nCoV's relationship to bat coronaviruses & recombination signals (no snakes) - no evidence the 2019-nCoV lineage is recombinant

Hi,

I have added the 2013 Yunnan bat sequence (much more closely related to the Wuhan2019-2020 virus than are the XC21 and ZC45 viruses) and built trees from complete genomes and some subgenomic regions chosen based on similarity plots.

57_Wuhan_Simplo800t_JP

From this type of data, we cannot say which viruses are “recombinant” and which are “pure”
or never recombined in their history. It is only clear that recombination has been happening in the evolution of these viruses.

My alignment is built from a sampling of complete genomes of only the SARS and “SARS-like” subclade of the Betacoronaviruses. It does not include MERS or other Betacoronaviruses. For the SimPlot (Stuart Ray software) I first gap-stripped the alignment.

I am now running an RDP4 (Darren Martin software) alignment on the gap-stripped set, and it is finding a lot of recombination. The recombination events that I found evident in SimPlot are also detected in RDP4, but I am a new user of RDP4 and it will take me a while to get up to speed with using it.

Brian Foley
HIV Databases at LANL

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Just to be clear our first post on Jan 22nd was to highlight there’s no evidence the new human lineage nCoV was recombinant, rather the, at that time, known to be related bat coronaviruses are clearly the recombinants. Since then a pre-print has come out from Wuhan-based researchers with senior author Zheng-Li Shi: https://www.biorxiv.org/content/10.1101/2020.01.22.914952v1 including a similarity plot. In this very important study Zhou et al. report a closer bat coronavirus to the nCoV lineage, RaTG13, in all of its genome confirming the nCoV lineage is not recombinant. The bat coronaviruses are themselves recorded to be frequently recombinant in the published literature so while interesting this is not a new finding. Update, Zhou et al’s paper is now available in Nature: https://www.nature.com/articles/s41586-020-2012-7.

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