Molecular analysis of a divergent isolate of Potato virus H from potato reveals novel evolutionary feature of Carlaviruses

A new Carlavirus in the family Betaflexiviridae was identified from potato plants showing yellow mosaic symptoms. The full genome of this Carlavirus comprises 8,429 nucleotides which shares the highest nucleotide identity (66.7%) with that of Potato virus H (PVH). The virus is closely related to PVH in the phylogenetic trees constructed based on the deduced amino acid sequences of RNA-dependent RNA polymerase (RdRp) and coat protein (CP). The CP of the virus had 71.1–73.1% nucleotide and 79.5–82.2% amino acid sequence identities with those of published PVH sequences, whereas the RdRp was distinctly different from PVH isolates, with about 52.5% nucleotide and 66.3% amino acid sequence identities. A highly divergent region underlying strong positive selection was identified in the RdRp coding region of the virus and other carlaviruses as well. We propose that the most conserved replicase domain at the C-terminal of RdRp is more suitable than the full RdRp for sequence-based species demarcation. The virus was classified as a divergent strain of PVH based on the nucleotide and amino acid sequence identities of the CP and replicase domain of the RdRp and similar host range to PHV.