Two Novel Parvoviruses in Frugivorous New and Old World Bats

Canuti, Marta; Eis-Huebinger, Anna Maria; Deijs, Martin; de Vries, Michel; Drexler, Jan Felix; Oppong, Samuel K.; Müller, Marcel A.; Klose, Stefan M.; Wellinghausen, Nele; Cottontail, Veronika M.; Kalko, Elisabeth K. V.; Drosten, Christian; van der Hoek, Lia

Fifty-nine reference nucleotide sequences and amino acid sequences were downloaded from the GenBank database and aligned together with the ones obtained in this study using ClustalX software version 2.0.12 [26] and the Cobalt Multiple Alignment Tool (http://www.ncbi.nlm.nih.gov/tools/cobalt/) for nucleotide and amino acidic sequences, respectively. Only complete coding sequences were included in the analysis. Alignments were manually edited when needed with BioEdit software version 7.0.5.3 [27] and then used for phylogenetic inference. The evolutionary distances were computed using the Maximum Composite Likelihood method for nucleotides [28] and the Poisson Correction [29] for proteins. Phylogenetic trees were constructed by means of MEGA software version 4.0.2 [30] using the Neighbor-Joining method [31] . To test the robustness of the analysis a bootstrap test (1000 replicates) [32] was performed and only clusters associated with a value higher then 75% were considered significant. Identities between and within sequences were calculated with BioEdit software version 7.0.5.3 [27] : the positions where both sequences have a gap did not contribute and positions with a gap in only one sequence counted as mismatch.