Molecular variability of twenty-one geographically distinct isolates of Carnation mottle virus (CarMV) and phylogenetic relationships within the Tombusviridae family

The complete nucleotide sequence of a Spanish isolate of Carnation mottle carmovirus (CarMV) has been determined. Phylogenetic analyses were carried out with the replicase, coat protein (CP) and the putative movement proteins (p7 and p9) of CarMV with the homologous proteins of representative members of the different genera included within the family Tombusviridae. These analyses revealed that phylogenetic trees obtained depended on the protein analyzed, and that the best correlation with taxonomy grouping was observed with the replicase and, to a lesser extent, with CP phylogenies. This result indicates that speciation has evolved as a consequence of different selection pressures to different genomic regions. In addition, the CP, p7 and p9 coding sequences of twenty-one CarMV isolates from nine different countries have been determined. Comparative analyses revealed that CarMV isolates separated in time and space show a very high genetic stability. A division in three protein motifs is proposed for the p7 movement protein, based on the homology data presented here and on our previous identification of RNA binding sequences and structural characterization of the protein. Interestingly, a remarkable covariation in the amino acid sequence was found for the CP between Pro(164) (located at the S domain) and Lys(331) (within the P domain), by which a change Pro(164) --> Ala correlated with a change Lys(331) --> Asn, strongly suggesting the existence of tertiary interactions between these two regions of the protein. In addition, this perfect covariation allows to segregate the 23 CarMV isolates characterised so far into two main groups that we propose to name as group PK and group AN for further studies.