Characterization of previously undescribed archaeal viruses and their coinfection dynamics

Spindle-shaped viruses infecting halophilic archaea (Haloarchaea) are among the most abundant viral morphotypes observed in hypersaline environments. Despite their abundance,
only two isolates, His1 and LSV-48N, have been described. Here, we characterize a novel spindle-shaped virus, Tebenquiche spindle-shaped Virus 1 (Tebi-SV1), isolated from a
Halorubrum strain (TLS6), deriving from a hypersaline lake in the Chilean Puna. Sequencing and electron microscopy of purified viral particles and cell cultures revealed the presence of a
second virus, Tebenquiche Pleomorphic Virus 1 (Tebi-PV1) that coinfects host cells. Together, Tebi-SV1 and Tebi-PV1 can infect across different genera of Haloarchaea. A search in public
databases, and gene sharing network analyses, revealed a small number of genomes related to Tebi-SV1, which together form a new virus family Almyrocitroviridae. Notably, some of these putative viruses also co-occur with pleolipoviruses in their host genomes. Halorubrum TLS6 did not lose either virus spontaneously and despite various efforts, we were unable to separate Tebi-SV1 and Tebi-PV1 from one another. We show evidence that Tebi-SV1 is dependent on Tebi-PV1, providing important insights into virus-virus interactions in archaea. Due to the extremophilic nature of this non-model system, extensive method optimization and the use of multimethod approaches was necessary to characterize the novel viruses, Tebi-SV1 and Tebi-PV1. Additionally, we provide insights to the different host cell entry and egress mechanisms that may be employed by the two viruses. This work demonstrates that co-occurrences of viruses and proviruses within one host system are not necessarily detrimental to the entities involved, rather that multiple elements can co-exist in concord.