Dear Sergei,

I have viral sequences from acutely infected individuals (~15 per person) that I am testing for evidence of recombination as indirect evidence of multiple variant transmission.  Some sequences have portions of the sequence with significant changes from the consensus in the individual that cannot be accounted for by selection or evolution in the short time they have been infected.  BUT, each parental strain was not necessarily amplified (the hypothesis would be one parent, and one recombinant was amplified).

When I uploaded one alignment into SBP from the first positive time point, there was no evidence of recombination.  If I upload an alignment of sequences from the 1st and 2nd timepoints (6 weeks later), then recombination is supported, and a breakpoint is identified in GARD.  The only difference including the second timepoint is the second parent was amplified, the other additional sequences nearly identical to those from the first. 

The way I understand SBP and GARD, trees are made with different portions of the sequences and if the trees are measurably different than recombination is supported.  With sequences from the first time point, the second half of the alignment would have 2 branches, but not the first.  Would you need 2 in both and sequences moving from one to the other?  Overall my question is, do you need both parents to get positive recombination? 

I don't understand why the first time point would not support recombination, when the second does, when the recombined sequences are identical at the 2 points.  Is it just more sequences? Or the absence of the parent?

I hope this makes sense!  I've included the highlighter plot of the sequences to show you what I mean, F1 is the first timepoint, F2 is the second.

Thank you,
Liz