Histo-Blood Group Antigens Act as Attachment Factors of Rabbit Hemorrhagic Disease Virus Infection in a Virus Strain-Dependent Manner
Figure 2
Evolutionary tree of RHDV strains and non-pathogenic rabbit calicivirus strains (RCV, RCV-A1 and MRCV) according to nucleotide sequences of the gene encoding the capsid protein VP60.
The 6 RHDV strains used in this study are marked with a dot (GenBank accession numbers: G1 JF438967, G2 FR823355, G3 FR823354, G4 AJ535094, G5 AM085133, and G6 AJ969628). The genetic group of each strain (G1 to G6 according to Le Gall-Reculé et al.[17] and Group 1 to 4 according to Kerr et al. [20]) is annotated. For the G1 strain, the genetic group is noted as defined in Muller et al. [19] (IB2a). Capsid sequences where recombination was previously detected were excluded from the analyses [76], [77]. The newly obtained sequences were checked for recombination using RDP3 [78]. Evolutionary distances were computed using the p-distance method. Alignment gaps and missing data were eliminated only in pairwise sequence comparisons (Pairwise deletion option). The European brown hare syndrome virus strain (GenBank accession number X98002) was used as an outgroup to root the tree. The tree was constructed using the neighbor-joining method [79] with the pairwise deletion option. Reliability of the tree was assessed by bootstrap with 1000 replicates and is indicated in the nodes for relevant clusters. Several genetic distance methods were used and similar results were obtained, but only p-distance is shown. The phylogenetic analyses were conducted in MEGA 4 [80]. Similar trees were obtained using the Maximum Likelihood (ML) method as implemented in Garli v1.0 [81].