Expansion of viral genomes with viral protein genome linked copies

Virus protein-linked genome (VPg) proteins are required for replication. VPgs are duplicated in a subset of RNA viruses however their roles are not fully understood and the extent of viral genomes containing VPg copies has not been investigated in detail. Here, we generated a novel bioinformatics approach to identify VPg sequences in viral genomes using hidden Markov models (HMM) based on alignments of dicistrovirus VPg sequences. From metagenomic datasets of dicistrovirus genomes, we identified 717 dicistrovirus genomes containing VPgs ranging from a single copy to 8 tandem copies. The VPgs are classified into nine distinct types based on their sequence and length. The VPg types but not VPg numbers per viral genome followed specific virus clades, thus suggesting VPgs co-evolved with viral genomes. We also identified VPg duplications in aquamavirus and mosavirus genomes. This study greatly expands the number of viral genomes that contain VPg copies and in-dicates that duplicated viral sequences are more widespread than anticipated.

Automated summary

This study developed a novel bioinformatics approach to identify VPg sequences in viral genomes and found 717 dicistrovirus genomes containing VPgs. VPg duplications were also identified in aquamavirus and mosavirus genomes. The results indicate that VPg duplications are more widespread than anticipated and suggest co-evolution between VPgs and viral genomes.