Codons and HIV

Brian Foley btf at
Mon Mar 16 15:01:41 EST 1998

TRKeske wrote:
> ... much mis-information deleted
> The only problem is that HIV-1 has (a-hem) 401,231 codons.
> The total possible combinations, I estimate, are on the order
> to 10 to the 308-th power.

	The HIV-1 genome is less than 10,000 bases in length.
There are closer to 4,000 codons than 400,000.

>  However, the subtype
> O virus was SIGNIFICANTLY closer to SIV, genetically,
> than the other known strains, and there is also significant
> genetic difference between HIV and SIV.  

	Sorry, wrong again.  HIV-1 M group and HIV-1 O group
viruses are approximately equal in their distance from the
two Chimpanzee SIVs which have been studied.  Likewise these
two Chimpanzee SIVs are equally divergent.
	HIV-2 is more closely related to SIVs from other 
primates, than to either HIV-1 or to Chimpanzee SIVs.

> ...
> The odds against  a large number of mutations all moving back
> to older strain would be astronomical.  It is similar to the fact
> of how human beings may surely continue to evolve into many
> different forms, but never precisely into monkeys.

	There is no such thing as "older strains" HIV strains
are here today and so are SIV strains.  Humans are alive today 
and so are monkeys.  We are all equally old.
	You are correct to guess that we tend to diverge over
time.  HIV and SIV continue to evolve in different directions,
and so do humans and monkeys.

> ...
> For example, an HIV subtype was found in Thailand in 1996
> that spreads much more easily through heterosexual intercourse.

	There is no solid evidence that HIV-1 subtype E is
any easier to transmit heterosexually than any other subtype
of HIV-1.  

> The subtype grows much more easily in the female reproductive
> tract than does the HIV subtype that currently predominates in the
> U.S.

	Not true.  All subtypes of HIV have been found to
infect the Langerhans cells.  There is more variablility
between different isolates of one subtype (in their ability to
infect these cells) as there is between any two subtypes.

> ...
> It would seem to be advisable that we continue studying
> these issues, until we can be confident that we have a
> very good handle on them.

	Keep on studying....
> Tom Keske
> Boston, Mass.

|Brian T. Foley               btf at                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos National Lab     |
|Los Alamos, NM 87544  U.S.A. |

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