Novel lineage of anelloviruses with large genomes identified in dolphins
Authors: De Koch Matthew D. , Krupovic Mart , Fielding Russell , Smith Kendal , Schiavone Kelsie , Hall Katharine R. , Reid Vincent S. , Boyea Diallo , Smith Emma L. , Schmidlin Kara , Fontenele Rafaela S. , Koonin Eugene V. , Martin Darren P. , Kraberger Simona , Varsani Arvind 
Published: December 2024

ABSTRACT

Anellovirus infections are ubiquitous in mammals but lack any clear disease association, suggesting a commensal virus-host relationship. Although anelloviruses have been identified in numerous mammalian hosts, their presence in members of the family Delphinidae has yet to be reported. Here, using a metagenomic approach, we characterize complete anellovirus genomes (
n
= 69) from four Delphinidae host species: short-finned pilot whale (
Globicephala macrorhynchus
,
n
= 19), killer whale (
Orcinus orca
,
n
= 9), false killer whale (
Pseudorca crassidens
,
n
= 6), and pantropical spotted dolphin (
Steno attenuatus
,
n
= 1). Sequence comparison of the open reading frame 1 (ORF1) encoding the capsid protein, the only conserved gene shared by all anelloviruses, shows that the Delphinidae anelloviruses form a novel genus-level clade that encompasses 22 unique species-level groupings. We provide evidence that different Delphinidae species can be co-infected by multiple anelloviruses belonging to distinct species groupings. Notably, the ORF1 protein of the Delphinidae anelloviruses is considerably larger than those encoded by all previously described anelloviruses from other hosts (spanning 14 vertebrate orders and including 27 families). Comprehensive analysis of the ORF1 sequences and predicted protein structures showed that the increased size of these proteins results from divergent elaborations within the capsid-distal P2 subdomain and elongation of the C-terminal domain of ORF1. Comparative structural and phylogenetic analyses suggest that acquisition of the P2 subdomain and its diversification occurred convergently in the anelloviruses associated with primate and Delphinidae hosts. Collectively, our results further the appreciation of diversity and evolution of the ubiquitous and enigmatic viruses in the family
Anelloviridae
.

IMPORTANCE

Anelloviruses are ubiquitous in mammals, but their infection has not yet been linked to any disease, suggesting a commensal virus-host relationship. Here, we describe the first anelloviruses associated with diverse species of dolphins. The dolphinid anelloviruses represent a new genus (tentatively named “Qoptorquevirus”) and encode open reading frame 1 (ORF1) (capsid) proteins that are considerably larger than those encoded by previously described anelloviruses from other hosts. Comprehensive analysis of the ORF1 sequences and predicted protein structures revealed the underlying structural basis for such an extravagant ORF1 size and suggested that ORF1 size increased convergently in the anelloviruses associated with primate and Delphinidae hosts, respectively. Collectively, our results provide insights into the diversity and evolution of
Anelloviridae
. Further exploration of the anellovirus diversity, especially in the host species that have not yet been sampled, is expected to further clarify their evolutionary trajectory and explain the unusual virus-host commensal relationship.