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.

Overall proportions of normalized read counts of viral families (excluding EAV and PhHV control reads, cut-off of �5normalized reads) detected by mNGS per patient are shown in Fig 4. Patients with viral pathogens (PCR target viruses) had significantly reduced proportions of bacteriophages when compared to patients without viral pathogen:0% and 79% bacteriophages respectively (p<0.001) bacteriophage reads vs. all viral reads, normalized reads excluding EAV and PhHV control reads. The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . Shannon diversity (normalized reads, excluding internal controls) was significant lower for all viral reads (P<0.001) and eukaryotic viruses (p = 0.028) in patients with viral pathogens (PCR target viruses positive). No significant association was found between the diversity scores, nor the percentage of bacteriophages, and the following parameters: disease severity, length of exacerbation, number of exacerbations during the study period, difference in FEV 1 , GOLD stage, smoking, CRP level, and the virus species (results not shown).