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 Earth's surface was divided into grid cells, each 10 latitude by 10 longitude. Thirty-four of these grid cells included areas from which bats were sampled (bats were identified down to the species level in thirty cells), and twenty-seven cells had samples testing positive for CoVs. If the coordinates listed for a particular bat were on the line between grid cells, it was arbitrarily included in the grid cell with higher latitude/longitude. Viral and host species richness for each cell was calculated by determining the total number of unique virus and bat species within each cell. Alpha diversity was calculated using the Shannon index (Jost et al. 2011 ), which was chosen over the Gini-Simpson index because it does not place disproportionate weight on dominant species. Since we do not know how representative our sampling was, the Shannon index was deemed the best approach. The effective number of viruses and bats in each cell was then correlated using Kendall's tau, since the values were not normally distributed. Sensitivity analyses were performed by shifting the grid cells in 1 increments and recalculating richness and effective species numbers.