Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.

Gene sequence data of viruses were obtained from GenBank (Table 1; see S1 Table for all Gen-Bank accession numbers). Following a broad and comprehensive survey of all virus genomic data available on GenBank, a total of 19 family-level virus data sets passed our selection criteria and were included in the analysis. These selection criteria, which are independent of whether the viruses have evolved by co-divergence or cross-species transmission, were: (i) the availability of virus sequence data that included a wide range of distinct and diverse virus species that is representative of the virus genera currently available; (ii) the availability of data with informative genomic regions that can be used to reveal evolutionary relationships (e.g. the RNAdependent RNA polymerase-see Table 1 ) and that were not so divergent as to prevent reliable sequence alignment; and (iii) the virus sequence data met a minimum length requirement of 100 amino acids following alignment and the removal of any ambiguously aligned regions.