Genomic characterization of a novel circovirus from a stranded Longman's beaked whale (Indopacetus pacificus)

Tissues from a juvenile Longman's beaked whale that stranded in Hawaii in 2010 were screened for viruses using a Next-Generation Sequencing (NGS) approach. From the NGS data, the full genome (1,849 bp) of a novel beaked whale circovirus (BWCV) was determined. Two open reading frames (ORF) were annotated, including ORF1 that encodes the capsid gene, ORF2 that encodes the replication-associated gene, and a 9-bp conserved nonamer on the apex of the open loop found in all circoviruses. Independent phylogenetic analyses based on amino acid sequence alignments of the two CV proteins supported the BWCV as a member of the genus Circovirus, branching as the sister species to the recently discovered canine circovirus. A sequence identity matrix generated from complete genome alignments revealed the BWCV displays between from 51.1 to 56.7% nucleotide identity to other circoviruses, which is lower than the 80% threshold proposed for species demarcation. Considering the genetic and phylogenetic analyses, we propose the formal species designation of beaked whale circovirus. An endpoint PCR assay targeting the BWCV genome confirmed the presence of the BWCV DNA in every tissue from which DNA was extracted, including spleen, muscle, left ventricle, left adrenal gland, liver, lung, cerebrum, cerebellum, and lymph node. An automated in situ hybridization assay utilizing RNAscope® technology and targeting the replication-associated gene resulted in labeling of individual cells morphologically resembling mononuclear leukocytes and cells of blood vessels in diaphragm, liver, lymph nodes, lung, pericardium, oral mucosa and tongue, adrenal gland, testis, aorta, intestine, stomach and heart. The clinical or pathologic significance of BWCV is undetermined, as are its host range, prevalence, and pathogenicity in cetaceans of Hawaiian waters and elsewhere.