A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses

Jia, Hengxia; Gong, Peng

Although we tried to survey the positive-strand RNA virus RdRPs in a comprehensive manner, there are still several limitations in our analyses. Firstly, the virus species that have not been assigned at the virus family level are not included in our analyses. Secondly, some virus families contain a large number of virus genera (e.g., 47 in Picornaviridae and 14 in Tombusviridae), suggesting high-level of genome and RdRP diversity within individual families. Moreover, RdRP primary structure diversity and genome-level diversity may not be consistent. The Flaviviridae is such an example with only four genera but three drastically different primary RdRP structures. Therefore, choosing one representative RdRP for each family (with the Flaviviridae as the only exception) may not be sufficient and ideal. Thirdly, the boundary estimation of the catalytic module is only a crude assessment. For example, the distance between the N-terminal boundary of the TaV RdRP catalytic module to the conserved motif F lysine is at least 100 residues longer than estimated distance using the 150-residue criterion used in our analyses (Ferrero et al., 2015) .