design: Total RNA was extracted from clinical samples using a combination of TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy columns (Qiagen, Hilden, Germany). The RNA was converted into cDNA by using Superscript IV First-Strand Synthesis Kit (Invitrogen). The concentration of each sample was determined using High Sensitivity reagents with Qubit 2.0 fluorometer (Invitrogen). There was no PCR amplification step. Samples were analysed by RT-qPCR in parallel and only samples with CT values below 25 were included. DNA libraries were prepared using the NexteraXT kit (Illumina, San Diego, CA, USA). DNA libraries were sequenced on the Illumina MiSeq in paired-end mode using the MiSeq 600 cycle v3 kit (Illumina). Raw sequence data were analysed and mapped using Genomics software package, workbench 10 (CLC Bio, Aarhus, Denmark). Raw reads were trimmed, and subsets of each trimmed dataset were assembled de novo to generate reference sequences for each data set. Basic trimming was done by CLC-bio software to generate FastQ files.