Shared mutations detected in complete genome consensus sequences and in viral sub-populations via cloning.

WT, Φnsp4 and Reenc3 represent the passaged WT, Φnsp4 and Φnsp1 Φnsp4 Φenv viruses. Viruses are represented by their name followed by ‘VERO’ for serial passages in Vero, ‘C6/36’ for serial passages in C6/36, and ‘ALT’ for alternate passages. All the mutations detected in complete genome consensus sequences during the passages were used (Table S4 in Text S1) as well as those used for the analysis of intra-population genetic diversity (Figure 8 and Figure S6 in Text S1).5′UTR designates the 5′ untranslated region.