FIG. 4.

Phylogenetic analysis of the coronavirus ORF1b replicase amino acid sequences. The HCoV-OC43 ORF1b protein (GenBank accession number AY391777) was compared to other coronaviruses and to an equine torovirus as an outgroup. Group 1, HCoV-229E (accession number AF304460), HCoV-NL63 (AY567487), PEDV strain CV777 (AF353511), and TGEV strain Purdue (AJ271965). Group 2, BCoV strain Mebus (U00735), MHV type 2 (MHV-2; AF201929), MHV strain Penn 97-1 (AF208066), and MHV-A59 (X51939). Group 3, IBV strain Beaudette (M95169), IBV strain LX4 (AY338732), IBV strain BJ (AY319651). SARS-CoV strain Frankfurt-1 (AY291315) is not classified in any of these groups but is most closely related to group 2 coronaviruses. Outgroup, equine Berne torovirus (EToV; X52374). Regions that were poorly conserved in the manually edited multiple protein sequence alignment were deleted from the alignment. All columns containing gaps were removed. The resulting alignment included 2,083 characters (1,122 being parsimony informative) and contained the meld of the following HCoV-OC43 fragments: 13686-13721, 13737-13793, 13797-13820, 13857-13889, 13869-13994, 14013-14090, 14127-14174, 14247-14390, 14397-14594, 14598-14756, 14766-14855, 14859-15230, 15243-15443, 15480-15674, 15684-15719, 15729-15764, 15786-15854, 15864-15989, 16023-16358, 16374-16715, 16719-16898, 16902-17093, 17115-17258, 17268-17336, 17340-17363, 17379-17501, 17535-17561, 17568-17825, 17925-18008, 18018-18032, 18069-18101, 18207-18440, 18450-18527, 18531-18563, 18576-18602, 18612-18929, 18942-19010, 19,026-19139, 19143-19259, 19284-19466, 19479-19625, 19686-19793, 20289-20318, 20370-20603, 20625-20708, 20718-20762, 20769-20885, 20907-21008, 21045-21125, 21135-21233, 21252-21296, 21309-21431, and 21438-21476. The frequencies of occurrence of particular bifurcations (percentage of 10,000 bootstrap replicate calculations) are indicated at the nodes.