MLV's... Can someone graphically show us and give us definitions?

[SickOfSickness]

On Dr Deckoff's blog someone named Baffled commented "Two things I would love to see developed are a glossary of terms and a family tree of viruses (who is related to whom)."

I thought that was a good point, so I am copying it here... maybe someone will be inspired... maybe it's too early?

 

[Bob]

Summary of MLV-related terminology

MLV = Murine Leukaemia Virus. MLV's are mouse retroviruses that cause cancer in certain mice.

MuLV - MLV's are also known as MuLV's.

mERV - Some types of MLV's are also known as mERV's (mouse endogenous retroviruses), but not all MLV's are endogenous.

XMRV is a human retrovirus and it is similar to (but not the same as) certain MLV's (mouse viruses). XMRV is not an MLV, but it is a human virus, known as an 'MLV-Related Virus' because of its similarities to certain MLV's. XMRV is an 'MLV-related virus' which was discovered in 2006 in prostate cancer patients.

XMRV = 'Xenotropic Murine Leukaemia Virus-Related Virus'
X = Xenotropic
M = Murine Leukaemia Virus (MLV)
R = Related
V = Virus

MLV-Related Virus indicates that XMRV is similar to MLV's (mouse viruses), but it is genetically different enough (i.e. it has mutated) to be classified as human viruses. XMRV has never been found in mice, so far. Human 'MLV-Related Viruses' (e.g. XMRV, PMRV) have now been found in prostate cancer patients and in ME/CFS patients.

PMRV = 'Polytropic Murine Leukaemia Virus-Related Virus' ('PMRV' could be used as a possible informal abbreviation, but it doesn't seem to have been used much):
In the NIH/FDA paper, Alter and Lo discovered new viral gene sequences, similar to XMRV, but which they say are more similar to 'polytropic' MLV's than to xenotropic MLV's. This is why the new virus gene sequences can't be called 'XMRV'. These new gene sequences have been referred to as 'Polytropic-MLV-related viruses'. The prefixes 'Xenotropic' and 'Polytropic' are used describe the behaviour of the MLV viruses (see below for explanation.)

HMRV = 'Human MLV-Related Viruses' = Judy Mikovits unofficially uses this new name for both XMRV's and PMRV's (i.e. 'HMRV' would describe all the known MLV-Related Viruses). It seems that the distinction between P-type and X-type related viruses might not be particularly significant for the purposes of researching ME, and the differences are not clear-cut as the XMRV genome is a hybrid of both Xenotropic MLV's and Polytropic MLV genes sequences.

HGRV = Human Gammaretrovirus = A proposed umbrella term for all human gammaretroviruses. Gammaretroviruses are a category of retroviruses which include MLV's. (XMRV and PMRV are the only known human gammaretroviruses). HIV is a 'lentivirus', not a gammaretrovirus.

Xenotropic (X-type) (XMRV = Xenotropic MLV-related virus):

Xenotropic = Cannot infect the cells of the original host species (i.e. mice) with complete, replicating viruses but can infect another species (i.e. humans) with complete and replicating viruses.

Polytropic (P-type) (PMRV = Polytropic MLV-related virus):

Polytropic viruses can infect both the cells of the original host species (i.e. mouse) and another species (i.e. humans) with complete and replicating viruses.


Extra Note:
Judy Mikovits has reportedly now found both Xenotropic and Polytropic MLV-Related Viruses in the ME patient samples from her original Science study. She sometimes refers to them collectively as 'HMRV'.

 

[Bob]

Phylogenetic Tree

See here for a diagram, extracted from the Alter & Lo paper, of a 'phylogenetic tree' (i.e. a virus family tree) of human MLV-related viruses and mouse MLV's.

Specifically, the diagram shows the relationship between the viral gag gene sequences detected in Alter's paper and XMRV's (XMRV variants) and MLV's.

The viral gag gene sequences from Alter and Lo's paper were detected in blood samples of CFS patients and blood donors and are labelled: CFS type 1, CFS type 2, CFS type 3, BD22, BD26, BD28.

http://www.cfids.org/mlv/phylogenetic-tree.pdf

 

[Bob]

Also, here's my blog entry:

MLV related viruses - a simpler explanation

http://www.forums.aboutmecfs.org/blog.php?b=518

 

[Bob]

hi sickofsickness, is that the sort of thing you were after?

 

[Otis]

See here for a diagram, extracted from the Alter & Lo paper, of a 'phylogenetic tree' (i.e. a virus family tree) of human MLV-related viruses and mouse MLV's.

Specifically, the diagram shows the relationship between the viral gag gene sequences detected in Alter's paper and XMRV's (XMRV variants) and MLV's.

The viral gag gene sequences from Alter and Lo's paper were detected in blood samples of CFS patients and blood donors and are labelled: CFS type 1, CFS type 2, CFS type 3, BD22, BD26, BD28.

http://www.cfids.org/mlv/phylogenetic-tree.pdf

Great stuff Bob. One thing to note is that Lo/Alter's sequences were partial sequences. Would complete sequences change their locations on the phylogenetic tree?

 

[Bob]

Great stuff Bob. One thing to note is that Lo/Alter's sequences were partial sequences. Would complete sequences change their locations on the phylogenetic tree?

Hi Otis, yes, my understanding is that the phylogenetic tree would change depending on what gene sequences are used.
As you said, Alter and Lo only detected gene sequences, and the have not sequenced the whole virus genome.
I understand that the phylogenetic trees are created by a computer program which calculates the position of the viruses on the tree, based on the gene sequences that are entered into the computer.
In the PNAS paper there are 3 different phylogenetic tree diagrams which, in each tree, place the different viruses in slightly different relative positions. I believe that this is due to slightly different sections of the gag gene sequences being used to create each tree. (That's my amateur understanding of it anyway.)