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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 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.

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Fig. 1: Methods to study viruses.
Fig. 2: Single-virus genomics workflow.
Fig. 3: Insights from SVG.
Fig. 4: Present and future of single-virus technologies.

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Acknowledgements

This work was supported by the Gordon and Betty Moore Foundation (grant 5334), the US National Science Foundation (NSF-OPP 1644155, NSF-OCE 1933289), the Spanish Ministry of Economy and Competitiveness (CGL2013-40564-R, RTI2018-094248-B-I00 and SAF2013-49267-EXP) and Generalitat Valenciana (ACOM/2015/133 and ACIF/2015/332).

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All authors researched data for the article, contributed to the discussion of the content and reviewed and edited the manuscript before submission. M.M.-G. and J.M.M. wrote the article.

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Correspondence to Manuel Martinez-Garcia.

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Glossary

IMG/VR database

Integrated data management and analysis system for cultivated and environmental viral genomes, which is publicly available for the scientific community.

Metagenomics

The study of sequenced nucleic acids obtained from bulk environmental samples (enriched in cells or viruses).

Tara expedition

Oceanic 3-year-long expedition around the world to investigate planktonic and coral ecosystems and the impacts of global change. More than 150 international scientists have taken part.

Auxiliary metabolic genes

Cellular host genes contained in the viral genome that modulate cellular metabolism during infection to improve viral replication.

Nucleocytoplasmic large DNA viruses

(NCLDVs). A group of large DNA viruses with genomes ranging from 150 kb to 1.2 Mb classified within the phylum Nucleocytoviricota. These viruses are referred to as ‘nucleocytoplasmic’ because they are often able to replicate in both the host cell nucleus and the host cell cytoplasm.

Contigs

High-confidence overlapped DNA sequenced reads that represent a consensus region of a genome.

Flow cytometry

Technique used to detect and measure some physical and chemical features of a population of cells, viruses or particles suspended in a fluid that flow one at a time through a laser beam, where the light scattered is detected along with other fluorescence features. The sample is often fluorescently stained with cell and/or virus markers.

Single amplified genomes

(SAGs). Genome sequences obtained from sequencing and assembly of the amplified genetic material from an individual sorted single cell.

Multiple-displacement amplification

Common whole-genome amplification technique used in single-cell genomics to amplify minute amounts of DNA. DNA synthesis and amplification is done by Φ29 DNA polymerase.

Virions

Complete virus particles, in their extracellular phase, that are able to carry out the infectious process. Typically, the viral genome is enclosed in a protein structure (capsid) and is sometimes surrounded by a lipid membrane.

Gene-transfer agents

Phage-like entities that contain only a random piece of the cellular genome, which is insufficient to encode its protein components.

Consensus sequences

The calculated order of the most frequent residues, either nucleotide or amino acid, found at each position in a sequence.

Ultradeep sequencing

DNA sequencing performed at very high coverage. ‘Deep sequencing’ refers to sequencing a genomic region multiple times, sometimes hundreds or even thousands of times.

Fosmids

Clone system based on the bacterial F plasmid usually in Escherichia coli that can hold a DNA insert of up to 40 kb in size.

Deep chlorophyll maximum

Region below the surface of water with the maximum concentration of chlorophyll.

Viral single amplified genomes

(vSAGs). Genome sequences obtained from sequencing and assembly of the amplified genetic material from an individual sorted single-virus particle.

Viral shunt

Mechanism mediated by viral infection and consequently cell lysis that prevents (prokaryotic and eukaryotic) marine microbial particulate organic matter from migrating up trophic levels by recycling it into dissolved organic matter.

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Martínez Martínez, J., Martinez-Hernandez, F. & Martinez-Garcia, M. Single-virus genomics and beyond. Nat Rev Microbiol 18, 705–716 (2020). https://doi.org/10.1038/s41579-020-00444-0

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