Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

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

Mutations of human rhinovirus (HRV) genome were explored in a lung transplant recipient infected with the same HRV strain for more than two years [91] . Analysis of complete HRV genome sequences by both classical and Illumina ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that HRV populations in the upper and lower respiratory tract were phylogenetically indistinguishable over the course of infection, likely because of constant viral population mixing. Nevertheless, signatures of putative adaptation to lower airway conditions appeared after several months of infection, with the occurrence of specific changes in the 5'UTR polypyrimidine tract and the VP2 immunogenic site 2 of HRV genome, which might have been relevant for viral growth at lower airway conditions [91] .