Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples. Detection of influenza A virus direct from human clinical respiratory samples

Detection of Influenza virus by application of Oxford Nanopore Technology to metagenomic sequencing of respiratory samples. Influenza reads limit of detection of 102-103 genome copies/ml in pooled samples, observing a strong relationship between the viral titre and the proportion of influenza reads. In clinical throat swabs, influenza reads detected from 27/27 samples with high-to-mid viral titres (Cycle threshold (Ct) values <30) and 6/13 samples with low viral titres (Ct values 30-40). No false positive reads were generated from 10 influenza-negative samples.