Re: Nucleic Acid Testing (was Re: Are we positive?)

From: Pat Fallon (
Date: Sun Aug 12 2001 - 20:28:19 MDT

>>Pat Fallon
>James Rogers

>>> How reliable are the "HIV tests?" (I've seen claims that
>>> there are more than 60 conditions or diseases that can
>>> cause false positives...

>>[...snip a very long list...]

>The problem is that the tests look for an immune response
>rather than for the viruses themselves...

As I understand it, it is expensive and time-consuming to actually isolate the
virus from every patients blood, so instead surrogate markers for the virus are
used for screening.

As long as the virus sample has first been properly isolated to a purity
sufficient to ensure that the proteins or genetic material to be used as
surrogate markers were extracted from that virus, and as long as the resulting
tests constructed using these markers are tested and calibrated against the
"gold standard" [viral isolation], then these tests can be useful diagnostic

No, the Perth Group [views summarized at and] argue that the problem with
these tests are that this virus was never properly isolated, and that it is
therefore incorrect to label the proteins and genetic material extracted from
the sample and used in the tests as being a marker for infection with a virus.

If you don't have a pure viral isolate, then it will be a case of garbage in =
garbage out no matter how fancy your lab techniques get.

Several of the Perth Groups points seem compelling to me.

1) In 1983 Luc Montagnier’s group at the Pasteur Institute claimed they had
isolated a virus from cultures obtained from patients at risk for AIDS, banded
it in density gradients, and that this band consisted of purified virus.(1)

However, neither Montagnier’s group nor anybody else published electron
micrographs of this band showing that it contained only objects with the
characteristics of viral particles. When Montagnier was asked in July 1997 by
French Journalist Djamel Tahi why such photos were not published, his answer was
because, even after "Roman effort", they could see no particles with "morphology
typical of retroviruses… I repeat we did not purify..."(2)

(2) Also in 1997 the leading science journal Virology published two papers that
provided stunning new data on the “isolation” of HIV.(3)(4) For the first time,
electron microscope images of “HIV” banded at the density required for
retroviruses were published. They revealed "major contaminants" in "pure HIV",
consisting of an excess of vesicles - particles of cellular proteins. [See the
photos for yourself at]

The samples Montagnier [and later Robert Gallo of the NIH] called "viral
isolates” contain a few objects that resemble retroviruses (the "HIV") plus lots
of other things, which clearly aren't viruses. Without a pure isolate of
virus-like particles, there is no way to extract proteins and genetic material
out of a molecular soup and know that they came from one group of particular
looking objects rather than another.

(3) Montagnier and Gallo claimed “isolation” citing three pieces of evidence:
detection of reverse transcription activity, detection of retroviral-like
particles in cell cultures, and antibody reactions. The Perth Group argues these
are logically insufficient:

First, reverse transcription activity is not unique to retroviruses, and in fact
RT activity in normal cells is promoted by the very conditions which Montagnier
and Gallo subjected their patients’ T-cells to.(5) Therefore, detection of RT
activity in these cultures was not proof that there was a retrovirus present.

Secondly, Gallo and Montagnier offered as evidence photographs of particles in
impure cell cultures and asserted that not only were they retroviruses, but they
were a specific retrovirus, “HIV.” However, as even Gallo admits,(6)
retroviral-like particles that are not infectious are common in cultures,
especially those subjected to the conditions that Gallo and Montagnier used in
order to cultivate “HIV.” Pointing to particles in impure cell cultures that are
viral-like was hardly proof that those particles were a retrovirus, let alone a
specific retrovirus, “HIV.”

Thirdly, Gallo and Montagnier offered antibody reactions as proof of isolation
of their virus from AIDS patients. They identified certain proteins in these
cultures as “HIV proteins.” This was done not by extracting those proteins from
the viral isolate, because there was no viral isolate. They had a soup
containing a few virus-like objects and a lot of contaminating cellular debris.

To decide which proteins extracted from this mix were from the virus-like
objects, they exposed the proteins to blood samples from both AIDS patients and
non-AIDS patients. If a protein caused an antibody response from an AIDS
patient, and no antibody response from a non-AIDS patient, they said that one
was an “HIV protein.” These proteins were then used in the antibody and Western
Blot tests. A Positive result is interpreted as indicating the presence of “HIV

However, antibodies cross-react, and AIDS patients have a much higher level of
circulating antibodies than in normal, healthy individuals. Thus AIDS patients
were likely to have antibody cross-reactions with any given protein more often
than non-AIDS patients. Also, false positives may be caused by vaccinations
against other diseases or current or past diseases.(7) Moreover, antibodies can
be raised against a non-viral protein, e.g. that of endogenous nature (arising
from within, not from infection). Identification of certain proteins as “HIV
proteins,” simply because they reacted with antibodies of AIDS patients and not
non-AIDS patients was insufficient proof that these proteins were actually from
a new virus, “HIV.”

The insufficiency of this evidence was first pointed out by Eleni
Papadopulos-Eleopulos, a medical physicist at Australia's Royal Perth Hospital.
In 1988 she published her paper, "Reappraisal of AIDS: Is the Oxidation Induced
by the Risk Factors the Primary Cause?", in which she stated, "Unlike other
viruses [HIV] has never been isolated as an independent stable particle."(8)
With the recent release of the photos showing no viral isolation, and
Montagnier’s admission that “…we did not purify”, it is hard to deny the logic
of her argument.

The inability to isolate the virus means no proteins which are viral and free
from contaminants have ever been obtained, thus no one can be certain what the
antibodies are that bind to the proteins. This is the heart of the problem
facing all HIV tests. The manufacturer of the most popular HIV test kit openly
acknowledges, "there is no recognized standard for establishing the presence or
absence of antibodies to HIV in human blood."(9)

>This is why Chiron's (CHIR) Nucleic Acid Testing (NAT) technology
>platform (Procleix), which is expected to receive FDA approved later
>this year is a considered to be a major advancement.
>Chiron's NAT technology will be the first general purpose platform
>that is capable of directly detecting the presence of viruses in the body.
>So that sort of answers your question. NAT should effectively eliminate
>false positives AND false negatives for HIV (and other viruses) in the body.

I found some press releases from Chiron online
[] that describe this NAT to be some
sort of a nucleic acid amplification test. Maybe I am mistaken. However, IF
HIV was never isoated, then how is it possible to consider the RNAs used
represents the genome of a unique retrovirus and to use these as probes and
primers for hybridisation, PCR or NAT tests to prove infection with this virus
and in fact to measure the viral load?

If no virus has been isolated, it follows that no nucleic acid has been isolated
from it either. Virologist Dr Stefan Lanka has described the complicated
procedures at the end of which something is produced which is called the nucleic
acid of HIV.

[begin quote]

1. In a tube....

HIV and its DNA can allegedly be made by the "bucketful",(24) but under very
surprising conditions which, inter alia, entail the use of extracts from plants
and other oxidising chemicals, which could not possibly exist in vivo.
Immortalised cell lines devised (and later patented) by the Montagnier and Gallo
groups are co-cultured with extracts from human cells or the cells themselves.
At the end of it all HIV itself is not actually obtained only reverse
transcriptase activity is shown to occur which is taken to imply
that the DNA that is found, must have been viral in origin.

The real explanation of what happens is as follows. In the mixture of cell
cultures and stressed human cells, RNA and reverse transcriptase come to be
produced in large amounts, because the cells have been specially selected and
treated to do this. The RNA is transcribed into DNA by reverse transcriptase,
and long pieces of DNA are produced which are said to be viral DNA. In fact they
are composed of unrelated pieces of expressed cellular RNA, transcribed into DNA
and linked together by a process of "template switching" (a well-characterised
property of reverse transcriptase).(25) This misleads ordinary researchers into
believing that they have actually produced viral DNA. It is said that this
linear DNA is the free or the non-integrated form of HIV, which furthermore is
said to be a unique feature of HIV, because a lot of detectable free linear DNA
has not been suggested in any other models of retroviruses.

2. Through selecting processes....

The resulting pieces of DNA too, are necessarily both shorter and longer than
the "correct" length of HIV. Pieces corresponding to the "correct" length of HIV
must be selected for size, because otherwise the purported DNA preparation would
be a mixture of various lengths, which would violate a cardinal rule of virology
that all nucleic acid of a particular virus be identical in size.

3. Through a detecting process....

Having artificially prepared DNA pieces of uniform length, they are still not
ready for presentation, because they consist of a mixture of all kinds of RNA
fragments transcribed into DNA and thus cannot be shown to represent unique
viral DNA. Accordingly, the mixture is subjected to a kind of key-and-lock
detection process called hybridisation, whereby pieces of DNA
are detected which complement more or less a probe of that which it is desired
to be shown to have been prepared.

4. Choosing a desired probe....

Since no DNA from HIV existed to hybridise with the prepared DNA, Gallo and
Montagnier simply used stretches of DNA from what they said was specific to
HTLV-I, a retrovirus Gallo had earlier claimed to have discovered, and which
they deemed suitable for this purpose. The DNA detected in this way was
replicated and certain stretches of it cloned and declared to be the DNA of
HTLV-III (later to be called HIV).

To summarise, the purpose of the exercise is to grow HIV, but it actually
produces a mixture of different lengths of DNA, contrary to theory which says
they should all be identical, and no virus at all. It is then claimed that the
"correct" DNA has been prepared by finding certain strands in this heterogeneous
mix by hybridising them with an HTLV-I DNA probe whose sequence is known and
defined also to be HIV. However, non-hybridising strands of DNA should not be
there at all, and the fact that they are, proves that a complete rag-bag of DNA
has been prepared, without any indication of what it is made up of.

It follows that "HIV" DNA must just be a laboratory artefact constructed to a
preconceived idea of what retroviral DNA should be, and this assessment does not
even raise the question why no virus can be obtained, whatever the experimental

Gallo and Montagnier's cloned HIV DNA

One cannot help asking why no-one had not long ago spotted the flaw in the
techniques employed by the Gallo and Montagnier groups. After defining some
segments of DNA to be "HIV"-specific, every researcher in the field worked
exclusively with short, cloned sequences (never the whole strand) on the
reasonable assumption that the original characterisation had been correctly
performed. From the isolation and identification procedure described above, it
follows that the resultant sequences vary widely from one preparation to the
next, which sequence analysts misinterpreted as the legendary capacity of HIV to

24 Tedder R.S. UCL Medical School London, 1994 personal communication

25 Guangxiang Luo and John Taylor. 1990. Template Switching by Reverse
Transcriptase during DNA Synthesis. J Virol 64, 4321-4328. Goodrich D.W. and
Duesberg P.H. 1990. Retroviral recombination during reverse transcription. PNAS
87: 2052-2056.

[end Stefen Lanka quote]

There are many Human Endogenous Retrovirus (HERV) sequences in the human genome,
thus in all of us (10).

They are there already, we don't acquire them by infection. For that reason, I
have always thought it confusing to call these sequences "virus" in the first

In 1997 some researchers found evidence that sequences specific for the
"hepatitis C virus" are demonstrable in the DNA fraction of peripheral blood
mononuclear cells from healthy, anti-HCV antibody-negative individuals and cell
lines of human origin (11). A similar finding has been announced concerning
"HIV". (12)

All of us have retroviral sequences in our genes that can be expressed under
certain circumstances. In the case of "HIV", the Perth Group argues that our
bodies, and cultures in labs, can be exposed to oxidative or other stress that
cause these sequences to "be activated" or express proteins. It is argued these
phenomenon are the result of, not the cause of, disease.

Pat Fallon

(1) Barré-Sinoussi F, Chermann JC, Rey F. (1983). Isolation of a T-Lymphotrophic
Retrovirus from a patient at Risk for Acquired Immune Deficiency Syndrome
(AIDS). Science 220:868-871
(3) Bess JW, Gorelick RJ, Bosche WJ, Henderson LE, Arthur LO. (1997).
Microvesicles are a source of contaminating cellular proteins found in purified
HIV-1 preparations. Virol. 230:134-144.
(4) Gluschankof P, Mondor I, Gelderblom HR, Sattentau QJ. (1997). Cell membrane
vesicles are a major contaminant of gradient-enriched human immunodeficiency
virus type-1 preparations. Virol. 230:125-133.
(5) 149. Tomley FM, Armstrong SJ, Mahy BWJ, Owen LN. (1983). Reverse
transcriptase activity and particles of retroviral density in cultured canine
lymphosarcoma supernatants. Br. J. Cancer 47:277-284. 150.
(6) Gallo, R. C., Wong-Staal, F., Reitz, M., Gallagher, R. E., Miller, N. &
Gillepsie, D. H. 1976. Some evidence for infectious type-C virus in humans. pp.
385-405, in Animal Virology, edited by D. Balimore, A. S. Huang and C. F. Fox,
Academic Press Inc., New York.
(7) Factors Known to Cause False-Positive HIV Antibody Test Results. Continuum;
4(3): 5. 64 references to conditions that can cause false-positive HIV test
(8) Medical Hypotheses (1988) 25: 151-162. Full text online at
(9) Abbot Laboratories, HIVABtm HIV-1 EIA, May 1998
(10) Lower et al. The viruses in all of us: Characteristics and biological
significance of human endogenous retrovirus sequences.
Poc. Natl. Acad. Sci. USA; 93: pp 5177-5184
(11) Dennin RH, Chen Z, Eur J Clin Chem Clin Biochem 1997 Dec;35(12):899-905
(12) Bryan Cullen, a Howard Hughes Medical Institute investigator at Duke
University, authored the paper in the November 9, 1999, issue of the Proceedings
of the National Academy of Sciences. As the HHMI newsletter summarized: "Buried
within the genetic blueprint of every human is a snippet of DNA that resembles a
gene sequence from the human immunodeficiency virus (HIV). Humans have been
carrying this unwanted genetic baggage around for more than 30 million years,
according to researchers from the Howard Hughes Medical Institute (HHMI) at Duke

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