Analysis of the lung virome under mechanical ventilation by high-throughput sequencing. Lung virome

The respiratory virome of 24 pulmonary samples (tracheal aspirate or bronchoalveolar lavage) in 9 patients was evaluated. For each sample, DNA and RNA libraries were generated in order to analyze the entire viral population. The Nextera DNA XT Kit (Illumina®, San Diego, CA, USA) and the RNA Seq Trio kit (Nugen®, San Carlos, California, USA) were thus used before 2 x 150 bp paired end sequencing on a NextSeq 500 platform (Illumina, San Diego, California, USA). The bioinformatics analysis was performed using the SURPI (“Sequence based ultra rapid pathogen identification”) computational pipeline. High throughput sequencing generated a total of about 1 billion reads, a majority of them corresponding to human reads (83%). Nevertheless, SURPI identified a total of 196580 viral reads. All the viruses detected by conventional methods were identified by high throughput sequencing. In addition, a large number of viruses not detected by PCR were detected by metagenomics as Herpesviridae Anelloviridae and phages. This feasibility study thus validates the strategy of a unique metagenomics protocol with the final aim of studying not only the bacterial microbiota but also the virome.