The metagenomic approach and causality in virology

Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

The term "metagenomics" indicates a joint analysis of microbial genomes in an environmental sample, not only from the genetic point of view but also in terms of function. 18 The term "viral metagenomics" involves the detection of the genome of all viruses present in environmental samples (e.g., fresh water lake, reclaimed water), 5, 20 or biological samples (e.g., respiratory tract aspirates, human and animal feces) 14,17,28 that could harbor a large diversity of viruses. This term is also used when the metagenomic approach is applied to identify the genome of a virus that can potentially cause a specific disease and/or a cytopathic effect in cell culture, when other common techniques failed to detect the virus. 24, 30 The metagenomic approach includes several steps, as follows: the purification and concentration of the viral particles (or the viral nucleic acid if the virus is found in the latent form or integrated into the host genome), nucleic acid extraction, reverse transcription of RNA to cDNA, random amplification of genomic sequences, sequencing of nucleic acid fragments, and sequence analysis using bioinformatics tools. 2, 12, 27 Nucleic acid fragments can be sequenced using the Sanger method after molecular cloning or using next-generation sequencing platforms, which are more sensitive and generate a much larger number of sequences than molecular cloning using a bacterial host. 2, 12, 16, 27