A Strategy To Estimate Unknown Viral Diversity in Mammals

Anthony, Simon J.; Epstein, Jonathan H.; Murray, Kris A.; Navarrete-Macias, Isamara; Zambrana-Torrelio, Carlos M.; Solovyov, Alexander; Ojeda-Flores, Rafael; Arrigo, Nicole C.; Islam, Ariful; Ali Khan, Shahneaz; Hosseini, Parviez; Bogich, Tiffany L.; Olival, Kevin J.; Sanchez-Leon, Maria D.; Karesh, William B.; Goldstein, Tracey; Luby, Stephen P.; Morse, Stephen S.; Mazet, Jonna A. K.; Daszak, Peter; Lipkin, W. Ian

Assumptions and caveats We considered the detection and discovery of viruses akin to the problem of detection and discovery of biodiversity, as is frequently the goal of ecological studies. The basic mechanism of species detection occurs from drawing samples by collection from some larger assemblage (61) . In this context, our samples are as described above, urine, throat, fecal, or roost urine taken from an individual bat or bat roost, which represent the biomes for our assemblage of interest. These methods require the assemblage of viruses under sampling to be closed for valid inference, that is, that the assemblage size and composition remained stable throughout the course of the study, an assumption we felt was justified. Although each of these sample types targets a unique biome of potential viral habitat from the host species, each with potentially differing efficacy for detecting any given virus, for the purposes of our analyses, we considered each sample a random and equivalent draw from the assemblage of viruses associated with this host species. We also assumed sample independence, even though multiple samples (e.g., urine and throat) were often drawn from the same individual host and sampled bat populations are likely to be geographically nonrandom. The consequence of this sampling strategy is that our analysis is blind to this additional source of geographical variation and occasional pseudoreplication, which means our virus accumulation results are specific to our sampling methodology and our extrapolations assume ongoing sampling with a similar average composition of samples. The results of additional analyses in which we isolated sample types and individuals and considered geographic variation are not presented herein.