Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

Barzon, Luisa; Lavezzo, Enrico; Militello, Valentina; Toppo, Stefano; Palù, Giorgio

In the diagnostic setting, metagenomic approaches could be used for systematic analysis of samples collected from patients with unexplained illness, especially in the context of outbreaks and epidemics [70, 71] . As mentioned in the above section, application of high throughput NGS methods in viral metagenomics can greatly enhance the chances to identify viruses in clinical samples, including viruses that are too divergent from known viruses to be detected by PCR or microarray techniques (reviewed in ref. [20] ). An attractive application of metagenomic approaches is the study of influenza, given the constant threat of antigenic drift and shift. Deep sequencing strategies can be used to monitor the emergence of mutations that confer virulence or resistance to antiviral drugs, to detect influenza viruses in clinical samples, and to identify viral quasispecies [22, 31, 32] . In addition, deep sequencing of clinical samples allows to identify and characterize not only novel pathogens but also the microbiota and host response to infection [32] .