Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung

Microbial communities in the lungs of cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) patients have been shown to be spatially heterogeneous. Viral communities may also vary spatially, leading to localized viral populations and infections. Here, we characterized viral communities from multiple areas of the lungs of two late-stage CF patients using metagenomics: the explanted lungs from transplant patient and lungs acquired post-mortem. All regions harbored eukaryotic viruses which may infect the human host, notably herpesviruses, anelloviruses, and papillomaviruses. In the highly diseased apical lobes of the explant lungs, viral diversity was extremely low and only eukaryotic viruses were present. The absence of phage suggests that CF-associated microbial biofilms may escape top-down controls by phage predation. The phage present in other lobes of the explant lungs and in all lobes of the post-mortem lungs comprised distinct communities, and encoded genes for clinically important microbial phenotypes, including small colony variants and antibiotic resistance. Based on the these observations, we postulate that viral communities in CF lungs are spatially distinct and contribute to CF pathology by augmenting the metabolic potential of the resident microbes as well as by directly damaging lung tissue via carcinomas and herpesviral outbreaks