Brian T Foley,
Los Alamos National Lab, Los Alamos, NM 87545 USA
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discussing the variability observed in HIV-1 M and O group genomes
compared to the variability in the genomes of other RNA viruses, the
Perth group wrote:
Can you please give us the name of two or three of these virologists who claim that RNA viruses don't differ by more than 1%?
On April 25th the Perth Group wrote:
On July 18th the Perth Group wrote:
On 21 August the Perth Group wrote:
It has been repeatedly pointed out to the Perth group, for example on Sept 5th by Chris Noble:
The figure of
1% refers to a study by Cattaneo et al. It refers to the intrahost
variation of the M protein coding sequence of the Measles Virus in the
brain tissue of patients suffering from SSPE.
that all RNA viruses are highly variable, and that the lentiviruses are not exceptional in their variability. Yet the Perth group continues to claim that there are virologists who claim that RNA viruses do not differ by more than 1%.
On Sept 22 the Perth Group wrote:
Steinhauer and Holland, are discussing "stabilizing forces" or negative selection, which is selection pressure on an organism to remain the same over time. The opposite forces are called positive selection, such as selection pressure by the host immune system to eliminate viruses that remain unchanged and allow mutant viruses to become dominant in the population. Both forces are operating on all viruses that are exposed to host immune systems, however a virus like the human influenza virus jumps from one host individual to the next before the first host individual has mounted much immune response. Retroviruses on the other hand remain in an infected host for life, and must evade the host immune response over a longer period of time.
A huge amount of work has been done in characterizing the evolution of lentiviruses both within a single host individual and over great distances of time (1-6). The results prove beyond any reasonable doubt that HIV-1, HIV-2, SIV-AGM, SIV-CPZ, SIV-SMM, FIV-Puma, FIV-housecat, EIAV and other lentiviruses are exogenous, rapidly multiplying retroviruses which face relatively strong selection pressures from their host's immune system. The env gene of HIV-1 is observed to evolve at roughly twice the rate of the gag gene of HIV-1, because the env gene is selected by both antibody (humoral response) and CTL (cellular response) host immune responses, while the gag gene is selected primarily by only CTL responses.
Viruses in freezers, or grown in cell culture, do not face the same immune selection pressures, which is why it was possible to determine that the H1N1 influenza virus which made a reappearance in humans in 1977 had been "dormant" and not circulating in man, bird or other animal during its 27 years of absence from the human influenza pandemic (7).
Endogenous retroviruses also do not evolve rapidly over time. The endogenous retroviruses found in chimpanzees and humans are nearly identical, despite the several millions of years of time seperating us from our most recent common ancestor.
1: Yang W, Bielawski JP, Yang Z.
2: Rodrigo AG, Mullins JI.
3: Ross HA, Rodrigo AG.
4: Halapi E, Leitner T, Jansson M, Scarlatti G, Orlandi P,
5: Howe L, Leroux C, Issel CJ, Montelaro RC.
6: Barouch DH, Kunstman J, Glowczwskie J, Kunstman KJ,
7: Laver WG, Webster RG, Chu CM.
Competing interests: None declared