Usurpativirus massiliensis, a new giant virus related to clandestinovirus

Giant virus discovery in 2003 revolutionized the virus paradigm. In 2015, we introduced a new host, Vermamoeba vermiformis, that led to the discovery of Faustovirus, Orpheovirus and two giant viruses (Clandestinovirus and a faustovirus) having distinct cytopathic effects despite being co-isolated from the same environmental sample and culture. This raised concerns about the possibility that the most "discreet" virus be overlooked. Here we report on Usurpativirus, a new giant virus closely related to Clandestinovirus and co-isolated with Faustovirus LCD7 in V. vermiformis. Its non-lytic replicative cycle was primarily overlooked in presence of the lytic Faustovirus. The Usurpativirus genome encode two tRNAs and 758 predicted proteins, and share 707 and 202 orthologs with Ushikuvirus and Clandestinovirus, respectively. We detected four histone-like proteins that further challenge the compaction of DNA from these large genomes into icosahedral capsids of approximately 240 nm, as well as four capsid-associated proteins, but we did not detect any predicted proteins involved in entry/fusion that could explain the special replication strategy of this virus. Scanning electron microscopy revealed two distinct morphologies for amoebae infected with Usurpativirus, which became either rounded with a smooth surface or more flattened with a wavy surface. In addition, virions were observed attached to the outside of the amoebae, which most often had a smooth surface and rarely an undulating surface after 6 days of infection. Finally, such co-infection with two distantly-related giant viruses questions on the possible interactions between each other.