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

Eleven PMVs were detected, including 10 novel viruses (PMV-1 from P. giganteus to and Nipah virus (PgPMV-11). These PMVs exhibited high sequence variation and clustered phylogenetically with either the rubulaviruses or an unassigned group related to the henipaviruses (Fig. 1 ). Within the AdV family, 14 viruses were discovered (PgAdV-1 to -14) . Thirteen were novel mastadenoviruses, while one virus (PgAdV-2) had 98% nucleotide identity to the aviadenovirus Fowl adenovirus E (Fig. 2) . Eight different AstVs were found (PgAstV-1 to -8), all of which were novel and clustered within the genus Mamastrovirus (Fig. 3) . Within the CoV family, four distinct viruses were discovered. The first two were closely related betacoronaviruses (PgCoV-1 and -2). The third was also a betacoronavirus (PgCoV-3) but was more distantly related and showed 97% nucleotide identity to bovine and human coronaviruses (human strains 4408 and OC43). The fourth CoV was a gammacoronavirus (PgCoV-4) with 91% nucleotide identity (97% at the amino acid level) to the avian Infectious bronchitis virus (Fig. 4) . Three novel PyVs were identified (PgPyV-1 to -3), all of which clustered with viruses in the genus Orthopolyomavirus (Fig. 5) . A total of 639 HV sequences were detected, which segregated into 13 distinct clades (PgHV 1 to 13) using hierarchical clustering (see Materials and Methods). None could be reliably classified within any existing genus, and they likely represent new groups within the Betaherpesvirinae and Gammaherpesvirinae subfamilies (Fig. 6) . One virus, PgHV-11, appears to be a recombinant between PgHV-10 and PgHV-13, with a breakpoint evident at approximately nucleotide 90. Upstream from this breakpoint, the sequences for PgHV-11 are related to PgHV-10, while downstream from the breakpoint, they are related to PgHV-13. Finally, two different BoVs were discovered (PgBoV-1 and -2), both of which showed Ͼ98% nucleotide identity to known human BoVs (Fig. 7) .