Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

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

When implemented into virus-discovery methods based on shotgun sequencing, next-generation technologies greatly enhance turnaround time and sensitivity. For example, the 454 system was implemented into a virus discovery assay based on an improved version of the VIDISCA protocol to minimize rRNA contamination [25] . Likewise, the association of NGS techniques with rolling circle amplification (RCA), another method for virus discovery, could greatly increase its performance. RCA employs the PhiX29 polymerase to selectively amplify small double stranded DNA (dsDNA) molecules and is used to amplify circular genomes of DNA viruses and bacteria plasmids [26] . Recently, RCA led to the identification and whole genome sequencing of novel human papillomaviruses and polyomaviruses [27] , including human polyomaviruses 6 and 7 (HPyV6 and HPyV7), detected in cutaneous swab specimens of healthy persons [28] , and trichodysplasia spinulosa-associated polyomavirus (TSPyV), detected in skin lesions from immunocompromised patients [29] .