To build on @dpark 's point, I'd also be mindful of sequencing artifacts when using the new Brazilian sequences for analyses. Given the high similarity between different isolates (>99.5%) even a small number of sequencing artifacts could be problematic. For example, KU321639 has an insertion at 10,446 in a 6C homopolymer that is almost certainly an artifact.
I'm not sure if this is true throughout S. America, but my understanding is that Ion Torrent is the most popular platform in Brazil in part because of a solid supply chain and better sales/marketing/support. Anecdotally, I've had a lot of problems with my collaborators getting Illumina supplies to Brazil in a timely manner. So I'd expect a lot of the upcoming sequenes from Brazil will be Ion and should be carefully evaluated for artifacts.