Representative amino acid sequences of the RNA-dependent RNA polymerases of all groups of positive-strand RNA viruses were aligned hierarchically, starting with the most closely related ones. This resulted in delineation of three large supergroups. Within each of the supergroups, the sequences of segments of approximately 300 amino acid residues originating from the central and/or C-terminal portions of the polymerases could be aligned with statistically significant scores. Specific consensus patterns of conserved amino acid residues were derived for each of the supergroups. The composition of the polymerase supergroups was as follows. I. Picorna-, noda-, como-, nepo-, poty-, bymo-, sobemoviruses, and a subset of luteoviruses (beet western yellows virus and potato leafroll virus). II. Carmo-, tombus-, dianthoviruses, another subset of luteoviruses (barley yellow dwarf virus), pestiviruses, hepatitis C virus (HCV), flaviviruses and, unexpectedly, single-stranded RNA bacteriophages. III. Tobamo-, tobra-, hordei-, tricornaviruses, beet yellows virus, alpha-, rubi-, furoviruses, hepatitis E virus (HEV), potex-, carla-, tymoviruses, and apple chlorotic leaf spot virus. An unusual organization was shown for corona- and torovirus polymerases whose N-terminal regions were found to be related to the respective domains of supergroup I, and the C-terminal regions to those of the supergroup III polymerases. The alignments of the three polymerase supergroups were superimposed to produce a comprehensive final alignment encompassing eight distinct conserved motifs. Phylogenetic analysis using three independent methods of tree construction confirmed the separation of the positive-strand RNA viral polymerases into three supergroups and revealed some unexpected clusters within the supergroups. These included the grouping of HCV and the pestiviruses with carmoviruses and related plant viruses in supergroup II, and the grouping of HEV and rubiviruses with furoviruses in supergroup III.


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