Two coinfecting archaeal viruses provide insights into virus-virus interactions

Abstract Virus–virus interactions can profoundly shape viral ecology and evolution, yet they remain poorly understood, particularly in haloarchaea. Upon characterization of a 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 were unsuccessful, suggesting a symbiotic relationship between Tebi-SV1 and Tebi-PV1. We discovered that virus abundances may 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 and expresses a type-4-pilin, that likely plays a role in regulating the interactions between the host and the viruses. Our findings highlight the complexity of virus-virus interactions and that resident viruses are important regulators of virus-host interactions.