London Calling 2023: Nanopore sequencing of wild virus particles reveals previously undetected phage and phage-parasitizing elements

Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. Nanopore sequencing of wild marine virus particle DNA recovered entire virus genomes in single-molecule reads, as well as phage satellites packaged in viral particles as concatemeric repeat elements. These diverse virus genomes and phage satellite concatemers could not be detected via short-read sequencing alone. The novel phage-parasitizing mobile elements were also found integrated within the genomes of dominant cellular hosts from the same habitats. Marine phage satellites were widespread in global oceanic virioplankton populations, suggesting their ubiquity, abundance, and temporal persistence worldwide. Their gene content and putative life cycles suggest that they exert significant impacts on host-cell phage immunity and defense, lateral gene transfer, and virus productivity. Similar phage parasites are predicted to thrive in virtually any habitat that also harbors bacteriophages.