Highlights d A family of human DNA viruses was identified and named Redondoviridae d Redondoviruses were the second most common virus in human respiratory virome samples d Some subjects with periodontitis and critical illness had higher redondovirus levels

In Table S1 of this article as originally published, the wrong sequence was mistakenly included for the pan-HCRV-AA qPCR assay probe during assembly of the table. The table has now been updated with the correct sequence (AAATGGAAGGGAGAGA GGCCTTTGG). This error does not alter the conclusions of the original paper. The authors apologize for any confusion or inconvenience this error may have caused.

Redondoviridae is a newly-established family of circular Rep-encoding single stranded (CRESS) DNA viruses found in the human oro-respiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from US urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61-82% prevalence, and an urban US population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species ( Brisavirus and Vientovirus ) in single individuals, persistence over time, and evidence of inter-genomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals, and encode a Rep protein implicated in facilitating recombination. IMPORTANCE Redondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and non-industrialized African populations from Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally-sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro , consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.

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Endobronchial stents are increasingly used to treat airway complications in multiple conditions including lung transplantation but little is known about the biofilms that form on these devices. We applied deep sequencing to profile luminal biofilms of 46 endobronchial stents removed from 20 subjects primarily with lung transplantation-associated airway compromise. Microbial communities were analyzed by bacterial 16S rRNA and fungal ITS marker gene sequencing. Corynebacterium was the most common bacterial taxa across biofilm communities. Clustering analysis revealed three bacterial biofilm types: one low diversity and dominated by Corynebacterium ; another was polymicrobial and characterized by Staphylococcus ; and the third was polymicrobial and associated with Pseudomonas , Streptococcus , and Prevotella . Biofilm type was significantly correlated with stent material: covered metal with the Staphylococcus -type biofilm, silicone with the Corynebacterium -dominated biofilm, and uncovered metal with the polymicrobial biofilm. Subjects with sequential stents had frequent transitions between community types. Fungal analysis found Candida was most prevalent, Aspergillus was common and highly enriched in two of three stents associated with airway anastomotic dehiscence, and fungal taxa not typically considered pathogens were highly enriched in some stents. Thus, molecular analysis revealed a complex and dynamic endobronchial stent biofilm with three bacterial types that associate with stent material, a central role for Corynebacterium , and that both expected and unexpected fungi inhabit this unique niche. The current work provides a foundation for studies to investigate the relationship between stent biofilm composition and clinical outcomes, mechanisms of biofilm establishment, and strategies for improved stent technology and use in airway compromise.