Table 1.

Advantages and shortcomings of the meta-omic sequencing approaches used in marine viral ecology studies. Adapted from [28].

	Method	Virus Nucleic Acid Detected	Shortcomings	Advantages
	Metaviromics or viral metagenomics	RNA or DNA viral genomes in the extracellular stage	RNA viruses targeted separately than DNA viruses Needs special enrichment for dsRNA and ssDNA Large DNA viruses are filtered out High-burst-size viruses can be overrepresented	Enriched for viral sequences, better assembly
	Metatranscriptomics	Transcripts of (+) and (−) ssRNA, dsRNA, ssDNA, dsDNA	High background of nonviral sequences Potentially fragmented assemblies Misses low-titre viruses Does not distinguish between (+) ssRNA viral genome and transcripts	Captures all types of DNA and RNA viruses simultaneously Captures active infection (for DNA viruses) Can capture RNA viruses without capsids
	dsRNA sequencing	ssRNA as replicative intermediate dsRNA genomes	Not as effective for (−) ssRNA and DNA viruses Cellular metatranscriptomes are removed in the enrichment process	Enriched for RNA viruses Can be used for detection of both extracellular (<0.22 µm fractions) and intracellular RNA viruses