A newly isolated giant virus, ushikuvirus, is closely related to clandestinovirus and shows a unique capsid surface structure and host cell interactions

The family Mamonoviridae , assigned in 2023, consists of three strains of medusavirus that infect acanthamoeba. A closely related species, clandestinovirus, which infects vermamoeba, was reported in 2021. Here, we report a newly identified clandestinovirus-like virus, named ushikuvirus, isolated from a freshwater pond in Japan. The ushikuvirus genome was at least 666,605 bp and contained 784 genes. Annotation revealed that a substantial proportion (58%) of open reading frames (ORFs) are ORFans, and 25% of ORFs are similar to those of other viruses in the phylum Nucleocytoviricota . Among ORFs sharing sequence similarity with other viruses, a large proportion (80%) were similar to the clandestinovirus sequences. However, ushikuvirus shows several remarkable features. (i) The capsid surface has multiple spike-like “cap” structures, some of which exhibit a fibrous structure. (ii) The infection cycle is longer than that of medusavirus and clandestinovirus, and the virus exhibits a unique cytopathic effect (CPE) that causes enlargement of host vermamoeba cells. (iii) The virus forms a viral factory for duplication and destroys the nuclear membrane of vermamoeba cells, a phenomenon not observed with medusavirus and clandestinovirus. These characteristics indicate that this newly isolated giant virus related to the family Mamonoviridae and Clandestinovirus may represent a key taxon for elucidating virus-host interactions and the evolution of this virus group.

IMPORTANCE

The family Mamonoviridae consists of only one genus, including three species: Medusavirus medusae , Medusavirus sthenus , and the recently described medusavirus euryale. These three medusaviruses have been reported to infect Acanthamoeba castellanii . Meanwhile, clandestinovirus, a closely related species in the family Mamonoviridae , infects vermamoeba. In these viruses, genome replication takes place in the nucleus of the host cell, and like eukaryotes, the genome encodes a full set of histones and has numerous spikes on the capsid surface. Here, we report a new member of this unique virus group, ushikuvirus, which displays distinct features including cytopathic effects in vermamoeba cells. These findings improve our understanding of the biological significance of the family Mamonoviridae and closely related taxa and provide a basis for elucidating the evolutionary relationships of giant viruses with their eukaryotic hosts.