Tale of Two viruses: Two coinfecting archaeal viruses provide insights into virus-virus interactions

Upon characterization of a novel spindle-shaped virus, Tebenquiche spindle-shaped Virus 1 (Tebi-SV1), isolated from Halorubrum strain TLS-6, we detected the presence of a second virus, Tebenquiche pleomorphic Virus 1 (Tebi-PV1), that coinfects host cells. Gene sharing network analysis revealed several genomes related to Tebi-SV1 in public databases, most of which also co-occur with pleolipoviruses in their host genomes. Attempts to separate the two viruses remained unsuccessful, suggesting a mutualistic relationship between Tebi-SV1 and Tebi-PV1. Virus abundances seem to be regulated through a shared operator sequence allowing Tebi-PV1 to keep Tebi-SV1 copy numbers low without excluding Tebi-SV1 from the host genome. Additionally, Tebi-PV1 encodes for a type-4-pilin, which we detected by proteomics, and likely plays a role in regulating the interactions between the host and viruses. Our findings highlight the complexity of virus-virus interactions and that residential viruses are important regulators of virus-host interactions.