"HIV" genomic variations 31 July 2003
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Eleni Papadopulos-Eleopulos,
Department of Medical Physics, Royal Perth Hospital, Western Australia,
Valendar F Turner, John Papadimitriou, Barry Page, David Causer, Helman Alfonso

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Re: "HIV" genomic variations

“HIV” genomic variations

In his rapid response “Re: HIV genome, clones and sequences” (24 July 2003), Christopher Noble wrote: “Even in influenza A, one of the examples of RNA viruses given by Papadopulos-Eleopulos, considerably more variation than 1% is seen.”

What does he mean by “considerably more variation than 1%”?   Is the variation closer to 40% than it is to 1%?  That is, would Christopher Noble please tell us what the actual % variation is?

Christopher Noble wrote: “This quote is again deceptive. Poliovirus has an extremely high mutation rate of approximately 10-4 to 10-5 substitutions per site per replication. Papadopulos-Eleopulos apparently does not understand the difference between mutation rates and evolution rates. The latter is highly dependent on the selective conditions.  Sabin was trying to produce a strain with less replication fitness. This is clearly not the normal selective conditions as can be seen with unfortunate results in cases of vaccine-related paralytic poliomyelitis.  In some individuals more than 100 genetic changes can be seen during a single passage of the Sabin strain.(2)”

In his reference 2 we could find no evidence to justify his claim.

Christopher Noble wrote: “I find the comparison between viruses and primates to be totally artificial and deliberately deceptive. A better comparison would be with the human papillomavirus (HPV) which shares many phylogenetic similarities with HIV including a large divergence of up to 50% between isolates.(3)”

The reason for our delay in answering Christopher Noble’s rapid responses is our difficulty in obtaining his reference (3) which is not available in any Australian library.   However, we feel that John Kirkham’s rapid response “Comparing HPV and HIV” (30 July 2003) adequately addresses this point.

In his rapid response “The HIV and “influenza A” virus genomes” (28 July 2003), Christopher Noble wrote: “The reappearance of a 1950 H1N1 influenza A strain in 1977 that Eleni Papadopulos-Eleopulos specifically referred to is indeed an exception.  Phylogenetic analyses have shown that this particular strain evolved at a much higher rate both before 1950 and after 1977. The period between 1950 and 1977 where little genetic change took place is quite clearly an abnormality.  Why does Eleni Papadopulos-Eleopulos specifically refer to the reappearance of this particular strain of H1N1 rather than other strains that have not shown this discontinuity?  Out of the hundreds of papers on the evolution of influenza viruses why does she choose this particular example?”

As we have already pointed out in our rapid response “The “HIV” and influenza A virus genomes” (26 July 2003):

(i)                  the quote concerning H1N1 influenza A was taken from a review on the evolution of RNA viruses.

(ii)                The evolution rate of H1N1 may be an exception in comparison with other influenza A viruses.   However, its evolution rate is not an exception regarding RNA viruses in general.  The reviewers obviously considered H1N1 to be a good example in addition to the other RNA viruses they reviewed and we quoted.

 Christopher Noble wrote: “Eleni Papadopulos-Eleopulos is once again extremely confused.  Antigenic change in influenza occurs by two different methods: genetic drift and genetic shift. The former is related to point substitutions while the latter is related to the reassortment of whole segments of the genome. The 0.2% per year that I cited is due to point mutations. In contrast it is genetic shifts that necessitate vaccine changes.”

 Christopher Noble then corrected himself in his rapid response “Re: The HIV and “influenza A” virus genomes: Correction” (29 July 2003) where he wrote: “In my last Rapid response I stated that it is genetic shifts that necessitate changes in the influenza virus. This was not correct.  While genetic shifts are responsible for the major influenza pandemics it is genetic drift that necessitates the more frequent vaccine modifications.”

 Irrespective of which is the truth, he still has not answered our question which is: “…how is it possible to have an "HIV" vaccine when there are differences of up to 40% at any given time in the "HIV" genome?”

 Christopher Noble wrote: “This is not true. The antibody tests have been modified precisely because they have failed to detected some cases of infection with divergent strains. The Vironostika HIV Uni-Form II now includes HIV-1 group O specific peptides.”

 The same antibody tests are used to prove “HIV” infection in everybody.    The Vironostika HIV Uni-Form II is an exception.

 Christopher Noble wrote: “Why does Eleni Papadopulos-Eleopulos continue with this empty rhetorical argument that only demonstrates her ignorance? I have previously given references showing that isolates of HPV show as much as 50% variation at the nucleotide level.  Has she read this article?  Does she want to deny the existence of HPV?”

 We are ignorant of the evidence which proves the existence of HIV.  Would Christopher Noble please enlighten us with some references?   Regarding HPV, John Kirkham’s rapid response “Comparing HPV and HIV” adequately addresses this point.

 Christopher Noble wrote: “But why not focus on influenza A as that is one of the examples she has used? The 'H1' in the nomenclature used to describe influenza A strains such as 'H1N1' refers to subtypes of the hemagglutinin gene. The differences between the subtypes H1-H13 is on AVERAGE 51% at the nucleotide level. (2). The hemagglutinin subtypes are all clearly still hemagglutinin. They all perform exactly the same biological function. The different Influenza A strains are all still Influenza A despite the large genetic variations in the hemagglutinin, neuraminidase and non-structural genes.”

 In his reference 2, the authors wrote: “The hemagglutinin gene is highly variable and can be classified into 13 subtypes (H1-H13) according to the immunological differences in hemagglutinin.  The average nucleotide difference among these subtypes is 51%…Subtypes H4-H13 have been found only in nonhuman species, but the other three subtypes infect humans as well as other organisms.”

 Let us be very clear on this point.   We are not considering genomic differences between immunodeficiency viruses of humans, monkeys, cats, etc.   We are only interested in the genomic variation in one immunodeficiency virus, the “human immunodeficiency virus”.  Neither are we interested in the genomic variation with time, that is, evolution of the genome, but the genomic variation at a given time.

 In his rapid response “Re: HIV genome, clones and sequences” (25 July 2003), Christopher Noble wrote: “She then cites Baba et al (3) as evidence against the hypothesis that it is the nef-deletion that is responsible for slow progression in these cases [Sydney Cohort cases]. In fact, if one reads the article it is evident that there is nothing at all to contradict the conclusions of the Sydney Cohort researchers.  Baba et al found that although infection with nef-deletion mutants did not lead to AIDS in adult macaques the same was not necessarily true in macaque neonates.  They agree 100% that the virus is attenuated by the nef deletion.  They argue, however, that nef-deletion mutants may still cause disease in specific cases such as neonates and as such these live attenuated strains are not suitable for vaccines.

I challenge Papadopulos-Eleopulos to provide any references that provide evidence that nef-deletion mutants are not attenuated.”

 According to Baba et al (1,2) the absence of AIDS in adults given nef-deleted SIV was due to “host factors” and not to the absence of the nef gene: “If virus replication is repressed by any mechanism or mechanisms, disease will not ensure, even if the virus contains the gene or genes that encode virulence.   We postulate that, in macaque neonates, replication of SIVΔ3 [nef , vtr, and NRE deleted SIV] was unrestricted and exceeded the threshold, whereas host factors limited replication in adults...In agreement with Shearer et al, we feel it is premature to consider nef-deleted viruses safe, even in adults.” (1,2)

 In a study entitled “Live attenuated, multiply deleted simian immunodeficiency virus causes AIDS in infant and adult macaques” by Baba et al, the authors wrote: “our findings confirm that the triply deleted SIVmac239Δ3 candidate vaccine retains its ability to cause AIDS, even in adults…Others have described repair or reversion of deleted nef sequences to restore a full-length open reading frame.   In contrast. each of our experimental animals that progressed to disease had proviral DNA that underwent progressive deletions in the nef-3’ LTR region over time.  In fact, we detected a 1:1 correlation between disease progression and the accumulation of additional deletions in this region…Our results indicate that full-length nef is not required for lentiviral virulence in neonatal or adult macaques.”(3)

 In regard to the Sydney Cohort, David Ho and his colleagues wrote: “Two studies, in particular, strongly support the notion that viral characteristics play a critical role in long-term nonprogression.  First, an astute epidemiological observation made by Learmont et al [the Sydney Cohort study] showed that six transfusion recipients of blood from an HIV-1 infected individual have remained clinically well and immunologically stable despite a decade of infection.  Likewise, the blood donor has remained healthy.  The existence of this cluster of long survivors raises the possibility that an attenuated strain of HIV-1 may have been transmitted.  Second, a set of elegant experiments carried out by Kestler et al showed that monkeys experimentally inoculated with nef-deleted SIV exhibited no sign of disease and maintained a low viral burden along with normal CD4+ T-cell counts.  These characteristics are very similar to what we have seen in long-term survivors of HIV-1 infection, thereby prompting us to investigate the possibility that defects in nef may be responsible for the well-being of our long-term survivors…our results would suggest that nef truncation or deletion is not likely to be a common explanation for the clinical stability of these subjects…We therefore conclude that deletion of or gross sequence abnormality within nef is not likely to be a common explanation for the well-being of long-term survivors of HIV-1 infection.” (4)

 In a study published in 2002 by researchers from the USA, Belgium and Australia, the authors wrote: “…we compared virus isolated from patient D36 [the blood donor in the Sydney Cohort study] prior to disease progression in 1995 (D36/95) and after progression but before therapy was initiated in 1999 (D36/99)…Sequence analysis of virus recovered from D36 in 1999 revealed additional deletions in the nef LTR regions, thereby reducing the possibility that restored Nef caused the onset of AIDS…In contrast, the increased cytopathicity of the D36/99 isolate reported here was not caused by a reversion or partial repair of the nef gene.  Sequence analysis showed that the deletion in the nef gene of the D36/99 isolate are even more extensive than that of D36/95.  Furthermore, immunoblot analysis of PBMC infected with D36/95 and D36/99 revealed that the two D36 isolates do not express a Nef protein that could be recognized by a polyclonal anti-Nef antibody”(5)


(1)   Baba, T W, Jeong, Y S, Pennick, D, Bronson, R, Greene, M. F, Ruprecht, R. M. (1995) Science 267:1820-1825.

(2)   Baba, TW, Liska, V, Hu, Y, Rasmussen RA, Penninck, D, Bronson, R, Greene, MF, Ruprecht RM. (1995) Science 270: 1220-1221.

(3)   Baba, TW, Liska, V, Khimani, AH, Ray, NB, Dailey, PJ, Penninck, D, Bronson, R, Greene, MF, McClure, HM, Martin, LN, Ruprecht RM. (1999) Nature Medicine 5: 194-203.

(4)   Huang, Y, Zhang, L, Ho, DD. (1995) J. Virol. 69: 93-100.

(5)   Jekle A, Schramm B, Jayakumar, P, Trautner, V, Schols, D, De Clercq, E, Mills, J, Crowe, SM, Goldsmith, MA. (2002) J. Virology 76:6966-6973.

Competing interests:   None declared