Single-virus genomics and beyond

Abstract

Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered.Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include, for example, targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology, and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.

Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics

“…In this way, the current state of the art of SVGs should be understood as a complementary tool to other existing viromic methodologies, allowing the recovery of key pieces from the complex virosphere jigsaw. The refinement of the viral sorting and sequencing methodologies and large-scale analysis will show the real scope of SVGs in the deciphering of the global virosphere [ 24 ].…”

“…For instance, the use of fosmid libraries [ 22 ] allowed the discovery of 99 bathypelagic viral contigs from two Mediterranean Sea sampling points (1000 and 3000 m depth). Another powerful approach has been SVGs [ 18 , 23 , 24 ], which sorts and sequences the genome of one virus at a time directly from as low as 1 mL of seawater, or even less [ 18 ]. SVGs has been employed to reveal novel highly microdiverse abundant viruses not only from marine samples but also from human salivary samples [ 25 ].…”

Viral discovery in the ‘realm’ of COVID‐19

“…Single‐virus genomics (SVG) ‐ flow cytometric sorting, whole genome amplification and sequencing ‐ now enables more complete genome sequences of these low‐abundance virions. The development of SVG, in particular, has delivered near‐complete genomes of large viruses previously thought to be cellular (Martínez Martínez et al ., 2020), and highly microdiverse genomes that previously could not be assembled (Martinez‐Hernandez et al ., 2017). These glimpses of full viral genomes also provide insight into viral microdiversity on a population level, lending insight into transmission and persistence (Gregory et al ., 2019).…”

Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics

“…Although it enables the en masse sequencing of entire viral assemblages and to some degree provides quantitative community assessment, the taxonomic assignments and phylogenomic analyses are limited by the relatively short-read assemblies and the lack of reference viral genomes in public databases [13]. Alternatively, the sequencing of individual virions [14][15][16] or viral DNA cloned into fosmids [17,18] enables us to obtain much larger DNA fragments, and even the entire genomes, from the environmental samples, although these approaches can either over-or underrepresent the most common members in the viral community [15,19]. In any case, the approaches mentioned above have mainly been used so far to represent a diversity of free viruses (in opposition to intracellular phages), implying that the host cells they have been infecting are already lysed and thus absent from the bacterial assemblages.…”

“…To overcome this issue and to establish possible associations between phages and bacteria, the single-cell sequencing and bioinformatic reconstruction of viral reads from within the single amplified genomes (SAGs) of the infected cells can be used [16,[20][21][22][23]. If successful, the mining of SAGs datasets not only makes possible the discovery of novel phage genomes [24], but, more importantly, elucidates the ecological relevance and enables a more robust classification of viral sequences [23].…”