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

A total of 12,793 consensus PCR assays were performed for the detection of viruses from nine different families/ genera, including coronaviruses (CoVs; n Ï­ 1,631), paramyxoviruses (PMVs; n Ï­ 1,108), hantaviruses (HTVs; n Ï­ 1,108), astroviruses (AstVs; n Ï­ 1,348), influenza A viruses (IFAVs; n Ï­ 1,108), bocaviruses (BoVs; n Ï­ 1,739), adenoviruses (AdVs; n Ï­ 1,902), herpesviruses (HVs; n Ï­ 1,741), and polyomaviruses (PyVs; n Ï­ 1,108) ( Table 1) . None of the samples were positive for IFAVs or HTVs, despite previous studies documenting their presence in other bat species (6) (7) (8) ; however, a total of 985 viral sequences representing the other seven viral families were detected in these bats. These sequences were segregated into 55 discrete viruses based on distinct monophyletic clustering (see Materials and Methods) ( Table 1) , and a virus was considered novel if the sequence identity to its closest relative was less than or equal to the identity between the two closest species for a given viral family (9) .