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

Of note was the detection of subgroup 2a CoV sequences in bats, humans and non-human primates from four different countries. This sub-clade is largely considered the rodent subclade (Lau et al. 2015; Wang et al. 2015; Tsoleridis et al. 2016 ), but here we detected sequences corresponding to the known virus betacoronavirus-1 in Pteropus medius from Bangladesh, Pteropus alecto from Indonesia, and from humans in China, and sequences corresponding to murine coronavirus in non-human primates from Nepal (these sequences were detected by four different laboratories, and no rodent samples were processed at the same time) (Fig. 2) . In addition, we report the discovery of several sub-clade 2b and 2c CoV sequence clusters (the SARS and MERS sub-clades, respectively) (Fig. 2) , and the detection of human coronavirus 229E-like sequences in hipposideros and rhinolophus bats sampled in ROC, Uganda, Cameroon and Gabon, supporting previous suggestions that 229E has zoonotic origins (Pfefferle et al. 2009; Hu et al. 2015) . Finally, we highlight the detection of avian-associated infectious bronchitis viruslike sequences (IBV) in bats and a closely related virus (PREDICT_CoV-49) in non-human primates from Bangladesh, as well as porcine epidemic diarrhea virus (PEDV) in bats (Fig. 2) . Again, we confirm that no livestock samples were processed in any of these laboratories that might have acted as a source of contamination.