We are sharing our initial analysis of the new #Wuhan #coronavirus (with @robertson_lab): #nCoV’s relationship to bat coronaviruses & recombination signals. Full analysis is here on virological: virological.org/t/ncovs-relati… @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett 
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett Focus of our analysis is on the Wuhan-Hu-1 virus (accession no. MN908947, released on GenBank by Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai, China) as all nCoV cluster together so will share the same evolutionary ancestry. 1/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett It’s clear from phylogenetic analysis the new human virus is most closely related to bat coronaviruses in the Betacoronaviruses genera. 2/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett While this is apparent from both the previously reported BLAST and full-genome phylogenetic analysis the closest related bat viruses (CoVZC45 and CoVZXC21) are in fact recombinants with shared breakpoints either side of ORF1b: (attached pic) 3/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett The phylogenetic clustering of the Wuhan-Hu-1 virus is consistently as a sister group to the SARS-related bat coronaviruses. Interestingly, a third bat coronavirus (Longquan_140) is a recombinant involving the Wuhan virus lineage in part of ORF1a. 4/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett This analysis has detected three bat coronavirus recombinants (two with shared breakpoints) involving the nCoV lineage indicating greater diversity in the Chinese Sarbecovirus group than previously appreciated. 5/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett The clustering of the related Sarbecovirus viruses from Kenya and Europe suggest the Wuhan virus is still part of the Sabecovirus sub-genre, and these recombination events probably occurred in bats. 6/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett Although. given the propensity of coronaviruses to switch hosts, involvement of another species cannot be discounted. 7/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett There is also a very good chance that a non-bat intermediate species is responsible for the beginning of the current outbreak in Wuhan. Given the tight clustering of the nCoV viruses in phylogenetic trees it seems most likely one event has occurred. 8/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett Several of these bat coronaviruses have been previously detected to be recombinant under-scoring the importance of doing appropriate analysis when analysing these viruses using phylogenetic methods. 9/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett Recombination, in this case between divergent coronaviruses circulating in bats, violates our assumption of a single evolutionary tree and so needs to be considered carefully when inferring coronavirus evolution from complete genome alignments. 10/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett We’re looking into the patterns of breakpoints to see if there’s any clues to the significance (or not) of these recombination events. 11/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett We’d like to thank the researchers and health professionals for making the nCoV data available. 12/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett Credit also needs to be given to the surveillance projects for generating the data that is now available for comparison and to the software developers for making the tools we’ve used freely available: 13/n
@robertson_lab @MackayIM @FluTrackers @HelenBranswell @Laurie_Garrett FigTree, available at: tree.bio.ed.ac.uk/software/figtr…; 2 GARD, available at hyphy.org; MAFFT, available at mafft.cbrc.jp/alignment/soft…; PhyML, available at atgc-montpellier.fr/phyml/; 2 and RDP4, available at atgc-montpellier.fr/phyml/ 14/n
