Global patterns in coronavirus diversity

Anthony, Simon J.; Johnson, Christine K.; Greig, Denise J.; Kramer, Sarah; Che, Xiaoyu; Wells, Heather; Hicks, Allison L.; Joly, Damien O.; Wolfe, Nathan D.; Daszak, Peter; Karesh, William; Lipkin, W. I.; Morse, Stephen S.; Mazet, Jonna A. K.; Goldstein, Tracey

For each reconstruction, the most recent evolutionary event leading to a virus-host association was recorded. Given that sorting is particularly sensitive to missing data (it indicates a loss on the tree when in fact it may simply be an artifact of under-sampling), we have excluded this event from our analysis. We also distinguished between two potential types of host switching, based on an assumption that there could be differences in zoonotic risk between viruses that only move between closely related bats (e.g. those within the same genus) and those that are able to make more substantive jumps into distantly related species (those in other host genera or families). We therefore use 'host switching' to refer specifically to viral lineages that have moved into a host belonging to another genus or family, and 'sharing' to indicate a viral lineage that has moved into a different host species of the same genus (without speciating). We selected host genus as the cut-off to be consistent with current conventions of taxonomic hierarchy, and verified that the number of species per genus is relatively consistent between regions. We further verified that the mean genetic distance between host species is consistent between regions (i.e. that the taxonomic distance a virus has to navigate when moving between any two species is roughly similar in all three regions).