Accompanying data for the paper

This zip file contains sequence alignments (*.phyl) and phylogenetic trees (*.tree) for the PB2 and RBCL protein-coding genes analysed in the paper. It also contains estimates of fitness values at codon sites for the two proteins. The fitness estimates can be used to calculate the relative non-synonymous substitution rate as explained in the paper (e.g. Eq 3.1)

Details of PCRs performed.

<p>400 nM concentrations of primers and 200 nM probes were used in all the TaqMan assays.</p

Details of sequences obtained.

<p>WB = Whole Blood.</p

Alignment between cfs1, MLV006, Pmv15 and Pmv22.

<p>The nine nucleotide differences between cfs1 and the other viral sequences are highlighted.</p

Maximum likelihood tree of gag sequences.

<p>The MLV RAxML tree for gag sequences lying between XMRV primers gagIF and gagIR was developed from the endogenous MLV sequences identified by Jern et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019953#pone.0019953-Jern1" target="_blank">[19]</a>, sequences derived from CFS patients by Lo et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019953#pone.0019953-Lo1" target="_blank">[5]</a> (shown in red and blue) and the sequences amplified in this study (in green). In addition to sequences from the RNA and DNA, “1F_131010” and “1F” are included. 1F_131010 was derived from the amplification of cDNA synthesized from RNA extracted from the tissue culture fluid supernatant of an XMRV culture, kindly provided by Professor M McClure. 1F was derived from the amplification of Balb/c mouse DNA (Sigma). Bootstrap values >50 are indicated.</p

Agarose gel analysis of R2 from experiment 1.

<p><i>gag</i> nested PCR for 80 cDNAs derived from blood donors and controls. Lanes 1A–1H ten fold dilution series of XMRV TCS (Lane 1A equivalent to 5.5×10⁶ to 5.5×10⁻¹ cDNA molecules/PCR – determined by Poisson distribution). Lanes 2A–11H 80 cDNAs derived from blood donor whole blood. Lanes 12A–12H ten fold dilution series of Balb/c DNA 10⁵ pg to 0.10 pg, negative.</p