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

The family <i>Mamonoviridae</i>, 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 <i>Nucleocytoviricota</i>. 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 <i>Mamonoviridae</i> and Clandestinovirus may represent a key taxon for elucidating virus-host interactions and the evolution of this virus group.IMPORTANCEThe family <i>Mamonoviridae</i> consists of only one genus, including three species: <i>Medusavirus medusae</i>, <i>Medusavirus sthenus</i>, and the recently described medusavirus euryale. These three medusaviruses have been reported to infect <i>Acanthamoeba castellanii</i>. Meanwhile, clandestinovirus, a closely related species in the family <i>Mamonoviridae</i>, 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 <i>Mamonoviridae</i> and closely related taxa and provide a basis for elucidating the evolutionary relationships of giant viruses with their eukaryotic hosts.