New WPI and CDC XMRV sequences in genbank

[Bob]

Well the cdc found it but they're adamant it's not in CFS patients...:headache:

They are unable to detect XMRV in the blood though, even in confirmed XMRV-positive prostate cancer patients...
So if they are unable to detect XMRV in the blood of prostate cancer patients, why are they so certain that they should be able to detect XMRV in the blood of CFS patients?
You'd think that they might ask themselves a question like that! Maybe they will though. I was very impressed with the wording of their prostate cancer study, and they did seem genuinely interested in investigating XMRV further.

 

[Kati]

how about looking for "it" in CFS patient's tissus... Sigh... hurry up already!!!

 

[alex3619]

Hi, a point is being missed here. Protein sequences are partially conserved, or the protein loses function. The underlying genetic sequences may vary a lot more than the amino acid sequences might indicate. Bye, Alex

 

[currer]

Hi,
From my posting on another thread,

The recent Switzer CDC paper found a widely varying replicating virus.
"The gag sequences from patient 5956 clustered with XMRV sequences from a prostate cancer patient (Vp88), a xenotropic mERV found on mouse chromosome 8, and a PMLV sequence found in a blood donor (BD28) by Lo et al."

 

[insearchof]

Hi, a point is being missed here. Protein sequences are partially conserved, or the protein loses function. The underlying genetic sequences may vary a lot more than the amino acid sequences might indicate. Bye, Alex

Hi Alex

This sounds interesting, can you expand a little on your comments?

Our lab is recognized for our research on a similar gammaretrovirus isolated from nonhuman primates, gibbon ape leukemia virus (GALV). GALV is the only gammaretrovirus other than xmrv found in primates. In collaboration with Frank Ruscetti at the NCI, Bill Switzer at the CDC and Suzan Winfield and Jessica Siegal-Willcot at the National Zoo, we are investigating the source animal for xmrv, and screening gibbon apes in US zoos for the presence of GALV and xmrv.

Speaking of interesting.....I will be keen to see the NIHs research on XMRV in Monkeys to see how much sequence diversity they find there
and how it compares to the sequence diversity of XMRV in humans. Though what such findings might tell us, is any ones guess.....but hopefully we will know a little more by then.

 

[Bob]

Hi,
From my posting on another thread,

The recent Switzer CDC paper found a widely varying replicating virus.
"The gag sequences from patient 5956 clustered with XMRV sequences from a prostate cancer patient (Vp88), a xenotropic mERV found on mouse chromosome 8, and a PMLV sequence found in a blood donor (BD28) by Lo et al."

So do we know what this means, exactly?

 

[currer]

Well I'm going to have to guess.
Patient 5956 gag sequences are on the first post in this thread. There are 361 codons found for this part of the retrovirus.
I assume that some sections of these codon sequences are the ones quoted as being similar to other sequences found previously by earlier researchers.

 

[Bob]

Well I'm going to have to guess.
Patient 5956 gag sequences are on the first post in this thread. There are 361 codons found for this part of the retrovirus.
I assume that some sections of these codon sequences are the ones quoted as being similar to other sequences found previously by earlier researchers.

So is Switzer saying that one of his new variants of XMRV has a closer similarity to one of Lo's PMRV's than any previous versions of XMRV?

 

[currer]

I think Switzer is saying that some sections of this gag sequence are similar to three separate previously discovered sequences from three different patients. ie. this gag sequence from patient 5956 has similarities across its' length to three other sequences found in three other patients.

It is not similar to one virus but similar in different parts to three other virus sequences found by various other researchers.

But yes he does admit that one of the sections he found on it is similar to Lo's pMLVs

(Edit. Ive just re-read the paper and the above is wrong. Sorry.
The entire sequence is similar to those three sequences.)

Does this make sense? I am on a learning curve here and would not want to mislead anyone.

Bob that quote came from Switzer's paper you spent a lot of time on last week. It was from the part where he discusses the sequence findings in detail. He discusses most of the found sequences, I think, if you want to look it up.

This is why that paper was so interesting. Because the XMRV Switzer found is very variable and seems to have mutated a lot, something contamination could not do. And he admits this.

 

[Bob]

I think Switzer is saying that some sections of this gag sequence are similar to three separate previously discovered sequences from three different patients. ie. this gag sequence from patient 5956 has similarities across its' length to three other sequences found in three other patients.

It is not similar to one virus but similar in different parts to three other virus sequences found by various other researchers.

But yes he does admit that one of the sections he found on it is similar to Lo's pMLVs

Does this make sense? I am on a learning curve here and would not want to mislead anyone.

Bob that quote came from Switzer's paper you spent a lot of time on last week. It was from the part where he discusses the sequence findings in detail. He discusses most of the found sequences, I think, if you want to look it up.

This is why that paper was so interesting. Because the XMRV Switzer found is very variable and seems to have mutated a lot, something contamination could not do. And he admits this.

Thanks for the info currer...

I was being a bit lazy, and didn't want to re-read the Switzer paper in detail!

More bed-time reading!

 

[omerbasket]

OK, I see now...from the XMRV Buzz article:





So: even sequence variability will have a counter-argument that such variability can be introduced during the culturing process.

And if it would be a biggerr sequence variablility - sequences that would be "only" 84%-96% (mostly about 95%) identical to VP62 - people like McClure and others would say that it is not the same virus (despite that fact that there are strains of HIV-1 that are "only" 85% identical to one another, and strains of HCV that are "only" 79% identical to one another).

 

[alex3619]

Hi Alex This sounds interesting, can you expand a little on your comments?

Hi insearchof. Amino acid sequences are the cutting edge of the biology - if they change too much the protein does not work, and the virus is non-viable. This does not mean they can't evolve, or gain new proteins through crossing with other viruses.

Each amino acid has a DNA or RNA code. That code can vary. The code can mutate several times, and still give the same amino acid. So the DNA can keep changing, but the viability of the virus is dependent more on the amino acid sequences - just tracking amino acid variation does not give a complete picture on the underlying genetic drift.

Amino acid substitutions with similar amino acids are less destructive than complete changes. Proteins often retain function in the new amino acid is very similar, although they can lose efficiency.

I have been thinking this is a small virus with limited genetic material, and limited options for variation compared to big viruses. This could mean that the expected rate for variation on large viruses is not valid for such a small virus. It just a thought, don't know if this last point is true or not.

Bye
Alex

 

[LJS]

What WPI is finding is very, very similar to VP62. I wonder if you cultured VP62 a few times if you would get basically what the WPI is finding.

Do the following steps to look for yourself..
1) go here: http://www.ncbi.nlm.nih.gov/nuccore/JF907638.1
2) Click 'Run BLAST' on the upper right
3) Click BLAST, the blue button at the bottom of the page

VP62, VP42, and 22RV1 is 99% similar to the WPI sequence...

I think these sequences hurt there case on XMRV and I find it hard not to think WPI's lab is contaminate with VP62 at this point. Why would others not be able to find XMRV if the XMRV the WPI is finding has so little variability from VP62? Other labs including Singh's lab have demonstrated that they can easily pick up VP62, there is basically no difference between VP62 and what the WPI is finding.

 

[eric_s]

There are different values here. What's the difference between your analysis, LJS, and the one i've linked to? Why the different result?

 

[Ecoclimber]

Maybe because:

181 ccacggacac ccggatcagg tcccatatat cgtcacctgg gaggcacttg cctatgaccc 181 acggacaccc ggaccaggtc ccatatatcg tcacctggga ggcacttgcc tatgaccccc
​

That is not how you do sequence alignments. You don't get good sequence until 20. Figuring out how to align 200 sequences that all have different start points would be maddening. That's why you have programs like Sequencher. This makes it a bit easier to see:
181 ccacggacac ccggatcagg tcccatatat cgtcacctgg gaggcacttg cctatgaccc
181 acggacaccc ggaccaggtc ccatatatcg tcacctggga ggcacttgcc tatgaccccc
becomes:
183 acggacac ccggatcagg tcccatatat cgtcacctgg gaggcacttg cctatgaccc
181 acggacac ccggaCcagg tcccatatat cgtcacctgg gaggcacttg cctatgaccccc

for sequences 1301 and 1302
because you couldn't fit everything into one screen shot, but that particular sequence is ~840-890, with the C I emphasized above clearly visible at 846. Its the only difference between VP62 and the 11 'new' sequences in that region.

 

[kday]

http://blast.ncbi.nlm.nih.gov/Blast...aBlast&LINK_LOC=nuccore&PAGE_TYPE=BlastSearch

Click here and run a blast by clicking the button "Blast" at the bottom and then you will be able to select between the 11 strains.

 

[LJS]

Here is another of WPI's sequences, this one is even more clear. It is really hard to come to any conclusion other than the WPI is finding contamination; see how the below cell line is 100% identical to 22RV1 which has already shown to be a contaminated lab cell line. If it was not a contaminate and a replicating virus from a human it should be significantly different from 22Rv1 or any of the other lab cell lines; like VP62, VP42, and VP35. If you take any one of these 11 sequences from the WPI independently and BLAST them you see they all line up basically identically with one of the know lab cell lines.
http://www.ncbi.nlm.nih.gov/nuccore/JF907639.1?report=GenBank

 

[currer]

OK so we have a variable retrovirus in prostate cancer, and one that isnt varying enough in ME/CFS!

I am going to the Invest in ME Conference in London tomorrow, J. Mikovits will be there, giving a talk along with other researchers.
I can ask her about this.
Any questions anyone? I'll put them forward for you.

I agree, at the moment things dont look good for XMRV and CFS.

 

[eric_s]

I've followed this link http://blast.ncbi.nlm.nih.gov/Blast...aBlast&LINK_LOC=nuccore&PAGE_TYPE=BlastSearch and run the program. They're not all identical to VP-62. I agree most of them seem to be very close to known sequences, but it's not to the same sequence in every case. And then, in many cases "query coverage" is not 100%, so what about the missing %? Also these new sequences seem to be only a small part of the entire genome, so is it possible to say anything after looking at them? Might not the rest of the genome show greater differences to the sequences that seem to match those parts?

And i'm no biologist or anything like that, so i don't even want to start running BLASTs and things like that, it just doesn't make sense, as i don't know anything about it, probably i will only come to wrong conclusions.

We need people who know what they are talking about analyze these things.

 

[eric_s]

OK so we have a variable retrovirus in prostate cancer, and one that isnt varying enough in ME/CFS!

I am going to the Invest in ME Conference in London tomorrow, J. Mikovits will be there, giving a talk along with other researchers.
I can ask her about this.
Any questions anyone? I'll put them forward for you.

I agree, at the moment things dont look good for XMRV and CFS.

Yes, please ask her, if you can. But i would not draw that conclusion (your first line) yet, after what i've seen here, and also don't forget about what Lo et al. found. So i wouldn't say there's no variation.