No significant evidence for recombination was found in the other strains or genes. We compared our result to the outcome of the screening performed by Yun et al. [16] that identified 11 recombinations within the 39UTR and the 39 end of the NS5 region, but did not include a LIV strain. Their observations could only be replicated when we used exactly the same settings, i.e. when detection was performed on ClustalW [40] aligned sequences, without Bonferroni correction for multiple comparisons. This suggests that the previously reported signal was not strongly supported and could have been caused by alignment problems, as UTRs are notoriously difficult to align due to spontaneous variations in length during laboratory passages [41, 42] .