesis), what they come up with is strangely far-fetched - especially to anyone who knows something of Africa (which Hahn and her supporters, it often seems, do not. Indeed, the word on the grapevine is that Hahn herself is freaked out by the prospect of visiting Africa.)
One of the techniques Hahn frequently uses in her arguments is to present hypothesis and speculation as if it were fact. For instance she claims that this article, and previous articles from her team, "provide for the first time a clear picture of the origin of HIV-1 and the seeds of the AIDS pandemic".
To my mind, this is a reckless over-statement. But for the record, this is the scenario that Hahn and her colleagues propose.
They posit a chimp-hunter or bushmeat-seller who becomes infected with SIV by blood-to-blood contact, probably while butchering or skinning one of the chimps from the south-eastern corner of Cameroon.
They further propose that the cross-species infection of this one person (the index case) single-handedly sparks the AIDS pandemic.
And, still sticking to the tenets of their discredited phylogenetic dating hypothesis, they propose that this happened some time around the 1930s.
They have to presume that this hunter or market-seller, the index case, does not spark any local outbreak of AIDS-like disease in Cameroon or in neighbouring Congo Brazzaville - or at least not one that was recognised and/or reported as an unusual condition by the French doctors who then worked in this area.
And because there is no correlation between the ranges of Hahn's Cameroonian chimps and the first recorded appearances of HIV-1 (which were exclusively in the Belgian Congo), she and her people have to hypothesise that someone quickly exported the virus, so that it was able to become established in Leopoldville (550 miles to the south-west by road, or more than 650 miles away by river), where they believe that the AIDS pandemic was somehow "spawned".
In fact, their article makes it clear that they believe that the index virus (or its descendants) was/were brought southwards by river. This means that they require that the first human infectee (or someone infected directly or indirectly by them) took at least two steamers down the Sangha and Congo rivers (travelling from Ouesso to Brazzaville to Leopoldville/Kinshasa and crossing two national boundaries in the process), and ended up delivering the virus to Leopoldville.
Hahn and Co. apparently believe that once this ancestral version of HIV-1 had arrived in Leopoldville, the various subtypes of HIV-1 somehow developed - first of all in isolation (presumably within different suburbs of that city!), and then, later, as an epidemic.
Then, at some later time, they propose, the different subtypes of HIV-1 began to meet up in the cells of infectees and to recombine, thus creating the recombinants and complex mosaic strains of pandemic HIV-1 that appear to have existed from, at the very latest, 1976.
So they have to postulate that first diversification and then recombination occurred in Leopoldville - and that all this happened before the various viral strains of pandemic HIV-1, such as the recognised subtypes, began to be exported outwards and around the world.
In other words, there are many rather substantial difficulties to their "chimpanzee bushmeat" hypothesis of origin.
However, as I shall show later, few if any of these problems apply to the hypothesis of origin that they all so dogmatically reject: the oral polio vaccine (OPV) hypothesis.
The Serological Evidence
The available serological evidence does not offer any support whatsoever to Hahn and Sharp's thinking. In fact, it runs quite strongly against it.
Here is a quick review of the relevant evidence that I have in my files, augmented by information from the excellent HIV/AIDS Surveillance Database, published by the US Bureau of Census.
In 1975-8, blood was taken from 340 pygmies (the greatest of all bushmeat hunters) from the borders of Congo Brazzaville and Central African Republic (CAR), who live just 100-150 miles to the north-east of the suspect Cameroonian chimps. Not one of these samples was found to be HIV-1-positive. Further surveys were conducted in CAR in 1986 among 280 members of the general population in Sangha region (which extends to as close as 50 miles from Hahn's chimps). Again, not one positive. Another much larger survey was conducted in 1984-7 among 782 pygmies from Sangha region and Lobaye region (immediately to the east), again without a single HIV-1-positive. This evidence strongly suggests that no HIV-1 derived from the Cameroonian chimp troops ever escaped northwards up the Sangha river, into the south-west of Central African Republic or northern Congo Brazzaville, despite the fact that there appears to be quite a heavy traffic of small boats on that part of the river. If Hahn and Sharp are right in their assumption that this south-eastern corner of Cameroon is the source of pandemic HIV-1, then these wholly negative findings are, to say the least, surprising.
So what about Cameroon itself? The south-east of Cameroon has such sparse population that little if any HIV-1 sampling has been done here. But a 1990 study of 125 pygmy adults from Djoum, in the south of Cameroon, but 200 miles west of the suspect chimp troops, found that just 2 were (1.6%) were infected with HIV-1. (It has been proposed that these two infections might have been the result of a pygmy travelling to a local town, having sex there, and later infecting another member of his group; in other words, that HIV-1 was imported from an urban area.) However, 1.6% is a fairly typical prevalence of HIV-1 for a rural area in 1990 in this part of sub-Saharan Africa.
There is therefore no serological data to encourage the Hahn/Sharp hypothesis in Cameroon itself. So let's look southwards, to Congo Brazzaville, which, indeed, is the country to which Sharp and Hahn hypothesise that HIV-1 "escaped", before ending up in Leopoldville in the Belgian Congo.
A large town, Ouesso, is situated on the River Sangha, just over the Cameroonian border in Congo Brazzaville, and some 30 to 50 miles south of the suspect chimp troops. Unfortunately, it seems that only a single HIV-prevalence survey has been conducted in Ouesso, and that quite late in the epidemic: it involved a survey of 300 pregnant women conducted in 1992, as part of a sentinel surveillance programme. 16 (5.2%) women were found to be infected with HIV (though the type, ie HIV-1 or HIV-2, is not recorded, which raises questions about the specificity of the test). To give some perspective, this is exactly the same HIV-prevalence as that encountered the previous year (1991) among 300 pregnant women in Impfondo (a much smaller town on the Oubangui river, 140 miles east of Ouesso, but inaccessible from there - and indeed, inaccessible by road from the outside world - due to impenetrable swamps). And it is much less than the HIV-prevalence of over 10% already being encountered in the capital, Brazzaville, by the mid-1980s.
In short, that 5.2% HIV-prevalence among typical sexually active adults (pregnant women) in Ouesso in 1992 represents a low to average HIV-prevalence for that year for an urban area in that part of sub-Saharan Africa. (Furthermore Ouesso is on a river, which increases transport links, and normally leads to higher HIV-prevalence.) It's worth noting that there was a lower HIV-prevalence (2.6%) encountered in the same year (1992) among 300 pregnant women in the smaller town of Owando, 150 miles south of Ouesso on the road to and from Brazzaville, at the point where the two-lane highway begins.
I should perhaps add that the first evidence of HIV-1 in the city of Brazzaville itself is not until 1981, which is two decades after the first evidence of HIV-1 in the Belgian Congo (later Zaire; now the Democratic Republic of Congo). There was one intriguing and fatal case of cryptococcal meningitis (CM) with gastric candidiasis in an 18-year-old woman living in the city of Brazzaville in 1958, conditions which, on their own, might be considered suggestive of AIDS. However, the appropriate antibiotics were only given to the patient in "modest" doses for a brief period, and she also suffered from severe anaemia and an "extremely brutal hepatitis". It is therefore likely that the latter diseases (and the less than adequate therapeutic regime) precipitated the CM, rather than any HIV infection. In short, there is no serological or clinical evidence from Congo Brazzaville to support Hahn's hypothesis of AIDS origin.
There is also some important and relevant recent data about SIV-like infection (rather than HIV infection) in humans. In the last few years, two American scientists, doctors Burke and Wolfe, have made an exhaustive search for evidence of SIV-like infection among hunter-gatherers from different parts of Cameroon (but almost exclusively from the south). It is reasonable to surmise that this study might have been connected to the Hahn research. However, they did not find a single SIV-positive sample among the 76 plasma tested. They found a host of other viruses, including several infections with a foamy virus which, like SIV, is a simian retrovirus. But they found no SIV.
Burke and Wolfe also tested 1,224 plasmas from a general population coming from urban and rural areas of Cameroon, where people "may handle [primate bushmeat] but are unlikely to have repeated contact with the blood or body fluids of freshly killed animals". Just one single plasma showed some indications of exposure to SIV (in this case SIV from a colobus monkey) by one of the assays used (ELISPOT), but the result was hardly convincing, for the plasma in question showed only weak cellular reactivity, and the authors were unable to amplify any SIV nucleic acids. Because other assays did not give positive results, this might have been a false positive, or it might be that they had genuinely detected one single human exposure to SIV in over 1,300 plasma, but that this exposure had failed to cause any productive human infection.
Burke and Wolfe's research, which appeared to be specifically designed to obtain data that lent support to the bushmeat theory of origin, actually did the exact opposite. There is still no data that directly supports the hypothesis that hunters can become infected with chimpanzee SIV through the handling and butchering of chimpanzee bushmeat.
None of the above data encourages the perception that HIV-1 was spreading southwards from south-eastern Cameroon, or Ouesso in Congo Brazzaville, to Brazzaville and Leopoldville at any point in the early twentieth century. In fact, there is not one jot of serological or clinical evidence that offers support to the Hahn hypothesis.
However, this is not what Hahn's principal collaborator, Paul Sharp, thinks. In a recent interview with Ed Susman of UPI, Sharp proposed that "there were probably thousands of people in the region" between Cameroon and Kinshasa who were already suffering from AIDS by 1959.
This is clearly an absurd claim. But if nothing else, it serves to demonstrate the frequently superficial nature of Sharp and Hahn's arguments, especially when they move outside their designated fields.
To borrow the words of a scientist who works in the same field, and who knows their work well, this type of analysis represents the "Hollywooding of Science".
It's extremely good that, after years of prevarication, the members of Beatrice Hahn's group have finally spelt out what they believe in. Because, as it turns out, their scenario of transfer and early spread, far from being the "clear picture" that Hahn claims, is in reality confusing and confused.
Instead of providing a clear history of "the origin of HIV-1 and the seeds of the AIDS pandemic", the scenario they advance is quite remarkably difficult and far-fetched.
I (and several scientists I have spoken with in the last few weeks) believe that Hahn and Sharp have got it wrong.
Their new chimp viruses are the closest yet to pandemic HIV-1 viruses, but they are not that close!
For them to claim, without supporting evidence, that it is "highly unlikely that other [chimp SIV] strains exist that are significantly more closely related to HIV-1 Group M…..than the viruses from [these Cameroonian chimp] communities" shows that their analysis continues to be highly speculative, especially when they have only fairly recently started sampling wild chimpanzee troops for the presence of SIV. (In fact, I believe they began their studies only after my late friend and collaborator, Bill Hamilton, had begun his similar researches around Kisangani in the DRC.)
Despite their latest efforts in Cameroon, which are indeed commendable (unlike their reporting of them!), less than 0.5% (or 1 in 200) of the chimpanzee troops in west central or central Africa have thus far been sampled. [This is my own estimate, calculated on the basis of current chimp population estimates and average troop sizes.]
Hahn and Sharp's findings thus far do not provide the source of the AIDS pandemic. And neither do they establish Pan troglodytes troglodytes (rather than Pan troglodytes schweinfurthii) as the natural reservoir of pandemic HIV-1….though they would like you to believe otherwise.
My own gut feeling (and those of several persons I have discussed this with) is that the "closest ancestor" to pandemic HIV-1 has not yet been found, and that it may be located some significant distance from south-eastern Cameroon.
If I had the money and resources that are available to Hahn's team (which is backed not just by US government grants, but by a $500,000 no-strings-attached "Distinguished Achievement Award" grant from Bristol-Myers Squibb), the chimpanzee troops that I would be most eager to sample as part of a search for a "closest ancestor" would include the following: Ptt troops from the Mayumbe region to the west of Kinshasa, (the one area in the Democratic Republic of Congo where Ptt chimps are found); Ptt troops from the region west of Ouesso, in northern Congo Brazzaville, in other words from the area directly to the south of Hahn's Cameroonian chimps; Ptt troops in Haute Sangha region, in the extreme south-western corner of the Central African Republic; Ptt and Pts troops from either side of the Oubangui river, in Congo Brazzaville and DRC respectively; Pts troops from the savannahs of northern DRC (around small towns like Ango and Bondo); Pts troops from eastern DRC (from around Mambasa); and Pan paniscus troops from the region to the south of Kisangani. Plus several places in between! (No reports of the SIV testing of any of these troops of chimps or bonobos have thus far been published.)
One last point before moving on. Because of the role that recombination may have played at the very beginning of the AIDS epidemic, the genesis of pandemic HIV-1 may not necessarily even require viral transfer to a human of the closest ancestral SIV strain from a non-human primate. [For that argument, see below.]
An Alternative Explanation of the New Data
At this stage I shall attempt a different approach. What I propose to do is to treat Hahn's claim that she has found the source of pandemic HIV-1 in south-east Cameroonian source as if it were true, and use it to advance what I believe is a far more viable hypothesis of how AIDS began than the one that she and Paul Sharp propose.
At least this hypothesis will be supported by known historical and scientific facts.
What this will, I hope, demonstrate is that Hahn's latest findings are at least as supportive of the oral polio vaccine (OPV) theory of AIDS origin as they are of the bushmeat theory…if not more so.
In order to make this work, I need to tell a story that, though it is moored in factual accuracy, is purely a work of the imagination. For this reason, the following section of this paper appears in italics, in order to underline that it is fiction, not fact.
Imagine that it is 1956. Imagine that five young Pan troglodytes troglodytes chimpanzees have been captured after a successful hunt by a group of pygmies in south-eastern Cameroon.
The young chimps (alive, but very frightened, for they have just witnessed the adults in their troop being slaughtered, one after the other) are bound at their wrists and ankles and hung loosely on poles. Then six of the young pygmy men set off on a long walk through the forest, towards the town of Ouesso, some forty miles to the south. Before the first day is over, one of the chimps has died. Two of the pygmies turn back with the animal's body, which will doubtless go in the pot when they rejoin their families. The other four pygmies march on, carrying the surviving chimps - a pole on each shoulder.
On the second afternoon, they reach the Ngoko river, which they cross by a dug-out canoe that is paddled, conveniently enough, by some friends of theirs. And at the end of the second day's march, they arrive at the edge of the forest, and can see the eery electric glow of the town or Ouesso ahead of them.
In 1956, Ouesso is a thriving place of over 30,000 people. It is also an important trading centre for palm products, rubber, animal hides and mahogany. Furthermore, it is a border post, and the northern terminus for year-round steamer navigation on the Sangha river.
Even though Ouesso is situated in a different country, Afrique Equatoriale Francaise (AEF), some of the young pygmy men know it quite well, for it is their habit to come here when they have something to sell to the townspeople. It is the only town or village of any size in the region. They have nothing like official papers, so their presence here, strictly speaking, is illegal. But it is now dark, and they have little difficulty in flitting out of the forest and into the fringes of the town. Here they know a Moslem man, Abdullah, who runs a small shop, and who is one of the few local traders to allow pygmies into his store. Abdullah knows that some of the French people in Ouesso like to keep chimpanzees as pets, and so he'd previously mentioned that he might be interested in buying a couple of young chimps. He had perhaps not expected four of them to be delivered just a few weeks later!
Abdullah gives the leader of the pygmies some salt and tobacco, and also a small handful of CFA francs, the local version of French francs. He lets two of them stay in the yard behind his shop, telling them to keep the young chimps fed and watered. And in the morning he leaves the shop in the hands of his son, and sets off to try to find some buyers for the chimps. However, he returns that evening tired and dispirited, having failed to interest even a single European in taking on a new pet. What is more, one of the chimps now appears to be poorly, after the trauma of the long journey through the forest.
Abdullah makes a decision. During the day, he has heard some rumours filtering up from down south of Belgians who want to buy young chimps. His son, Salah, is already booked to set off down the Sangha river on the steamer that leaves in a few days' time; he is delivering a shipment of mahogany poles to a place on the main thoroughfare in the region: the River Congo. Abdullah asks his son if he will take the chimps with him, and try to sell them on. Salah agrees, and he asks the pygmies to go back to the forest, and to bring some wood to make cages.
While all this has been going on, the other two pygmies have been enjoying themselves. Although not used to money, they have adapted rather quickly to the freedoms it provides. They make a few small purchases to take back to the forest, and they find a place to stay, not far from Abdullah's yard. They also find some female company, young women who are descendants of Bantu/pygmy unions in the past. By the second night, neither of the two pygmy men sleeps alone.
[At this point, let me cut across to the other hypothesis, Hahn's hypothesis, for a moment, and imagine that one of the pygmy hunters has been scratched rather badly during the hunt, and in the process, has unknowingly acquired a chimpanzee virus, an SIV, that has infected his blood-stream. My question to Beatrice Hahn is this. Ouesso is a large town, just two day's journey on foot from where her chimps are living in the forest. Once that virus, that chimp SIV, has - as she postulates - infected a local hunter, and once that hunter has arrived in Ouesso and, as her hypothesis seemingly requires, has passed it on to someone else in that town through sex, is it really likely that these events would not have sparked an outbreak of HIV infection then and there? (Ouesso is the one conurbation of any size in this region. On both sides of the border around Ouesso all is thick forest, but the fact that the Sangha is navigable for steamers as far north as the town makes this the effective entry and exit point to the region for humans. The other relevant detail here is that the local hunters in south-eastern Cameroon are almost all pygmies, and pygmy hunters from Cameroon - or in fact rural Cameroonians in general - would not themselves be travelling down to Leopoldville in the colonial era. Therefore, if one adopts the Hahn scenario, the virus does apparently need to be passed on in Ouesso.) So, to sum up, if Hahn's hypothesis is correct, why do we not see an eruption of HIV-1 infection in Ouesso, or somewhere a little to the south of Ouesso, at around the same time - or before - the eruption in Leopoldville? And remember: Hahn believes that the virus actually arrives here in the 1930s, not the 1950s. Yet we see no trace of HIV-1 in the vicinity of Ouesso until the 1990s.]
At this point let us leave the pygmies behind. Abdullah and Salah are now the owners of two rough wooden cages and four young chimpanzees, (for the sickly chimp has started eating, and has quite suddenly regained her health). A few days later the chimps, now packed two to a cage, are carried down to the docks on a cart, and then loaded on board the steamer. Over the next two days they and Salah are transported slowly down the Sangha river, as it weaves to and fro through the swamps, eventually to debouch almost 300 miles later into the River Congo, which is this point is a much vaster river, roughly five miles across from shore to shore.
On either side of the Sangha's mouth there is a small steamer station and customs post - the downstream one at Mossaka, and the upstream one at Loukolela. Salah is heading for the latter, where he is selling his mahogany to a Frenchman who owns a small woodyard. The Frenchman doesn't want to buy any chimpanzees, but he passes Salah on to an African friend of his from the Belgian Congo, Joseph, who is visiting Loukolela unofficially for a couple of days. A deal is struck, and Salah is relieved and happy, for he knows that he has more than doubled his father's money.
By contrast with the Sangha junction a few miles downstream, the River Congo at Loukolela is at its narrowest point for hundreds of miles in each direction, and there is a constant flow of traffic across the river to a small port in the Belgian Congo with an almost identical name: Lukolela. This is where Joseph is normally based, and where he makes a decent living dealing in a range of goods, ranging from beer to bicycles. He waits until night has fallen, and then, accompanied by the four chimps in their cages, he crosses the river in a small boat. Joseph knows something that Salah doesn't, for news passes up and down the Congo as fast as the flow of the huge brown stream. And word has filtered down from Stanleyville that there are doctors in that city who are willing to pay a good price (in African terms) for chimpanzees; to do what with, no-one knows nor cares. By Friday morning, Joseph is to be found sitting at a table at his favourite river-front bar, and occasionally scanning the horizon downstream.
Every week during the fifties, every Friday, the huge Otraco river steamer, with its several barges linked behind, calls at Lukolela on its long journey eastwards towards Stanleyville, where it arrives the following Wednesday. For those five days, as the many-jointed ferry chugs its way through the rain forest, it is a floating city of people, animals and cargo. The Europeans travel in segregated luxury aboard the main steamer, but the Africans have to sleep where they can on the decks or in the bowels of the barges behind. Those barges have everything. They have bars selling local brews; they have tiny restaurants; they have live animals and smoked animals that are brought out in dug-outs from both shores and sold for food - or (in the case of the live ones) as future food, or as pets. And they even have their own discreet red-light district, where a man can purchase the services of a woman for five minutes, or for longer if he chooses. The prostitutes entertain dozens of men each day, and this is an era long before condoms, at least in African society. Officially, the Belgians are very strict about controlling sexual activity and the spread of venereal disease. Unofficially, the captain and crew tend to turn a blind eye to what goes on aboard the African barges.
(Much later, in 1983, the wonderful American writer Helen Winternitz took the same journey by river-steamer up the Congo river from Kinshasa, formerly Leopoldville, to Kisangani, formerly Stanleyville. And she wrote a book about it: "East Along the Equator"; [The Bodley Head/Sceptre: London, 1987]. On pages 74-75 of the paperback edition, she writes about the death of a child passenger, "a sickly boy who had been too thin for too long". Winternitz ascribes the death to malnutrition, but the boy's mother was working as one of the on-board prostitutes, and it is hard to imagine that she had been unable to afford to feed her child. This moment in 1983 was just before the recognition that there was an AIDS epidemic in Africa, and I think the account is rather significant. The tale is recounted as something rather unusual; there is no recognition of a new disease, a new pattern. If AIDS had already been "spawning" in Leopoldville/Kinshasa for fifty years - as Hahn and Sharp and Korber believe it must have been - then surely it would have emerged onto the world stage before then, and one of the first places for it to emerge would surely have been aboard one of the great Kinshasa-Kisangani ferries, with their populations of thousands. To sum up: this sad death of a prostitute's child in 1983 was probably not the first AIDS death on board one of the great river-ferries. However, given the lack of interest or recognition it aroused, it sounds as if it might have happened relatively early in the epidemic, rather than fifty years into it. Remember, when AIDS first arrived in the Rakai district of south-western Uganda, it was immediately recognised as a new condition by local people, and given a new name: "Slim".
But back to Joseph and the chimps. On the Wednesday, just before noon, the steamer swings slowly into its final destination - the docks in Stanleyville. By this time the chimps, still in their cages, but well fed and watered by their new owner, have travelled just over a thousand miles from their forest of origin in south-eastern Cameroon. They have been carried upside-down through the forest on poles, they have travelled on board two steamers, and (though they don't know it) they have crossed two national boundaries.
To Joseph's relief, it turns out that the rumours are true. As his two cages are unloaded, he is approached by a European man, who immediately begins negotiations. The man from Loukolela tries to hold out for a higher price, but the European (another Frenchman, it seems) starts to walk away, and Joseph has to call him back. A minute later, the chimps have been sold on again, this time for the princely sum of 500 Belgian francs each - the equivalent of about ten American dollars a head.
The next day, the Frenchman, who is named Gilbert Rollais, takes the four young chimps on their final journey. It involves a 20-minute drive by Land-rover, followed by a 500-yard ferry-trip across the Lindi river, and then a further one mile hike to reach a place that has only just been created in the rainforest, after four months of bulldozing and construction. The Africans know it as "Camp Polio", but Rollais and his Belgian doctor friends call it Lindi camp.
The young chimps are needed for some important research that the director of the local medical lab in Stanleyville, Ghislain Courtois, is undertaking into poliomyelitis. Courtois is apparently working with an American scientist too, a man called Professor Koprowski. Rollais has been told that they need as many chimps as he can supply, though he is not entirely sure why this is, given that the polio research of Courtois only seems to require a handful of animals.
Once inside Lindi camp, Rollais takes the chimps to one of the two large hangars, with its walls built of local sticks and mud, blended with banana leaves, and inside which there are forty newly-constructed iron cages. Then the African keepers put each of the four young chimps inside a different cage. The two pairs of young chimps have got used to each other's company during their long safari, and separating them causes screams of distress. But Rollais orders that each chimp be given a new cage-mate - this being one of the chimps or bonobos that he's already collected during his hunting expeditions near Banalia and Ponthierville, on the northern and southern sides of the Congo river. He knows that when the young chimps arrive in the camp, they are usually frightened, upset, and off their food. He finds that the best way to persuade them to eat is to give each new chimp a cage-mate, an animal that is already familiarised, and which can show the newcomer how easy it is to eat the unusual foods, like sugar-cane, that the keepers push between the bars. Admittedly the chimps tend to fight a bit to begin with. Often they have to swap them around a couple of times before they find two animals that get along. By doing this, Rollais and the Belgian who runs the camp, Robert Daenens, have managed to prevent any fatalities.
Later, when the newcomers are relaxed, he will arrange for them and their cage-mates to be put in the "play-cage", which is twenty feet long, ten feet high and ten feet deep. The young chimps love that; they play and groom each other, and fights only happen quite rarely.
Though not himself a scientist, Gilbert Rollais knows a bit about chimp taxonomy. He knows that most of the chimps in Lindi are from the two species local to Stanleyville. These are Pan troglodytes schweinfurthii (the local subspecies of chimpanzee from the north bank of the Congo river), and Pan paniscus, the pygmy chimpanzee or bonobo from the south bank. Just three years earlier, Rollais was employed as the chief animal catcher in AEF, a job which he had done since 1949. He made several expeditions up to Ouesso and its neighbouring forests, and is well aware of how abundant chimpanzees are in those regions. That's partly why he had put out the word that he and his colleagues in Stanleyville were looking for young chimpanzees from any source. So he was not at all surprised that chimps from AEF - and even Cameroon - were beginning to turn up at the Stanleyville docks.
A few weeks after this, an unusual epidemic begins going round Lindi camp, killing many of the chimpanzees. One of the doctors from the laboratory, a man called Osterrieth, swiftly diagnoses it as being caused by an organism known as Klebsiella pneumoniae. The disease kills forty of the bonobos and a few of the common chimps in the space of three weeks. Rollais is told that he needs to get hold of replacements just as fast as he can. The following Wednesday he is back down at the docks, awaiting the steamer from Leopoldville.
Which Scenario Better Fits the Facts?
Of course the story that appears in italics on the last few pages is a dramatised account…even if the factual details that underpin it are accurate, having been based on careful research over several years. I do not normally employ drama or fiction as a way of getting my point across, but on this occasion it seemed justifiable. The reason? To point out just how much more plausible this scenario of origin is than the Beatrice Hahn scenario.
Of course, Hahn thinks the opposite. In a recent National Public Radio (NPR) broadcast in the US, Hahn is quoted as saying that her new evidence about south-eastern Cameroon "lays [the OPV hypothesis] to rest". The commentary continues: "If the vaccinators did use chimp kidneys to make their polio vaccine in a Congolese lab near what is now called Kisangani, Hahn says [they] would not have been of the subspecies that harbors the pandemic virus ancestor." Hahn adds: "Well, you would have to come up with a pretty convincing scenario that would explain how chimpanzees or the viruses from the south-eastern corner of Cameroon end up around Kisangani."
That, of course, is what I have just tried to do (though my drama of the caged chimps, as it happens, was written some days before Hahn's thoughts were broadcast on NPR).
So let's compare the two hypotheses. I believe that Hahn has to propose a series of quite far-fetched events.
Firstly her chimp-hunter cannot afford to infect more than one or two people locally, in or around southern Cameroon or Ouesso; for had he done so, then there surely would have been some evidence of an early disease outbreak in that region. Instead he (or someone infected directly or indirectly by him) has to up sticks and travel more than 600 miles, across two national boundaries, to end up in Leopoldville. Once arrived in Leo, he (or she) has to infect other people with the newly-acquired chimp virus. But for Hahn's idea to work, this new virus needs quickly to diversify, and to create separate strains that are genetically quite distinct from each other - including the strains that are now called the HIV-1 Group M subtypes (A to K). Later, these subtypes have to meet up in the bodies of infected persons and to recombine, in order to create recombinant and mosaic forms of the virus. And only then can any of these early strains of HIV-1 begin to escape from Leopoldville/Kinshasa, and to spread elsewhere in the Congo, and across to Rwanda and Burundi, where their presence can be recognised retrospectively from the 1970s onwards. All of these rather far-fetched things need to happen for Beatrice Hahn's scenario of origin to come true.
By contrast, look at the story of the caged Cameroonian chimps. Just like Hahn's story, it requires movement across national borders on at least two occasions. But to my mind, it would have been easier for chimps to have been moved in this way during the colonial era than for colonised Africans to have done the same. I would accept, however, that one could argue that particular point either way. So let's leave that aside, and instead look at the rest of the two scenarios, which at this point begin to diverge markedly.
For Hahn's scenario, the means of transport (the ferries) was there, but the "magnet" was not there, for it's hard to argue persuasively that during the 1930s Leopoldville would have been of any interest to Cameroonians, or to people from the northern end of the AEF territory of Moyen-Congo (now Congo Brazzaville).
For the "caged chimp" scenario, the means of transport (the ferries) was there, and the "magnet" was definitely there: the fact that in the 1950s Koprowski and Courtois and the designated "chimp-catcher", Rollais, were desperate to procure common chimpanzees (ie Pan troglodytes, of whichever subspecies) has been revealed in contemporary documents, and reported by three different witnesses (including Rollais himself). Witnesses from the 1950s (and, indeed, from the 1980s) report that chimps were regularly brought up to Stanleyville/Kisangani on the river-steamers, to be sold at the docks. In the second half of the 1950s, this process is likely to have been accelerated, because the LMS doctors were known to be paying good money for them.
But is it possible to prove whether there were any Pan troglodytes troglodytes among the chimps present at Lindi camp? The one significant published paper  by any of the protagonists about the capture and maintenance of the chimps and bonobos of Lindi camp was written by Ghislain Courtois, and published retrospectively in 1967, and it fails to give a definitive answer to the question. Courtois begins by describing the three chimp species or subspecies that were to be found in the old Belgian Congo: Pan troglodytes troglodytes (around Tshela in the far west), Pan troglodytes schweinfurthii and Pan paniscus. Having provided a sketch-map of the three ranges, he writes the following: "In view of the position of Stanleyville, and the geographic ranges of the different species, we were therefore able to make our choice from Pan troglodytes schweinfurthii (Pts) or Pan paniscus (Pp)." Elsewhere in the article he writes: "these were the two varieties of chimpanzees…that could interest us". The somewhat ornate phrasing is interesting, and it is noticeable that on both occasions it allows Courtois to avoid specifying whether or not any Pan troglodytes troglodytes were present in the camp.
But if Ptt chimps had been present, why might he have wanted to avoid mentioning such a thing? Well, we know that many of the Lindi apes died soon after arrival in the camp from Klebsiella pneumoniae, and that even back in those days the Stanleyville doctors concluded that the Klebsiella infection had probably been facilitated by some prior viral invader; they apparently suspected an adenovirus. Nowadays, Klebsiella pneumoniae is well-known as an opportunistic infection that has frequently appeared during outbreaks of simian AIDS, following the cross-species transfer of SIV in American primate facilities. This suggests that SIV (especially one that crosses from one subspecies or species to another, which would be expected to impact on viral pathogenicity and infectivity) would have been an extremely good candidate for the mystery viral invader. 1967 was long before anyone knew of the existence of SIVs. But is it possible that Courtois, even with his fairly rudimentary viral knowledge, might have deduced what was going on? If so, it might be that by the time he wrote the 1967 paper, Courtois had guessed that the presence of "non-indigenous chimps" at Lindi camp might have been the source of the viral problem - and therefore decided that any mention of Ptt at Lindi would be a detail that was better omitted.
Apart from this, the records of Lindi camp are extremely sparse, and only provide details about 54 chimps, or 13.5% of the 400 unfortunate animals that were "used" [their term] in the polio programme. But from those records, we know that one chimp from Coquilhatville (now Mbandaka, just upstream from Lukolela) was present at Lindi camp from April 1957 onwards, and that (rather unusually) she was still alive two years later. Furthermore, it seems from the experiments that were conducted on these animals that all 54 of them were Pan troglodytes (common chimps) rather than Pan paniscus (pygmy chimps or bonobos). Because the district around Coquilhatville faces the ranges of both Pan troglodytes subspecies, Ptt and Pts, on the opposite bank of the Congo river, it is clear that the Coquilhatville chimp could have been either a Pan troglodytes troglodytes or a Pan troglodytes schweinfurthii. But that is still somewhere short of proof.
However, in recent weeks dramatic new evidence has emerged that provides the hard proof that had previously been lacking. I recently located a medical paper which reveals that the Laboratoire Medical de Stanleyville doctors were indeed experimenting with at least one Pan troglodytes troglodytes chimpanzee. Other published and unpublished papers in my possession reveal some of the prior history of this Ptt chimpanzee. They reveal that it (and seven Pts chimps) were part of a group of sixteen chimpanzees which were obtained by Gilbert Rollais between August 1959 and February 1960. They were apparently not involved in the polio or hepatitis experiments, but they were used in atherosclerosis experiments beginning in the latter month. We know that Lindi camp closed in January 1960, and that at that date the surviving Lindi chimps, numbering about 60 in total (and including all, or most, of the subset of 16), were transferred to a hangar immediately behind the Stanleyville laboratory, the LMS, and that this hangar became the main chimpanzee holding centre from that point on.
It is therefore likely, but not certain, that the Ptt chimp spent at least a few months at Lindi camp before it closed. But in any case, whether this particular chimp ever stayed at Lindi camp, or only arrived at the LMS in February 1960, is unimportant. The vital thing is that it is now proven that the LMS doctors included some Pan troglodytes troglodytes chimps (perhaps even some from Cameroon!) among their experimental animals.
The question of the sources of the chimps at Lindi and the LMS is vitally important, because viruses from those chimps might have been spread throughout the two facilities. This is because co-caging of chimps was routine at both Lindi and the LMS, and in both places the chimps and bonobos were allowed to play together (at Lindi in a large group cage). Several witnesses have reported that there used to be frequent fights between the animals, and thus the ideal conditions were created for onward transmission of viruses such as chimp SIVs, at both venues.
But which chimp SIV strains might have been passed on? Beatrice Hahn wants to insist that the presence in Stanleyville of Ptt chimps (and indeed, of south-eastern Cameroonian Ptt chimps) is necessary for the OPV theory to remain viable. (And because she believes that no Ptt chimps were present in Stanleyville, she argues that her latest findings repudiate the OPV/AIDS theory.)
I do not concur with Hahn's analysis, not least because, as previously explained, I am far from convinced that she has established Ptt as the reservoir of pandemic HIV-1, or that she has identified the true "source of pandemic HIV-1" in south-eastern Cameroon. But in any case, we now know for certain that at least one Ptt was present among the experimental animals in Stanleyville - and the presence of that one chimp disposes of Hahn's argument. (In reality, of course, it is likely that there were more Ptt chimps in Stanleyville than just this one.)
In addition, I have several further documents (both from the 1950s and the modern era) that are relevant to this important subject. I am still seeking confirmation of certain important details, so I shall not attempt to include this further information now. Suffice it to say, however, that additional details about the chimpanzee subspecies housed at Lindi and Stanleyville are likely to be forthcoming at a future time.
The Recombination Factor
In 2004, a CDC team led by the head of the retrovirology lab, Tom Folks, published an excellent article entitled "Recombinant Viruses and Early Global HIV-1 Epidemic." They had tested nearly 4,000 serum samples originally obtained in the early to mid-1980s in Kinshasa. Folks's team found that all of the major subtypes of HIV-1 were present, and that 37% of all HIV-1-infected sera showed evidence of recombinant or multiply recombinant (ie mosaic) HIV-1 viruses…an apparently extraordinary finding for so early in the epidemic.
They concluded their abstract: "We propose that the HIV epidemic was well established in central Africa by the early 1980s and that some recombinant viruses most likely seeded the early global epidemic." [My italics.]
It will be recalled that Leopoldville/Kinshasa is not only Professor Hahn's chosen "spawning ground" for HIV-1; it was also one of the main venues for CHAT vaccination in the late 1950s. Indeed, it is my belief that Leo/Kinshasa was one of several spawning grounds for AIDS, not the only one.
However, for Hahn's "infected chimp-hunter" scenario to achieve this level of HIV-1 diversification by the early 1980s is very difficult indeed. Basically, her index virus (the one that arrived in Leo with the chimp-hunter, or someone infected by the chimp-hunter) has first of all to diversify, for some reason, into a whole host of different viral subtypes. And then those subtypes have to start recombining on a massive scale. Indeed, it seems that all this has to have happened before any of these viruses starts arriving in other venues - something which we know had begun happening by 1976 at the very latest.
(Strangely, though, the only other places in Africa to become infected with pandemic HIV-1 during the years up to 1979 seem to have been former Belgian territories - like elsewhere in the Democratic Republic of Congo, and 1,000 miles to the east, in Rwanda and Burundi. Hahn cannot explain why those early HIV-1 viruses did not escape north (to Congo Brazzavile, Gabon and Cameroon) or south (to Angola) before the 1980s, but only to old Belgian colonial holdings. I propose that it's because only the Belgian territories were vaccinated with Koprowski's OPV, CHAT.)
But let me return to the creation of the recombinant viruses that seeded the pandemic. I believe it is extremely hard to imagine that if all this rampant viral diversification, and then recombination, had been going in Leo between the 1930s and 1970s, as Hahn proposes, that none of these viruses managed to escape from Leo until the 1970s. (After all, it is not only in Leopoldville that people had sex in those decades.)
By comparison, these very same conditions (the emergence of several subtypes, and rampant recombination between the subtypes) represent no problem at all to the OPV theory. Indeed, it is exactly what the theory predicts.
First of all you need many different strains of immunodeficiency virus (whether in humans or chimps) coming into contact with each other in the same place. Hahn argues that this happens in Leo, after just one single human infected with chimp SIV arrives in that city (from Cameroon or Congo Brazzaville), and the virus diversifies from there.
But where better for such a thing to have happened than in the largest chimpanzee colony the world had ever seen up to that point - at Lindi camp, just outside Stanleyville, which, in the course of three and a half years, housed more than 500 chimps and bonobos from a wide range of different localities?
Courtesy of the work of Dr Hahn and Sharp, it seems that between 10% and 13% of Pan troglodytes troglodytes chimps and approximately 20% of Pan troglodytes schweinfurthii chimps are likely to be naturally SIV-infected in the wild. Since most of the 400-odd chimps and bonobos that were directly involved in the polio research at Lindi and the LMS are known to have been Pts chimps, it is likely that between 60 and 80 of these animals would have been naturally infected with SIV on arrival at the camp. Because the chimps came from different venues spread across at least 200,000 square miles of rain forest, these SIVs must have included some widely differing strains, including, it now seems probable, some Pan troglodytes troglodytes strains. Indeed, as I have proposed in my italicised section above, these may have included some of those Ptt SIV strains from south-eastern Cameroon that Hahn thinks are the very closest relatives to pandemic HIV-1.
My belief, however, is that for the OPV scenario to work, it is not requisite that any of the Cameroonian Ptt SIVs, or indeed any Ptt SIVs at all, were present at Lindi camp or at the LMS. The Pan troglodytes schweinfurthii (Pts) chimps found all around Stanleyville on the north bank of the Congo have their own SIV strains, and these strains have exactly the same nine genes that also appear in the Ptt SIVs and in pandemic HIV-1. It's simply that the OPV hypothesis works even better if there were also some Ptt chimps in Stanleyville or at Lindi. And we now know that there was at least one of them present.
Back to recombination. First of all, these differing strains of SIV would have started recombining in the cages, and in the group-cage, at Lindi camp, where chimps from different places met - and often fought. (Fighting is now recognised as the prime mode of onward SIV transmission between different primates.)
But in this scenario, how do the chimp SIVs get to infect humans? For various reasons I do not want to reprise all the evidence now, but some of it has already appeared on this web-site, and some other parts appear in the documentary film, "The Origins of AIDS".
However, let me summarise. We now know from several different witnesses from Lindi camp that the LMS doctors were routinely harvesting blood and organs, including kidneys, from the Lindi chimps. Furthermore, they were regularly draining the chimps of much of their blood on the day before they were sacrificed. Sometimes as many as four or five animals were "sacrificed", as they put it, on a single day. We know from LMS employees (including the Belgian head technician of the lab) that they were making chimp tissue culture "for a long time" at the LMS, and that this tissue culture was being supplied to the head of virology, Paul Osterrieth, who was (although he denies it) in charge of the polio vaccines. Osterrieth was also, according to the witnesses in his own laboratory, in charge of preparing further batches of the polio vaccine (in other words, growing them in the chimpanzee tissue cultures). We also know from documentary evidence that a procedure used by the LMS researchers to keep their chimp cells alive involved using "isologous sera" (the sera of other chimpanzees) as a growth and maintenance medium. (This alone would have provided materials from at least two different chimps in a culture, which allows the theoretical possibility of SIV recombination. However, such sera would almost certainly have contained pooled material from several different animals, which provides an even better opportunity for in vitro recombination between different SIV strains).
A retrovirologist with considerable experience in this field has informed me that the presence in a tissue culture of cells from chimpanzees coming from two different species or subspecies, or even from two different troops would by itself be sufficient to activate the T-cells in that culture, and therefore to allow SIV growth, replication - and recombination. (This is because different chimp troops would almost inevitably contain animals that were not matched immunologically, with respect to MHC, or major histocompatability complex. In other words, HIV or SIV growth in vitro does not require the addition of a special agent such as "T-cell growth factor", which Robert Gallo used to grow HIV-1 in vitro in the 1980s, and which, some have argued, would have been required as an ingredient in the Stanleyville tissue cultures for the OPV/AIDS theory to remain viable. In reality, all it would require would be the addition of SIV-infected cells or sera from chimps coming from two different parts of the rain forest.) Furthermore, since, as Robin Weiss himself has reported, all early tissue cultures contained a small percentage of macrophages, it is likely that the SIVs therein would have prospered anyway, which renders the question of MHC haplotype irrelevant.
The major point is that chimpanzee SIVs would have replicated and recombined in such a tissue culture, and that a proportion of SIV virions (how big a proportion would depend on the specific preparation techniques used for each tissue culture and vaccine batch) would be expected to survive through to the final vaccine. Since Dr Osterrieth is in denial about all this [see below], it is impossible to know exactly how the Stanleyville vaccine batches were prepared, and impossible to do a trial run to test how much SIV in such batches might have survived. But the virological message is this. If the Stanleyville vaccine was indeed prepared in chimp cells and chimp sera, there is no reason to suppose that SIVs, including recombined SIVs, would not have survived through to the final vaccine that was given to humans.
As reported above, there is eye-witness evidence confirming every step of the process whereby tissue cultures were prepared from the Lindi/Stanleyville chimps. But most crucially of all, there are three witnesses who were directly involved with the chimpanzee experiments (two Belgians and an American) who confirm that the LMS doctors were indeed making polio vaccines locally in the Belgian Congo, using cultures from the Stanleyville chimpanzees. Others who were only indirectly involved have confirmed this.
Dr Osterrieth, by contrast, claims that he couldn't possibly have prepared polio vaccine in the Stanleyville laboratory: that they didn't have the means or equipment to do this. But that is patent nonsense.
Provided glassware is kept clean and the work is done in sterile conditions, making vaccine batches of polio vaccine is not - and was not - a difficult procedure.
Indeed, during 1957 Osterrieth was being trained in these very techniques by Koprowski's assistant, Tom Norton, in the labs at the Wistar Institute in Philadelphia. Furthermore, by the time he returned from the US, Osterrieth was working in the virology lab of the new LMS building which opened in September 1957. It was a brand-new custom-built lab, 100 metres long and two storeys high, and funded (it seems) by mysterious sources (for the Congolese government had no spare cash for such indulgences).
And there is more. Between 1953 and 1957, a Polish vet, Alexandre Jezierski, working in his small veterinary lab at Gabu in eastern Belgian Congo, did exactly what Osterreith claims was "impossible" to do in Stanleyville. Without very much fuss, Jezierski prepared tissue cultures from the cells of fifteen different African primate species, including the chimpanzee. He then went on to prepare polio vaccines (both inactivated and oral) in at least five of these primate tissue cultures.
The only difference was that Jezierski's locally-made vaccines were given to only 21 African "volunteers". As it turns out, the OPVs he gave them were not dangerous, having (by good fortune) been grown in colobus cultures.
By contrast, the batches of CHAT polio vaccine that were locally-prepared at the LMS were given to up to one million Africans in 31 known vaccination venues spread around the Belgian Congo, Rwanda and Burundi. Including, of course, Leopoldville, where every African child up to the age of five was vaccinated, a total of 76,000 kids.
The correlations between the 31 different CHAT vaccination venues and the places where HIV-1 first emerged in Africa (all of which are found in villages and towns in the DRC, Rwanda and Burundi) are "highly significant". That means there is less than a 1 in 1,000 chance that these correlations are caused by coincidence alone.
Given the foregoing, it seems highly probable that many or all of the vaccine batches that were locally-prepared in Stanleyville would have contained not just attenuated poliovirus, but also a range of recombinant and mosaic versions of various strains of chimp SIV.
As a result, chimp SIV strains, including recombinant strains, would have been spawned right across the vaccinated towns and villages of the DRC, Rwanda and Burundi….including, of course, in Leopoldville.
But the recombination factor does not end there, for once chimp SIV strains had been seeded in different groups of vaccinees, further in vivo recombination would have occurred through the more traditional means of people having sex with each other. Indeed, it is even possible that some of the CHAT vaccinees were people (perhaps bushmeat-sellers or chimp-hunters) who had previously been exposed to Pts or Ptt SIV through bushmeat. If they were, then transient infection with just a single SIV strain via the bushmeat would very probably not have caused any illness. But what if a chimp SIV strain from the polio vaccine and a strain of chimp SIV acquired from bushmeat recombined in vivo, in the body of an infected chimp-hunter somewhere in the Belgian territories of Africa?
What did Tom Folks's group write? "We propose….that some recombinant viruses most likely seeded the early global epidemic."
The events at Lindi camp, where almost 400 chimps were sacrificed for (largely undocumented) poliomyelitis research during the course of two terrible years, and the creation at the LMS of living oral polio vaccines that were prepared in the cells and sera of these same chimps, surely provides the recombination factors that are so clearly missing from Beatrice Hahn's scenario.
After sixteen years of historical and scientific research into the origins of AIDS, I feel very confident that this is how the AIDS pandemic started.
A Single or Multiple Source?
There is one other key detail to deal with. Hahn and Co. insist that the pandemic began with a single chimp virus infecting a human.
I disagree. I believe that it began after several different variants of chimp SIV (almost certainly of recombined chimp SIVs) transferred to humans at almost the same point in time (ie within the course of approximately three years), via the different batches and trials of locally-prepared CHAT oral polio vaccine.
The geneticists' methods of modelling do not postulate such a scenario; in other words, they automatically reject it. That doesn't make it wrong, however. On the contrary, their failure to consider this possibility reflects only the limitations of their thinking, and of their methodology.
Dr Hahn's new Pan troglodytes troglodytes chimpanzee SIVs from Cameroon are genetically closer to pandemic HIV-1 than any other primate SIVs previously reported.
However, they hardly represent the "cradle" of pandemic HIV-1, or "dead ringers" for the AIDS virus, as she and her group would have us believe.
A far likelier explanation for bridging the genetic gap between the viruses is recombination in vivo among the collectively-caged chimpanzees of Lindi camp, and recombination in vitro, in Stanleyville, Belgian Congo, between chimp SIVs (very probably including Pan troglodytes troglodytes SIVs) that were growing unseen and unrecognised in tissue cultures that were prepared at the LMS from chimpanzee cells and sera. These same chimpanzee tissue cultures were used in the LMS virology department to prepare locally-made batches of CHAT oral polio vaccine, that were then administered to up to one million African "volunteers" in 31 known central African trials. 
These OPV trial venues are the places where pandemic HIV-1 and AIDS first emerged in the world - and they are hundreds of miles away from the chimps of south-eastern Cameroon favoured by Beatrice Hahn.
I believe that this is a far likelier explanation for how AIDS began than the arguments so dogmatically advanced by the key proponents of the bushmeat hypothesis.
Ed Hooper. 16/06/06, updated 5/08/06.
 B.F. Keele, B.H. Hahn et al., "Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1", [Science Express: 10.1126/science.1126531, and Science, 2006; 313; 523-526.].
 P. M. Sharp, "Where AIDS Came From" [Webcast]; 13th Conference on Retroviruses and Opportunistic Infections; Denver, CO, February 5-8, 2006.
 F. Deinhardt, Lindi Databook, 1959.
 M.M. Vastesaeger et al.; "L'atherosclerose experimentale du chimpanze. Recherches preliminaires"; Acta Cardiol.; 1965; Supp. 11; 283-297.
 "The Age of AIDS", PBS documentary, 2006. M. Carmichael, "How it began: HIV before the age of AIDS"; article available on PBS web-site, at: http://www.pbs.org/wgbh/pages/frontline/aids/virus/origins.html.
 "The Origins of AIDS"; MFP/Galafim documentary, 2004.
 A. Andre, G. Courtois. G. Ninane, P.M. Osterrieth et al.; "Mise en evidence d'antigenes de groupes sanguins A, B, O et Rh chez les singes chimpanzes"; Ann. Inst. Past.; 1961; 101; 82-95.
 M. L. Kalish, T. M. Folks et al.; "Recombinant Viruses and Early Global HIV-1 Epidemic"; Emerg. Inf. Dis.; 2004; 10; 1227-1234.
 The remaining HIV-prevalence data for CAR, Cameroon and Congo (Brazzaville) were obtained from the HIV/AIDS Surveillance Database; International Programs Center, US Bureau of the Census; January 1997 edition.
 National Public Radio, "Weekend Edition", broadcast June 4, 2006, 12:00 PM EST. Transcript, with headline: "Origin of AIDS Linked to Colonial Practices in Africa."
 F. van Heuverswyn, "Natural Reservoirs of Chimpanzee Lentiviruses Closely Related to HIV-1 Groups M and N" [Webcast]; 13th Conference on Retroviruses and Opportunistic Infections; Denver, CO, February 5-8, 2006.
 E. Hooper, "Dephlogistication, Imperial Display, Apes, Angels, and the Return of Monsieur Emile Zola. New developments in the origins of AIDS controversy, including some observations about ways in which the scientific establishment may seek to limit open debate and flow of information on 'difficult' issues"; Atti dei Convegni Lincei; 2003; 187; 27-230.
 G. Courtois, "Sur la réalisation d'une singerie de chimpanzés au Congo"; Proceedings of Symposium international sur l'avenir des animaux de laboratoire; Lyon 1966, 235-244; (Institut Merieux, Lyon: 1967).
 J. Kingdon, The Kingdon Field Guide to African Mammals; (Academic Press, San Diego: 1997), p. 10.
 "P. Gagneux, P.A. Morin et al., "Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time", Phil. Trans. Roy. Soc. Lond. B; 2001; 356; 889-897.
 M. Worobey, B. Hahn et al., "Contaminated polio vaccine theory refuted" [letter]; Nature; 2004; 428; 820.]
 P.M. Sharp, G.M. Shaw and B.H. Hahn, "Simian Immunodeficiency Virus Infection of Chimpanzees"; J. Virol.; 2005; 79(7); 3891-3902.