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 analyses were performed using all unique associations between viruses and their respective hosts (limited to bats). Alpha-CoV sequences and beta-CoV sequences were analyzed separately, since each appears to have diversified independently within bats. This gave us a total of four reconstructions (alpha-Quan, alpha-Watanabe, beta-Quan, beta-Watanabe). Only one instance of each virus-host association was included, even if multiple instances of the same association were observed (i.e. our analysis does not account for the frequency of detection). Associations were excluded if the host was not identified to the species level or if the cytochrome B sequence did not exist in GenBank or could not be amplified by PCR. The topology of the virus tree was inferred from the topology of the full tree for consistency, since subsets of sequences often produce different arrangements.