Competition assays comparing the relative fitness of homologous and nonhomologous recombinants.

<p>Each of the four nonhomologous selected CV-B4/MAD4 recombinants presented in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005266#ppat.1005266.t002" target="_blank">Table 2</a> were competed against the homologous recombinant CV-B4/MAD4 B.38, the recombination site of which is located in the spacer between IRES domains dIII and dIV (CV-B4 nt 240 / MAD4 nt 234) (A to D), and against the parental cVDPV MAD4 (E to H). Viruses were mixed at a 1:1 ratio and HEp-2c cells were inoculated in triplicate at an MOI of 0.01 TCID50/cell for three passages. At each passage, the progeny RNA was amplified by RT-PCR and the relative amount of each competitor was evaluated by measuring the intensity of the bands on agarose gel electrophoresis (ImageJ 1.47 software, NIH) corresponding either to the nonhomologous recombinant or to its homologous competitor. The ratio of band intensity for the nonhomologous recombinant versus the homologous competitor is shown for each well for the three passages (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005266#ppat.1005266.s006" target="_blank">S6 Fig</a>). An increase in this ratio indicates that the nonhomologous recombinant is more fit than the homologous one. Error bars indicate the standard deviation (Student’s t-test, n = 3; *<i>P<0</i>.<i>05</i>, **<i>P<0</i>.<i>01</i>, ***<i>P<0</i>.<i>001</i>).