Limited consensus of marine viral diversity observed across techniques

Viruses are fundamental to many aspects of life influencing ecosystem functions. The `lenses´ we use for exploring the viral diversity have expanded, yet at the same time each has limitations that constrain our view of the uncultured virosphere. Here, using the same surface seawater sample, we compare short- and long-read viromics (i.e., Illumina, PacBio–HiFi and MinION sequencing) along with high-throughput single-virus genomics (SVG) to explore the consensus between approaches to uncover the extant viral diversity. Overall, ≈42,000 viral contigs (> 10 kb) were obtained, resulting in ≈12,500 and ≈23,400 viral clusters at the genus and species level, respectively, and predominantly infecting Flavobacteriaceae and Pelagibacteracea. At the viral family level, SVG recovered viruses with a more distinct taxonomic profile compared to other methods . At lower taxonomic resolution, only < 1% of all species and genera, including some of the most abundant one, were captured by all methods; reaching a value of ≈2% when only viromics -with or without hybrid assemblies- were considered. When exploring how the different methods resolve the co-occurring genomic microdiversity within species using as reference one of the most abundant and microdiverse virus, the uncultured pelagiphages vSAG 37-F6 discovered by SVG, none of the methods separately were able to assemble the complete genome; which was only achieved by combining all datasets. Similarly, neither of the viral clusters at the strain level was recovered by all methods. Our data suggest that the inherent bias of each method still represents a challenge for the recovery of viral diversity.