Genomic characterization of a RdRp-recombinat nebovirus strain with a novel VP1 genotype

Nebovirus is a new genus within the family Caliciviridae and is a causative agent of calf diarrhea. The limited nebovirus genomic sequences that are currently available has hampered understanding of nebovirus genetic evolution. The aim of the present study was to determine the genomic characterization of strain Bo/LZB-1/17/CH, which was previously identified as being similar to the novel genotype strain Bo/DijonA216/06/FR based on partial capsid sequences. Our results show that the complete RNA genome of strain Bo/LZB-1/17/CH is 7453 nucleotides (nt) in length and shares 79.0%-83.5% nt identity with all available nebovirus genomes in the GenBank database. A phylogenetic analysis based on its complete genome sequence revealed that strain Bo/LZB-1/17/CH clustered into an independent branch. Two interesting characteristics were observed in the genome of strain Bo/LZB-1/17/CH. First, the major capsid protein (VP1) of strain Bo/LZB-1/17/CH shares 96.6% amino acid (aa) identity with strain Bo/DijonA216/06/FR but shares only 75.2%-76.8% aa identity with other nebovirus strains and has an even lower identity in the P2 domain (61.1%-65% aa identity). Second, the RNA-dependent RNA polymerase (RdRp) of strain Bo/LZB-1/17/CH is more closely related to NB-like strains than it is to strain Bo/DijonA216/06/FR, and a recombination event was identified within the 3′ end of the RdRp in strain Bo/LZB-1/17/CH. In conclusion, the results in this study indicate that strain Bo/LZB-1/17/CH may represent a novel nebovirus strain. To the best of our knowledge, this is the first description of a recombinant event in nebovirus RdRp.