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

Estimate of total viral diversity (richness) in P. giganteus in Bangladesh. Previous attempts have been made to predict the total number of unknown viruses in humans by analyzing temporal trends in viral discovery (13, 14) . However, these assessments principally consider the emergence of disease-causing agents rather than an ecological assessment of virodiversity. Here, we ® measured viral richness using nonparametric species discovery curves, which are commonly used in biodiversity studies (10, 13, (15) (16) (17) and rely on the frequency of rarely occurring species to measure the completeness of discovery (15) and make statistical estimations of the undiscovered fraction (10) . Our estimate of the viral carrying capacity of P. giganteus as 58 viruses (for the nine viral families assayed) was robustly supported, with the cumulative number of new viruses slowing toward an asymptotic trajectory and with statistical estimators showing reliably asymptotic behavior. Given that our total discovery effort revealed 55 of the estimated 58 viruses, we suggest that most have now been identified and that the remaining viruses in P. giganteus in Bangladesh are extremely rare. However, we make the qualification that this estimation of richness is likely a minimum and that additional viruses will almost certainly be found through the expansion of viral family testing and the use of high-throughput sequencing. While we cannot infer a great deal about the biology or taxonomic relatedness of the undiscovered diversity, our estimate of viral richness does allow useful considerations of the efficacy of viral discovery efforts in this species. In general, surveys for undiscovered diversity present diminishing returns, since the commonly occurring species are quickly identified, while the rare species require an increasingly large sampling effort. Here, the Chao 2 estimator predicted that 85% of the total richness could be achieved if another~500 samples were screened but that a further 5,500 would then be required to find the remaining 15%. Considering that only very rare viruses would exist within this final fraction and assuming that this rarity reduces both exposure and the chance of transmission, the public health advantage gained by knowledge of their biological properties or taxonomy may not be sufficiently high to justify the cost of their discovery. Similar estimations were made for each of the viral families individually. For example, 13 HVs were discovered in a total of 1,741 samples, with an estimated 8,503 additional samples needed to identify just 2 more predicted viruses (100% of the estimated). Equally, 11 PMVs were identified in 1,108 samples, with one additional virus projected from a further 773 samples. In both cases, an extremely limited return is expected from a costly discovery effort.