nCoV-2019 Spike Protein Receptor Binding Domain Shares High Amino Acid Identity With a Coronavirus Recovered from a Pangolin Viral Metagenomic Dataset

SARS-CoV-2 coronavirus nCoV-2019 Evolutionary History
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Recombination does look like something coronaviruses do in the extreme! The new more complete pangolin virus genome from Xiao et al of the South China Agricultural University seems to confirm this, see https://www.biorxiv.org/content/10.1101/2020.02.17.951335v1. Note, the 'as close as 1%’ they reported in their press release for the pangolin virus was misleading as other viruses are also very close in the region they reported as 1% similar, see their Table 1:

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(annotations in red added by Xiaowei Jiang). It is still an interesting paper. The evidence is definitely accumulating that the pangolin is the intermediate host.

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Does SimPLot ignore gaps in alignments?

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I used a gap-stripped alignment for my similarity plots. So yes, the simplot I posted ignored gaps, because they were already stripped out.