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

The emergence of SARS and MERS has driven a need to understand more about the diversity, ecology and evolution of coronaviruses, particularly at so-called 'hotspots' of zoonotic emergence (Jones et al. 2008; Drexler et al. 2014) . To this end, we surveyed the diversity of CoVs from twenty countries in Latin America, Africa, and Asia to identify global factors driving viral diversity and to look for regional differences in factors that contribute to the risk of emergence, such as host switching. In total, we identified sequences from 100 discrete phylogenetic clusters, ninety-one of which were found in bats. Our data suggest that the diversity of bat CoVs has been driven primarily by host ecology. First, viral richness was strongly correlated with bat richness, suggesting that most CoVs will be found in regions where bat diversity is highest. Second, we showed that CoV diversity separates into three distinct communities by region, echoing the distribution of bats and suggesting an ecological dependence on their hosts. And third, we identified particular associations between viral subclade and bat family, indicating that CoVs have evolved with (or adapted to) preferred families. Collectively, these data show that the global diversity and distribution of CoVs in bats is nonrandom and is driven by variation in the biogeography of bats.