The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

van Rijn, Anneloes L.; van Boheemen, Sander; Sidorov, Igor; Carbo, Ellen C.; Pappas, Nikos; Mei, Hailiang; Feltkamp, Mariet; Aanerud, Marianne; Bakke, Per; Claas, Eric C. J.; Eagan, Tomas M.; Hiemstra, Pieter S.; Kroes, Aloys C. M.; de Vries, Jutte J. C.

Of the 23 qPCR positive samples, 22 tested positive with mNGS, resulting in a sensitivity of mNGS of 96%. Only one sample, that was rhinovirus positive by qPCR (Cq 38), could not be detected by mNGS ( Table 3) . Coverage of reference genomes was high (93-100%) with the exception of three samples: 30% coverage of rhinovirus C (1,401,120 mapped reads, accession AY391777.1). A coverage plot of all reads against this reference strain (Fig 1) showed good horizontal and vertical coverage (read coverage depth 428). The original OC43 qPCR amplification appeared to have been inhibited, and repeated OC43 qPCR confirmed the positive mNGS result (Cq 25). Sensitivity, specificity and predictive value. The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). Calculations were made using different cut-off values of respectively �0, �15 and �50 normalized read counts. With a cutoff of �15, the sensitivity was 92% and specificity 100% and the positive predictive value (PPV) increased to 92%. The negative predictive value (NPV) was 100% for all cut-off levels.