Intra-population genetic diversity of CHIKV.

<p>Minimum spanning trees were used to depict the intra-population genetic diversity of CHIKV. Each panel represents all the clones sequenced in one region of one virus passage from one method: (<b>A</b>) E3/E2 region of the Φnsp4 virus passaged in C6/36 cells, (<b>B</b>) E3/E2 region of the Φnsp1 Φnsp4 Φenv virus alternatively passaged, and (<b>C</b>) E1 region of the Φnsp1 Φnsp4 Φenv virus serially passaged in Vero cells. Each circle represents one variant and its size corresponds to the number of clones with the same nt sequence. The original sequence is represented by the biggest circle except in panel (c) where it is the circle at the top. Mutation positions are indicated in each branch. For the point mutations, the nt present in each viral population is shown. For the 6 nt deletion found in the viruses serially passaged in C6/36 cells at nt positions 8556/61 (panel <b>A</b>) which was considered as a unique event, (i) the word ‘Del’ indicates that it is present in the nearest viral population, (ii) no modification compared to the original sequence are represented by U, (iii) C and A indicate the presence of the 8566u>c and 8566u>a mutations, respectively.