Would the mystery VP62 XMRV virus please step forward.
The Genbank holds two VP62-XMRV full length sequences. One (DQ399707.1) is from the first XMRV paper Urisman et al. (2006), the second (EF185282.1) is from Dong et al. (2007). The second is two partially overlapping sections of XMRV from VP62 that have been fused together.
There is also however a mysterious third sequence.
What makes this third VP62-XMRV (NC_007815.1) peculiar is why, on the 3rd July 2011, this sequence was update/replaced by a PreXMRV-1 sequence with the accession number NC_007815.2?
The mysterious third VP62-XMRV sequence
PreXMRV-1 had been first mentioned in Paprotka (2011) and speculated by those authors to be a parental virus to a hypothetical virus that would be several switching events away from being the “consensus” 22Rv1-XMRV virus. More on the issues around the missing env gene for the “consensus” 22Rv1-XMRV GenBank sequence can be found here.
Interestingly this PreXMRV-1 sequence that replaced a VP62 sequence, is identical to another PreMXRV-1 sequence (FR871849.1). Both are said to relate to Paprotka et al. (2011). They are both said to be from the same mouse hosts, NU/NU and HSD. And they both have the same identical date, 3rd June 2011.
NC_007815.1
http://www.ncbi.nlm.nih.gov/nuccore/NC_007815.2
FR871849.1
http://www.ncbi.nlm.nih.gov/nuccore/FR871849.1
Two particular details on the entry for the PreXMRV-1 virus, which replaced the third VP62-XMRV virus, do stand out above many others.
Firstly, the locus tag for the gag gene is called "pXMRV-1_gp1". pXMRV1 happens to be the name used for an XMRV plasmid. Is there any relationship?
The second and most significant is for the locus tag on the env gene, which is called "XMVV62_gp4". This is of interest because it is the same name given to the locus tag on the env gene for the VP62-XMRV virus that this PreXMRV-1 virus has replaced.
PreXMRV-1
There have always been questions raised about the PreXMRV-1 virus due to the statement in Paprotka that indicates the use of more than one source for complete sequencing of this punitive virus.
“The complete sequence of PreXMRV-1 was determined from the early passage xenografts, the NU/NU and Hsd strains, and the CWR-R1 cell line.“ – (Paprotka, 2011)
And the failure to provide any details on cloning and identification of PreXMRV-1 despite the inclusion of details for the virus named PreXMRV-2.
"Cloning and identification of Prexmrv2. A fragment of mouse DNA containing the gag leader with the characteristic 24‐base deletion, the 5’ LTR, and flanking mouse DNA was amplified and cloned with the aid of the Genome Walker kit (Clontech). From the flanking sequence, primers C12_1f and C12_4r were developed (Fig. S2) and used in combination with the internal primers shown in Fig. S2 to amplify Prexmrv2 sequences for detection and sequencing." – (Paprotka, 2011)
Furthermore, there is the issue of genome integration of a particular PreXMRV-1 sequence, which appears to be different to these two identical PreXMRV-1 sequences, into a strain of mice not used to create the 22Rv1 cell line. Further details on this can be found here and here.
Where did the 3rd VP62-XMRV come from?
The date on this third VP62-XMRV sequence is the 8th December 2008. The study title is Urisman et al. (2006). It is said to have been a direct submission to the Genbank and part of the CONSRTM NCBI Genome Project.
We have been unable to find if this sequence was ever claimed by a study, but believe that the first reference to it was in Smith et al. 2010. http://www.retrovirology.com/content/7/1/70
Although on the VP62-XMRV entry it states that, “This sequence has been updated”, and despite on the PreXMRV-1 update it says that, “this sequence version replaced gi:89889045”, when attempting to access the gene or protein information for this third VP62-XMRV sequence, there is line that says, “This record was discontinued”.
Considering that the record has the title of the Urisman (2006) paper entered into its details, and the update is for Paprotka et al. (2011) perhaps Dr Silverman, Dr Pathak and Dr Coffin should now explain why a PreXMRV-1 sequence has replaced a VP62-XMRV sequence and what the reasoning is for this replacement?
Studies that we have found to have mentioned or used this third VP62-XMRV sequence are listed below. Use of this now obsolete sequence raises questions about the validity of data derived from it.
STUDIES
Desarrollo de un nuevo sistema de transferencia génica basado en un gammaretrovirus humano.
Daniel Cervantes Garcia
http://eprints.uanl.mx/2687/1/Tesis_Daniel_Cervantes_Garc%C3%ADa.pdf
Susceptibility of the Human Retrovirus XMRV to Antiretroviral Inhibitors: Discussion Robert A Smith, Geoffrey S Gottlieb and A Dusty Miller http://www.medscape.com/viewarticle/729233_4
PCR and serology find no association between xenotropic murine leukemia virus-related virus (XMRV) and autism
Brent C Satterfield, Rebecca A Garcia, Fiorella Gurrieri, Charles E Schwartz. http://www.molecularautism.com/content/pdf/2040-2392-1-14.pdf
Detection of XMRV in normal and tumor tissue of prostate cancer patients from the Southern United States is dependent on specific PCR conditions
Bryan P. Danielson, Gustavo E. Ayala, and Jason T. Kimata
http://ukpmc.ac.uk/articles/PMC3058280
An Endogenous Murine Leukemia Viral Genome Contaminant in a Commercial RT-PCR Kit is Amplified Using Standard Primers for XMRV
Eiji Sato, Rika A Furuta and Takayuki Miyazawa
http://www.retrovirology.com/content/7/1/110
No Evidence of Murine-Like Gammaretroviruses in CFS Patients Previously Identified as XMRV-Infected Konstance Knox, Donald Carrigan, Graham Simmons, Fernando Teque, Yanchen Zhou, John Hackett Jr., Xiaoxing Qiu, Ka-Cheung Luk, Gerald Schochetman, Allyn Knox, Andreas M. Kogelnik, Jay A. Levy
http://www.sciencemag.org/content/suppl/2011/05/31/science.1204963.DC1/1204963s.pdf
Phylogeny-Directed Search for Murine Leukemia Virus-Like Retroviruses in Vertebrate Genomes and in Patients Suffering from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Prostate Cancer
Jonas Blomberg, Ali Sheikholvaezin, Amal Elfaitouri, Fredrik Blomberg, Anna Sjo ̈sten, Johan Mattson Ulfstedt, Ru ̈diger Pipkorn, Clas Ka ̈llander, ChristinaO ̈hrmalm, and Go ̈ran Sperber
http://www.hindawi.com/journals/av/2011/341294/
Disease-associated XMRV sequences are consistent with laboratory contamination Stéphane Hué, Eleanor R Gray, Astrid Gall, Aris Katzourakis, Choon P Tan, Charlotte J Houldcroft, Stuart McLaren, Deenan Pillay, Andrew Futreal, Jeremy A Garson, Oliver G Pybus, Paul Kellam and Greg J Towers
http://www.retrovirology.com/content/7/1/111
“xenotropic” gammaretroviruses and their XPR1 receptor
Christine A Kozak
http://www.biomedcentral.com/content/pdf/1742-4690-7-101.pdf The mouse
Early Events in Retrovirus XMRV Infection of the Wild-Derived Mouse Mus pahari
Toshie Sakuma, Jason M. Tonne, Karen A. Squillace, Seiga Ohmine, Tayaramma Thatava, Kah-Whye Peng, Michael A. Barry and Yasuhiro Ikeda http://jvi.asm.org/content/85/3/1205.full.pdf
