Evidence for Novel Hepaciviruses in Rodents

Drexler, Jan Felix; Corman, Victor Max; Müller, Marcel Alexander; Lukashev, Alexander N.; Gmyl, Anatoly; Coutard, Bruno; Adam, Alexander; Ritz, Daniel; Leijten, Lonneke M.; van Riel, Debby; Kallies, Rene; Klose, Stefan M.; Gloza-Rausch, Florian; Binger, Tabea; Annan, Augustina; Adu-Sarkodie, Yaw; Oppong, Samuel; Bourgarel, Mathieu; Rupp, Daniel; Hoffmann, Bernd; Schlegel, Mathias; Kümmerer, Beate M.; Krüger, Detlev H.; Schmidt-Chanasit, Jonas; Setién, Alvaro Aguilar; Cottontail, Veronika M.; Hemachudha, Thiravat; Wacharapluesadee, Supaporn; Osterrieder, Klaus; Bartenschlager, Ralf; Matthee, Sonja; Beer, Martin; Kuiken, Thijs; Reusken, Chantal; Leroy, Eric M.; Ulrich, Rainer G.; Drosten, Christian

The high degree of sequence homology of the RNA-dependent RNA polymerase (RdRp) genes between all members of the family Flaviviridae enabled a more comprehensive comparison of the novel viruses. In a Bayesian phylogeny of these genes across the flavivirus family, the rodent viruses formed a monophyletic sister-clade to HCV ( Figure 4A ). Topological robustness was assessed by the fixation, in parallel Bayesian phylogenies, of two alternative topological hypotheses, the first involving monophyly of HCV with the canine/ equine viruses and M. glareolus clade 1, and the second assuming a separation of HCV and the canine/equine viruses from all rodent viruses and GBV-B. A Bayes factor test comparing the total model likelihood traces of these analyses indicated borderline-significant preference of the second hypothesis over the first (Log10 Bayes factor = 2.94). Figure 4B provides a comparison of RdRp-based amino acid distances within and between Flaviviridae genera.