First dozen post-Polynesia genomes

Continuing the discussion from Initial Zika Phylogeography:

NJ tree, TN93. Rooted on PF genome.

Probably not enough variability to really say - but not quite the structure I’d have guessed. Haiti is 2014.

Thanks Derek. This is similar to the tree I got. Looking at this, it seems plausible that Zika was spreading in Brazil before May 2015. Also likely multiple introductions into Brazil (although could be multiple exports). @nuno_faria has some estimates in this post -

Wonder how the first of the_ WHO Zika Open_ papers squares with potentially earlier introductions. I confess I’ve read it a few times and am struggling to understand it. Are they saying that microcephaly increases began as long ago as 2012, or are they saying that the microcephaly rate has always been higher than the received wisdom?

TMRCA is shifting slightly earlier with latest data. Will post update soon.

This is a very interesting result. We should consider that Brazil could be the first country to detect the ZIKV circulation, but not necessary the entrance point of ZIKV in the Americas. At the same time is possible to note that the American clade displayed a low support. When we added the Brazilian sequences KU321639 to our analyses the support of the American clade is also reduced. That sequence may have some editing problems?