Environmental Shotgun Sequencing (ESS). (A) Sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds.
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain viral diversity in the environment that is often missed in studies targeting specific potential reservoirs. It reveals important information on virus evolution and the genetic diversity of the viral community without the need for isolating viral species and cultivating them in the laboratory. This approach has created improvements in molecular epidemiology and accelerated the discovery of novel viruses.
^David M. Kristensen1, Arcady R. Mushegian1, 2, Valerian V. Dolja3 and Eugene V. Koonin4, New dimensions of the virus world discovered through metagenomics. Trends in Microbiology, Volume 18, Issue 1, 11-19, 25 November 2009.
^Bernardo P, Albina E, Eloit M, Roumagnac P.. Pathology and viral metagenomics, a recent history.[Article in French].Med Sci (Paris). 2013 May;29(5):501-8.