Jeffrey L Evans,
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Although it was nice to hear from Brian Foley after a long suspension of our discussion, I'm not sure why he chose to do so privately, rather than post here. His comment on one line of my previous post follows:
>>"It was not to be - I'm still without an example of another genome-insinuating, exogenous, infectious entity."
>What are you talking about here???
>Several hundred different exogenous retroviruses have been characterized in detail:
>HTLVs, STLVs and a few other T-cell leukemia viruses are certainly exogenous. They, like the lentiviruses are "complex" retroviruses with regulatory genes in addition to the Gag-Pol-Env genes found in all retroviruses. So far, nobody has ever found a complex retrovirus in an endogenous state (found in the germ-line DNA).
>There are many exogenous retroviruses of livestock and fowl that are of huge economic importance in the agricultural industry. The Avian Leukosis/Sarcoma Viruses are just one example. Look up all the research that has been done in recent years on the "J subtype" of ALV for an introduction.
This is quite similar to the response I received from Brian two years ago, quoted below, and in both instances I probably did not make my context sufficiently clear, having occupied it for so long. My apologies, but I meant an example of an exogenous human retrovirus which would be accepted by both sides of the "isolation and characterization" issue. Otherwise, examples like HTLV are just an instance of using a thing to prove itself, depending upon your perspective.
Assuming agreement on an "old style" centrifugation - EM - characterization retroviral candidate as a starting point, it might be more interesting and relevant to begin comparing the degree of variability scattered around the consensus genome of HIV and the mutually acceptable example. At least it would be more interesting to me than another repetition of the HPV to HIV comparison.
Having now taken the time to read some posts here from previous months, I'm reminded that no such mutually agreed example exists. For starters, Brian Foley does not concede that ANY human retrovirus has been identified by the full Pasteur Institute protocol championed by the Perth Group, nor, does it appear, do they. Which leads inevitably to the question of whether any exogenous human retrovirus has yet to be discovered.
In the process of giving up on this attempt to find common ground, I was struck by a consistency across two years which somewhat surprised me. Mr. Foley still claims the absence of a particular retroviral type sequence in the germ line as sole and sufficient proof of exogenous origin, just as he did two years ago.
Brian Foley, 7/16/2001:
"Endogenous viruses are by definition in the germ-line. Exogenous viruses might enter either the germ-line DNA, somatic cell DNA, or both. If an exogenous virus entered the germ-line DNA, and then the cell(s) which were infected were successfully fertilized and developed into complete organisms which could reproduce, the virus would now be said to be endogenous in those individuals descended from the infected germ- line cell(s)."
"Most viruses do not enter the host genome at all, germ-line or somatic cell. Most viruses which do enter the somatic cell DNA, are observed to very rarely enter the germ-line DNA and become endogenous. "For example, there is good evidence that HTLV-I and HTLV-II have been infecting humans and other primates for hundres of thousands of years, and yet there is no evidence of any HTLV or STLV in the germ-line of any primate. Likewise we have no exact count, but we can estimate that there at least thousands of different retroviruses on earth, and eukaryotes have been living with these retroviruses for hundreds of millions of years, and in that time several hundred of the retroviruses have become endogenous."
"So we observe hundreds of endogenous retroviruses in the human genome. Most of them are present in many copies which are either thought to be, or have been proven to be, duplicated after entry into the germ-line, rather than each copy representing a seperate capture of an exogenous virus. None of the human endogenous retroviruses has been shown to have been captured into the human germ-line in the last 100,000 years. All are thought to have entered the primate germ-line millions of years ago, some have relatively solidly known dates of entry, based on the observation that chimpanzees, humans, and gorrillas have them incorporated into the same genomic location but other primates which diverged before the lineage leading to humans and gorrillas diverged do not have this endogenous virus."
I probably shouldn't start something I may not have time to finish, so anyone with the latest research on HERVs would be greatly welcome. However, I was not aware of any lingering controversy regarding the existence of internally generated retroviral type sequences which do not originate in the germ line. If that's not endogenous (by definition), what other word is available?
Competing interests: None declared