From Science Express, 31 May 2011.
Konstance Knox1,2, Donald Carrigan1,2, Graham Simmons3,4, Fernando Teque 5 , Yanchen Zhou3,4, John Hackett Jr.6, Xiaoxing Qiu6, Ka-Cheung Luk6, Gerald Schochetman6, Allyn Knox1, Andreas M. Kogelnik2 , and Jay A. Levy5,*
+ Author Affiliations
1Wisconsin Viral Research Group, Milwaukee, WI 53226, USA.
2Open Medicine Institute, Mountain View, CA 94040, USA.
3Blood Systems Research Institute, San Francisco, CA 94118, USA.
4Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
5Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA 94143, USA.
6Abbott Laboratories, Abbott Park, IL 60064, USA.
*↵To whom correspondence should be addressed. E-mail: Jay.Levy@ucsf.edu
ABSTRACT
Murine-like gammaretroviruses (MLVs), most notably XMRV [xenotropic murine leukemia virus (X-MLV)–related virus], have been reported to be present in the blood of patients with chronic fatigue syndrome (CFS). We evaluated blood samples from 61 patients with CFS from a single clinical practice, 43 of whom had previously been identified as XMRV-positive. Our analysis included polymerase chain reaction and reverse transcription polymerase chain reaction procedures for detection of viral nucleic acids and assays for detection of infectious virus and virus-specific antibodies. We found no evidence of XMRV or other MLVs in these blood samples. In addition, we found that these gammaretroviruses were strongly (X-MLV) or partially (XMRV) susceptible to inactivation by sera from CFS patients and healthy controls, which suggested that establishment of a successful MLV infection in humans would be unlikely. Consistent with previous reports, we detected MLV sequences in commercial laboratory reagents. Our results indicate that previous evidence linking XMRV and MLVs to CFS is likely attributable to laboratory contamination.
Received for publication 1 March 2011.
Accepted for publication 16 May 2011.
the details show that this was again not a replication study and used the VP62 clone. Without poitives we are left without the necessary evidence that the assays even work. Lombardi used a Nested RT-PCR. Not Nested PCR or RT-PCR. Which makes a great deal of difference to results. After that the conditions would not be the same either.
This is why
If anyone is wondering why an assay that can find a low copy number of the VP-62 clone can’t find wild-type virus, the answer is relatively simple.
The chemophysical properties of the DNA are different
high levels of oxidative stress caused by HGRV infections and commonly found in studies investigating patients with ME cause oxidative modification of nucleotide bases. The most common is the addition of a hydroxyl functional group or deamination. This (for reasons involving sterochemistry and something called twisting) means that the stacking energy and hydrogen bonding which hold complimentary nucleotide bases together are dramatically reduced. This can be compensated for by using increased levels of magnesium and lowering annealing temperatures. Another strategy is to use an RNA template to begin with. MLV viruses can’t replicate in resting cells so xmrv will exist in such cells as preintegrative complexes and integrated highly methylated proviruses. ROS oxidation induces a pattern of base substitution or inversion in the provirus affecting primer annealing.The presence of certain oxidised bases or even abasic sequences can stop taq polymerase “in its tracks” leading to an absence of product.Unless PCR reagent concentrations and cycling conditions are adjusted accordingly the virus will escape detection. silverman was able to adjust his assays to find gag sequences which were already present and was fortunate enough to isolate XMRV from RNA hence largely avoiding these issues
The effect of activating PMBCs would be to allow the integration of “fresh” proviruses as the preintegrative complexes are nowhere near as prone to oxidative damage. This would also allow the creation of viral RNA