The recombination breakpoints in our analysis are from an analysis with GARD in the Hyphy package using the 11 sequences listed in the diversity plot. In recombination analysis the exact locations of breakpoints detected will differ depending on the reference sets used and the method/software used. There’s also other recombination events in the bat coronaviruses (widely reported) that could be causing issues and we detected these both with GARD and RDP. This post’s purpose was to focus on the nCoV lineage. We will provide full details of our analysis in a pre-print very soon.