Re: Re-phrasing our two questions to Brian Foley 11 May 2004
Previous Rapid Response Next Rapid Response Top
Brian T Foley,
HIV Researcher
Los Alamos National Lab, Los Alamos, NM 87545

Send response to journal:
Re: Re: Re-phrasing our two questions to Brian Foley

The Perth group wrote:
“…
Unfortunately he gave a lengthy response and a long list of inappropriate references but did not answer our questions.
…”

It is unfortunate that the Perth group denies that the references I provided were appropriate. If they read the content of those papers, they would not need to keep repeating their questions, which are answered in those papers.

The Perth group wrote:
“…
Would please Brian Foley read Gallo and Montagnier group’s 1984-1985 papers (1,2,3) and tell us if it is true that the “HIV” poly(A)-RNA, , that is, the “HIV” genome, originated from the 1.16g/ml band? Yes or No?
…”

Yes, there were HIV-1 M group subtype B poly-adenylated RNA genomes in many of the 1.16g/ml bands that were analyzed by the Gallo and Montagnier labs (those that came from infected cell lines, but not from uninfected cell lines). There were also some polyadenylated subgenomic RNAs in the 1.16 g/ml bands, which were produced by cellular splicing machinery which removed introns from the viral genome to make mRNAs that can be translated to produce Tat, Rev and other viral proteins which cannot be produced from unspliced full-length genomic RNAs. These three papers cited by the Perth group [1,2,3] are only a small sampling of the many papers published by the Gallo and Montagnier labs in the 1984-1985 time period. I would advise the Perth group to do more reading on this subject, if they wish to understand why the Gallo and Montagnier groups were given credit, over other labs such as the one that Jay Levy worked in, for being the first two labs to “isolate” the virus which became known as HIV-1 M group subtype B.

I assume that when the Perth group refers to “the” HIV genome, they are speaking of one or more of the genomes that were cloned and sequenced by the Gallo and Montagnier labs. In that case, not all of these clones were derived DIRECTLY from any 1.16 g/ml band. As I clearly stated before, most molecular clones of HIV-1, including those that were sequenced in 1985, did not originate directly from any 1.16 g/ml band. For example, if the Perth group could read and comprehend the papers they cited, they would know that the Lambda-HXB-2 and Lambda-HXB-3 clones in [3] originated from two of the several HIV-1 M group subtype B genomes which were integrated into the genomic DNA of one particular HIV-infected infected H9 cell culture. These two molecular clones of HIV-1 M group subtype B virus are not identical, as is readily apparent from the restriction maps in figure 2 of [3], but they are nearly identical, as would be expected from two clones which originated from pooled sera from several HIV-infected people, and were passed into clone 9 of HT cells (H9) as stated in [2]. Likewise the HIV genomes found in the Lambda-HXB-2 and Lambda-HXB-3 clones were nearly identical to the Lambda-BH-5, Lambda-BH8 and Lambda-BH-10 clones, each of which originated from circular pre-integration complex DNAs isolated by the procedure of Hirt et al. [4,5]. This extrachromosomal DNA was probed with radiolabeled cDNA made from the HIV-1 RNA isolated by oligo-dT column from HIV-infected cells, after “double banding” meaning that the first 1.16 g/ml band was reloaded and recentrifuged [4].

The Alizon paper [1] reports the cloning and preliminary analysis of 3 subgenomic fragments of HIV-1 M group subtype B cDNA, called plasmid-LAV13, plasmid-LAV75 and plasmid-LAV82. The Alizon paper states that an HIV-infected cell line called FR8 was used, and cites a 1984 Levy paper [6] . It is not 100% clear whether Alizon is citing Levy as the source of the LAV-infected cell line that was used, or only the source of the procedure used to purify HIV-1 RNA in order to make the cDNA. At any rate, yes, these 3 clones (although not infectious, as they are not full-length genomes) were in fact derived directly from virion particles isolated from one or more 1.16 g/ml sucrose density bands.

If the Perth group had read and comprehended the Arya paper [2], they would know that in this case, yes the authors obtained their HIV-1 genomic RNAs, from which they made cDNAs, from the 1.16 g/ml band of sucrose-density gradient-purified virions. The Arya paper does not report cloning any of their cDNA, they only labeled it and used it to probe HTLV-1 and HTLV-II cloned genomes in an effort to determine how closely or distantly related HIV-1 is to these other two complex retroviruses. However, [3] reports the cloning the integrated proviral genomic DNA from these very same cells, as discussed above.

The Perth group wrote:
“…
Is it true that by infectious molecular clone of a virus is meant the introduction of the viral genome (molecular clone) into suitable cells leading to the appearance of virus particles identical (regarding both appearance and composition) to the ones from which the genome was obtained? Yes or No?
…”

Yes, as I have said twice or more times before already. The clone must produce virus particles that are identical by serology, morphology, protein sequences, RFLP, Southern blotting, etc. to the parental virus, and the particles must also be infectious. If a cloned viral genome does not meet these criteria, it is not an INFECTIOUS molecular clone of the virus, be it HIV-1 or any other virus. Morphology by electron microscopy is the least important of those criteria, because as I have stated many times before, all lentiviruses look alike by electron microscopy. Also, it is not always possible to detect the difference between infectious and non-infectious virus particles by electron microscopy.

References

1. Alizon M, Sonigo P, Barre-Sinoussi P, Chermann JC, Tiollais P, Montagnier L,
Wain-Hobson S. (1984).
Molecular cloning of lymphadenopathy- associated virus.
Nature 312:757-760.

2. Ayra SK, Gallo RC, Hahn BH, Shaw GM, Popovic M, Salahuddin SZ,
Wong-Staal F. (1984).
Homology of genome of AIDS-associated virus with genomes of human T-cell
leukemia viruses.
Science 225:927-929

3. Shaw GM, Hahn BH, Arya SK, Groopman JE, Gallo RC,
Wong-Staal F. (1984).
Molecular characterization of human T-cell leukemia (lymphotropic) virus type III
in the acquired immune deficiency syndrome.
Science 226:1165-1171.

4: Hahn BH, Shaw GM, Arya SK, Popovic M, Gallo RC, Wong-Staal F.
Molecular cloning and characterization of the HTLV-III virus associated
with AIDS.
Nature. 1984 Nov 8-14;312(5990):166-9.
PMID: 6095086

5: Hirt B.
Selective extraction of polyoma DNA from infected mouse cell cultures.
J Mol Biol. 1967 Jun 14;26(2):365-9.
PMID: 4291934

6 : Levy JA, Hoffman AD, Kramer SM, Landis JA, Shimabukuro JM,
Oshiro LS.
Isolation of lymphocytopathic retroviruses from San Francisco patients
with AIDS.
Science. 1984 Aug 24;225(4664):840-2.
PMID: 6206563

Competing interests: None declared