Did Africans get HIV from
chimps?
Not likely, asserts biophysicist Eleni
Papadopulos-Eleopulos in her latest paper rejected
by Nature
The science journal
Nature continues its de facto policy of rejecting all submissions
that question the HIV-causes-AIDS model. Its editors recently rejected
the following commentary composed by the AIDS research team headed
by Australian biophysicist Eleni Papadopulos-Eleopulos.
The rejected article addresses a recently
published letter by scientists who claimed to have discovered the
original human source of HIV: a simian "immunodeficiency"
virus (SIV) newly identified (by them) from a particular subspecies
of African chimpanzees. The authors declared that the genetic sequencing
of their new SIV closely resembles that of HIV. And since the chimpanzees
live in the same region as some humans who test "HIV-positive,"
the authors concluded that the humans there somehow contracted HIV
(or what became HIV) from those chimpanzees.
Not so fast, say the Australians. The published
authors presented no evidence that they had isolated any virus,
so there's no basis for claims of a new viral species or a viral
genome. Nor did they demonstrate a close similarity between the
perported SIV and HIV gene sequences. To the contrary, the published
sequences differed significantly. As for the possibility of trans-species
transmission, the Australians note that none of the presumably infected
chimpanzees had managed to transmit the purported virus to their
own children or sex partners.
Most scientists consider Nature the
world's leading research publication. Papadopulos-Eleopulos's carefully
argued letter typifies the high quality of dozens of AIDS reappraising
submissions, including several of hers, that Nature
has rejected over the years. and the sloppy, implausible letter
she criticizes exemplifies the poor quality of the dozens of pro-HIV
submissions Nature publishes each year. A comparison
of the two suggests that when Nature's editors consider
the topic of AIDS, they practice poor judgment and censorship. --
Editor
IN A LETTER to Nature (Feb.
4), Gao et al .claimed to have proven:
(i) the existence of a new simian immunodeficiency
virus (SIVcpz), in a chimpanzee, by identifying the virus's genome;
(ii) that the chimpanzees in which his group found
this SIV belong to a certain subspecies, P.t. troglodytes (their
chimpanzee, Marilyn, as well as two of the other three chimpanzees
in which to date a SIVcpz was reported, GAB1 and GAB2);
(iii) that these chimpanzees live in the same area
of Africa with humans who are said to be infected with certain genetic
groups of HIV ("the natural range of P.t. troglodytes coincides
uniquely with areas of HIV-1 group M, N and O endemicity");
(iv) the humans there acquired their HIV from the
chimpanzees ("HIV-1 infection of humans occurred as a result
of cross-species transmission of SIVcpz from P.t. troglodytes");
and
(v) those chimpanzees are the original source for
humans of HIV ("P.t. troglodytes is the primary reservoir for
HIV-1").
A close analysis of the evidence on which Gao's group bases its
claims raises several issues that contradict those claims:
(a) Marilyn was "wild-caught in Africa (country of origin unknown),
exported to the United States as an infant." [1]
Two of the chimpanzees, GAB1 and GAB2, originated in Gabon. GAB1,
who was 4 years old when reported HIV-1 positive, was caught when
she was "about 6 months" and was kept with another 49
wild-caught animals at the International Centre of Medical Research
(CIRM) in Gabon. GAB2, who was also reported HIV-1 positive, was
about 2 years old when she was shot in the wild, kept in a village
for 2 days and then was brought to CIRM, "where it died of
its wounds one week later." [2]
In the 1989 study, where the "HIV-1 seropositivity"
of GAB1 and GAB2 was reported, the authors (which included one of
Gao's co-authors, Peeters) concluded: "...on examination, none
of the people caring for the animals and none of those living in
the village showed antibodies to HIV/SIV. Furthermore, the region
where the chimpanzee was captured is known to have a low seroprevalence
rate.... It has been suggested that human AIDS retroviruses originated
from monkeys in Africa. However, this study and other previous studies
on SIV do not support this suggestion." In other words, by
the time that "HIV infection" and AIDS had already reached
their peaks in the US, Europe, and Australia, the number of individuals
proven HIV seropositive in Gabon were few if any.
A 1990 study published in Nature by
researchers from CIRM and the Pasteur Institute, including Wain-Hobson,
where the authors described "the molecular cloning and sequencing"
of SIVcpzGAB1, states: "In Gabon, only 2 out of 83 chimpanzees
tested were seropositive, indicating that SIVCPZ is not widely dispersed
in this region.... Of more than 250 chimpanzees caught over the
last 15-20 years in West Africa, none was seropositive. This might
explain the absence of naturally infected chimpanzees in captivity
in the US as virtually all are of West African origin." [3]
How is it possible to espouse "prevalence
in the natural host," "geographic coincidence," and
"plausible routes of transmission" as evidence to substantiate
the claims that HIV-1 originated in P.t. troglodytes and that this
sub-species is the natural reservoir for HIV-1?
(b) The three P.t. troglodytes -- GAB1, GAB2 and Marilyn -- were
said to be infected with HIV-1/SIVcpz on the basis of an antibody
test. However, given that:
(i) as Philip Mortimer points out,
"...it may be impossible to relate an antibody response specifically
to HIV-1 infection." [4]
(ii) when the blood was collected
none of the animals was perfectly healthy although none had AIDS.
(iii) the only way to prove the specificity of
an antibody test is to use the virus isolation as a gold standard.
Although no effort has been spared, no SIVcpz could be isolated
either from GAB2 or Marilyn (see comments below for GAB1).
(c) How is it possible to claim proof for infection on the basis
of an antibody test?
(i) If GAB1 and Marilyn were infected then, given
that the animals were brought to the colony as infants where no
other animals or humans working there were infected and, according
to Weiss, "Chimpanzees in captivity are mostly taken from the
wild before they become sexually active and so rarely harbor SIV,"
how did these two chimpanzees become infected? [5]
(ii) Since the three chimpanzees found positive
were all female, and since HIV/SIV is acquired following sexual
maturity, how did they become infected?
(iii) If the animals were infected with a virus
SIVcpz and this was transmitted to humans, why was this not transmitted
to any other of the 49 animals at CIRM where GAB1 was kept or to
the 93 animals in the colony where Marilyn was kept, not even to
her 6 living offspring or her mates? (By the age of 26 she had a
total of 14 pregnancies). [6]
(d) The additional "lines of evidence" that Gao used to
substantiate transmission are based on genomic studies. Gao claimed
to have shown that "All HIV-1 strains known to infect man,
including HIV-1 groups M, N, and O, are closely related to just
one of these SIVcpz lineages, that found in P.t. troglodytes."
Indeed, if all these HIV-1 and SIVcpz strains represented one and
the same virus, then their genomes will have to be "closely
related." In fact they should represent a unique molecular
entity. Even in the genomes of RNA viruses, including influenza,
which are considered to be most variable, a 1% sequence difference
is considered to represent "extreme variability." [7]
This is because small genetic differences lead to significant phenotypic
differences. For example the difference between the human and the
chimpanzee genome is less than 2%.
In the 1989 study of SIVcpzGAB1 Peeters wrote:
"Nucleic acid hybridization experiments appear to indicate
that the virus is different from HIV-1 and HIV-2." A 1990 Nature
paper by researchers from CIRM and the Pasteur Institute, including
Wain-Hobson, states: "Several regions of the chimpanzee sequences
were more than 50% divergent with respect to HIV-1BRU. Some parts
of the gag gene were almost as varied as the hypervariable regions
in env.... The vpu gene found only in the type 1 viruses was particularly
different (64% divergent to HIV-1BRU).... It is also apparent that
the SIVCPZ genome was not simply a more diverged HIV-1 isolate....
It is not possible to conclude that SIVCPZ was the precursor to
HIV-1, if indeed infection ever passed in that direction. Even given
this premise the vpu data indicates that SIVCPZ was not the immediate
precursor." [3]
In a 1994 study of the SIVcpzGAB2, Peeters wrote:
"The genetic distance between SIVcpz-gab [SIVcpz GAB1) and
SIVcpz-gab2 is 14.1%. Genetic distances to the HIV-1 genotypes A,
B and D strains are 13.7 to 16.3%, whereas distances to group O
HIV-1 strains are 15.4 to 18.5%." Contrary to Gao, in 1994
Peeters concluded: "On the basis of their respective distances
to each other and to the HIV-1 strains, SIVcpz-gab and SIVcpz-gab2
can be assigned as representative for two distinct genetic lineages
of HIV-1-related chimpanzee lentiviruses." [8]
By 1993 it was reported that "in the A-G HIV-1
genotypes the intra-genotypic gag distances averaged 7%, whereas
the inter-genotypic distances averaged 14%.... The maximum level
of variability in gag is still well below that observed for the
envelope region of HIV-1." [9]
The HIV-1 group O has "65% similarity to HIV-1
and 56% similarity to HIV-2 consensus sequences. The env
gene of MVP-5180 [HIV-1 group O] had similarities to HIV-1 and HIV-2
of 53 and 49% respectively.... Comparison of the MVP-5180 amino
acid sequences with that of the Gabon chimpanzee virus showed similarities
of 70, 78 and 53% in the gag , pol and
env genes, respectively." [10]
As far as the genomic differences between HIV-1
group N, on the one hand, and group M and O on the other is concerned,
it suffices to quote from the 1998 study where its existence was
first reported. "Proviral DNA amplification with several sets
of HIV-1 group M and O primers was attempted on pelleted end-cultured
cells. Amplification was negative with eight different group M env,
gag or pol primers and five group O env or gag primers." [11]
How is it possible to claim proof for the existence of a unique
molecular entity which constitutes the genome of a unique retrovirus
HIV-1/SIVcpz?
(e) The only way to prove that an RNA (and its cDNA) is the genome
of a retrovirus is to demonstrate that it comes from a retrovirus
particle and such RNA codes for its proteins. This can be done only
by obtaining the particles separate from everything else, purifying,
isolating them. [12]
In the 1989 study, where Peeters reported the isolation
of SIVcpzGAB1, stimulated peripheral blood lymphocytes "from
healthy human donors" were co-cultured with the same type of
cells from the chimpanzees. Supernatant from the co-culture was
centrifuged for 10 minutes at 400.000g. Detection in the pellet
of reverse transcriptase activity, using An(dT) [12-18] as template
primer, was considered proof for SIVcpzGAB1 isolation. Such a method
for viral isolation is no different from claiming that elevations
in serum liver enzymes proves the existence of gallstones and, moreover,
that the gallstones have been isolated from the patient and are
in the surgeon's hands separate from everything else. The SIVcpzGAB1
"genome" was obtained either by hybridizing the RNA present
in the pellet (they presented no proof that the pellet contained
even retrovirus-like particles), where one would expect to find
ample cellular RNA, with probes "from HIV-1oyi, a Gabonese
HIV-1 strain," or from "SIVCPZ-infected human lymphocytes,"
again using HIV-1oyi as a probe. The "genome" thus obtained
was compared with the genome of HIV-1BRU.
We could find no details as to how the HIV-1oyi
"genome" was obtained. HIV-1BRU is the "HIV-1"
which, according to Weiss, was "discovered by Barre-Sinoussi
and her colleagues in 1983." The senior author of the 1983
Barre-Sinoussi study, Luc Montagnier, in 1997 not only acknowledged
that they did not isolate HIV-1BRU, but their "pure" virus
from where they chose some RNA and called it HIV RNA, did not even
contain particles with "morphology typical of retroviruses."
[13]
The only evidence ever presented as proving the existence of the
SIVcpzGAB2 genome was reported by Peeters and his associates. They
write: "From this chimpanzee we have been unable this far to
isolate a lentivirus, but some of the primary peripheral blood mononuclear
cells (PBMCs) have remained available in a frozen state. To investigate
the genetic relationship to the SIVcpz-gab isolate [SIVcpzGAB1],
proviral DNA was extracted from these primary PBMCs [no mention
is made how it was possible to extract the proviral DNA from the
chimpanzee DNA], and a 280-base pair (bp) fragment of the pol gene
was amplified by a nested polymerase chain reaction (PCR). Subsequently,
PCR fragments were cloned and sequenced." [8] No mention is
made as to how they obtained the PCR primer. Gao et al used "consensus
sequences" as primers and the following method: "Here
we used the polymerase chain reaction (PCR) to amplify HIV- or SIV-related
DNA sequences directly from uncultured (frozen) spleen and lymph-node
tissue obtained at autopsy in order to characterize the infection
responsible for Marilyn's HIV-1 seropositivity. Amplification and
sequence analysis of subgenomic gag (508 base pairs (bp)) and pol
(766 bp) fragments revealed the presence of a virus related to,
but distinct from, known SIVcpz and HIV-1 strains. Because virus
isolation from the autopsy tissues was unsuccessful, we used PCR
to amplify and sequence four overlapping subgenomic fragments that
together comprised a complete proviral genome, which we termed SIVcpzUS."
However,
(i) The specificity of the PCR for HIV has never been proven. The
only way to obtain such proof is to use virus isolation as a gold
standard. Even if one accepts the claims for SIVcpzGAB1 isolation,
it is agreed that, although no effort has been spared, SIVcpz could
not be isolated from the other two animals. This means that the
PCR results obtained for the genomes of SIVcpzGAB2 and SIVcpzUS
are false.
(ii) Even if they were specific for retroviruses; given that:
(a) The genome of all humans and animals contain retroviral proviruses,
i.e., genomes of the endogenous retroviruses. [14]
(b) There are homologies between the genomes of different retroviruses,
especially in the gag and pol genes. In fact, according to Montagnier
and Wain-Hobson, the gag and pol genes "are generally conserved
among retroviruses." [15]
(c) In not one of the studies which claimed proof for the existence
of the SIVcpz genomes did the authors use controls.
(iii) How is it possible to claim that the sequences detected in
the DNA "of SIVcpz-infected human lymphocytes," the PBMCs
of GAB2 and in Marilyn's "spleen and lymph-node tissue"
were those of an exogenous retrovirus which is transmitted from
one chimpanzee to another and from chimpanzee to humans and not
those of an endogenous retrovirus?
(iv) Since there is no proof that the three chimpanzees ever came
in contact with HIV-1-infected humans or animals or that they transmitted
such a virus to other humans or animals, is it not more "plausible"
to conclude that if these animals did harbor a retrovirus, the retrovirus
was endogenous?In analyzing the "SIVcpz" molecular biology
one cannot help reflecting upon the words of Sir John Maddox, "Is
there a danger, in molecular biology, that the accumulation of data
will get so far ahead of its assimilation into a conceptual framework
that the data will eventually prove an encumbrance? Part of the
trouble is that the excitement of the chase leaves little time for
reflection. And there are grants for producing data, but hardly
any for standing back in contemplation." [16]
Signed,
Eleni Papadopulos-Eleopulos (1)
Valendar F. Turner (2)
John M. Papadimitriou (3)
David Causer (Senior Physicist) (1)
Bruce Hedland-Thomas (1)
Barry Page (1)
Charles Geshekter (4)
Etienne DeHarven (5)
Helman Alphonso(6)
Todd Miller (7)
1) Dept of Medical Physics, Royal Perth Hospital, Western Australia.
bruce.hedland-thomas@rph.health.wa.
gov.au;
2) Dept. of Emergency Medicine, Royal Perth Hospital, Western Australia;
3) Dept of Pathology, University of Western Australia;
4) Dept. of History California State University, Chico, California;
5) Professor (Emeritus) of Pathology, University of Toronto, Canada.
6) Head, Department of Research, Universidad Metropolitana Barranquilla,
Colombia
7) Assistant Scientist,Department of Molecular and Cellular Pharmacology,
University of Miami School of Medicine, Florida, USA
Eleni Papadopulos-Eleopulos, Biophysicist, Department
of Medical Physics, Royal Perth Hospital, Wellington Street, Perth
6001, Western Australia.
www.virusmyth.com/aids/perthgroup;vturner@cyllene.uwa.edu.au
REFERENCES
1. Gao, Nature 397, 436-441 (1999).
2. Peeters, Aids 6, 447-51 (1992).
3. Wain-Hobson, Nature 345, 356-9 (1990).
4. Mortimer, Med. Internat. 56, 2334-2339 (1989).
5. Weiss, Nature 397, 385-386 (1999).
6. Gilden, Lancet i, 678-679 (1986).
7. Steinhauer, Annual Rev. of Microbiology 41, 409-433
(1987).
8. Janssens, AIDS Res. and Human Retrov. 10, 1191-2,
1994.
9. Louwagie, AIDS 7, 769-780 (1993).
10. Gurtler, Journal of Virology 68, 1581-5 (1994).
11. Simon, Nature Medicine 4, 1032-7 (1998).
12. Toplin, Spectra , 225-235 (1973);
13. Tahi, Continuum 5, 30-34l; 1998 (available at: www.virusmyth.com
/aids/ data/dtinterviewlm.htm.
14. Lower, Proceedings of the Nat'l Academy of Sciences
93, 5177-5184, 1996.
15. Wain-Hobson, Nature 313, 743 (1985).
16. Maddox, Nature 335, 11 (1988).
RETHINKING AIDS HOMEPAGE
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