Single Virus Genomics

Bacteriophage lambda While single cell studies have focused on bacteria and cyanobacteria, single virions have yet to be isolated and genomically described using similar mechanisms. Viruses are ubiquitous and the most numerous and diverse biological entities on our planet. Nearly all aspects of our lives are influenced by viruses through shaping the environments that surround us, our immune responses and even our genomes. The field of environmental viral metagenomics has gained momentum over the past several years; however, sequencing of individual environmental viral genomes is currently dependent on the establishment of cultivable virus-host systems. With this in mind, if less than one percent of microbial populations can be cultured using standard microbiological techniques due to incongruencies in direct counts versus cultivatable microbes, then only a very small number of viruses have the likelihood of being genomically described. Currently, viral genomic sequences are lacking in public databases, with the exception of human viruses and those of agricultural and industrial significance (e.g. Lactococcal phages). Clearly, a better understanding of virus diversity and evolution will not be achieved until the genomes of a broad range of viruses are available.

This paper introduces an approach for isolating and characterizing the genomes of viruses called “Single Virus Genomics” (SVG). The benefits of SVG will be far-reaching, enabling novel virus discovery in a variety of clinical and environmental settings, altering our understanding of virus evolution, adaptation and ecology and facilitating the interpretation of viral genomic and metagenomic data by providing suitable reference genomes.

Single Virus Genomics: A New Tool for Virus Discovery. 2011 PLoS ONE 6(3): e17722. doi:10.1371/journal.pone.0017722
Whole genome amplification and sequencing of single microbial cells has significantly influenced genomics and microbial ecology by facilitating direct recovery of reference genome data. However, viral genomics continues to suffer due to difficulties related to the isolation and characterization of uncultivated viruses. We report here on a new approach called ‘Single Virus Genomics’, which enabled the isolation and complete genome sequencing of the first single virus particle. A mixed assemblage comprised of two known viruses; E. coli bacteriophages lambda and T4, were sorted using flow cytometric methods and subsequently immobilized in an agarose matrix. Genome amplification was then achieved in situ via multiple displacement amplification (MDA). The complete lambda phage genome was recovered with an average depth of coverage of approximately 437X. The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable.

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