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

Co-phylogenetic reconciliation analysis was used to investigate the evolutionary mechanisms driving the virus-host associations observed, for example host switching, viral sharing, or co-speciation (see 'Methods'). Overall, host switching was the dominant mechanism, followed by co-speciation (Fig. 5) . When analyzed by region, host switching (inter-genus transmission) remained dominant in Africa and Asia, but not in Latin America. Despite fewer host-switching events in Latin America, there was a concomitant increase in virus sharing (intra-genus transmission). This suggests that viruses are still switching hosts in Latin America but preferentially move between closely related species, while in Africa and Asia viruses cross between more distantly related species. To assess the sensitivity of our results to our chosen method (i.e. use of a pre-defined cost scheme in the program Jane), we repeated the analysis for the Quan alpha-CoV and beta-CoV reconstructions using CoRePA, a parameter-adaptive approach that estimates an appropriate cost scheme without any prior value assignment. Comparing the results, we noted 91% agreement between Jane and CoRePA in alpha-CoV reconstruction (thirty-four events, of which thirtyone agreed), and 100% agreement in the beta-CoV reconstructions (twenty-six events, all of which agreed). We further note that the cost scheme calculated in CoRePA was 0.7 for host switching and 0.1 for co-speciation-supporting the default cost scheme used in Jane (i.e. that host switching should be considered more 'costly' than co-speciation).