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

Novel viruses. The current study significantly enhances our knowledge of the viruses harbored by P. giganteus, for which only two viruses had been previously described, Nipah virus and a GB virus-like flavivirus (21, 22) . A total of 50/55 of the viruses discovered in this study were considered novel, while 5/55 have been reported previously (PgBoV-1 and -2, PgCoV-3 and -4, and PgPMV-11). Additional discussion of the 50 novel viruses is provided in the supplemental material. Here, we discuss a number of important limitations that must be considered in the interpreta- tion of these results. First, the use of consensus PCR limits surveillance and discovery to viruses related to those targeted in these assays. Second, variations in virus concentration can also influence the probability of detection. Third, we evaluated the diversity of viruses in a limited set of compartments and tissues, and unbiased sequencing was not used as a secondary method of capturing diversity. The classification of viruses is also significant, as redefining the genetic limits between one virus and another would change the total number and prevalence of viruses discovered and would impact our estimations of viral richness. We have tried to address this by using monophyletic clades as a taxonomic surrogate, which obviates the variable and polythetic criteria set by the ICTV for species demarcations.