S seems unlikely. Another notable characteristic of the XMRV clade is
S seems unlikely. Another notable characteristic of the XMRV clade is its asymmetry (B 1 asymmetry statistic = 24.47, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28242652 p < 0.002). This is an expected property of families of endogenous mobile elements [23]. Phylogenetic asymmetry implies that whenever replication occurs, one daughter sequence tends to be inactive whilst the other continues to proliferate. This phenomenon arises naturally when one (or a few) active endogenous viruses in a genome generate inactive copies by re-infection [23], but is difficult to explain under a hypothesis of host-to-host transmission. Extreme cases of strong selection among genetically diverse variants can cause asymmetry [28], although in this case, the lack of XMRV genetic diversity is incompatible with this possibility. Whilst our observations cannot conclusively prove that XMRV is not a human pathogen they appearconsistent with the hypothesis that XMRV is not an exogenous virus transmitting among individuals. Instead, multiple lines of evidence suggest that the full length clones of XMRV originated from the 22Rv1 cell line. PCR contamination could arise directly from 22Rv1 cells or from cells inadvertently infected with the 22Rv1 derived virus. We speculate that the 22Rv1 cells became infected with XMRV during their passage through athymic mice [29]. Data in Figure 1 demonstrate that mouse DNA could also contaminate patient samples as a variety of mice PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26552366 encode sequences, with endogenous MLV proviruses, that are detected with PCR protocols that are designed to detect XMRV. It is quite possible FCCP site therefore that previously published findings are explained by contaminated PCR where the patient samples were contaminated by mouse DNA or DNA from cells infected with MLV-X including that from 22Rv1 cells. A recent study amplified polytropic MLV sequences rather than XMRV from chronic fatigue patient samples [30] and healthy donors. Unfortunately the MLV sequences described there were too short to carry out a thorough phylogenetic analysis, and we have therefore not included them here. It is difficult to retrospectively establish whether prior studies have contaminated patient samples. Importantly, assay contamination cannot be assessed by detection of murine DNA alone since MLVs contaminate a significant proportion of nonmurine cell lines common in laboratories [1,30]. PCR contamination has previously been found to underlie erroneous association between retroviruses and human disease underlining the difficulties associated with detecting pathogens by PCR [31,32].Pairwise Genetic Distance (nucleotide substitutions per site)0.0.0.012 0.Conclusions We conclude that future screens for MLV-related sequences use more rigorous PCR containment procedures, such as those used to reliably recover ancient DNA [33], or manage contamination by controlling for its inevitable frequency, for example by screening equal numbers of controls prepared and stored identically, together with test samples [34]. Positive samples must be sequenced and those that are identical to known endogenous murine sequences, or plasmids present in the host laboratory, should be treated with caution. Whilst true association of XMRV with human disease would be of great medical importance, it is imperative that such an association is rigorously established before it impacts on diagnosis and patient care. We suggest that XMRV as a human virus does not conform to this criterion. MethodsTaqman PCRPCR of mouse genomic DNA was performed using primers/probes a.
