TY - JOUR T1 - Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples JF - bioRxiv DO - 10.1101/676155 SP - 676155 AU - Kuiama Lewandowski AU - Yifei Xu AU - Steven T. Pullan AU - Sheila F. Lumley AU - Dona Foster AU - Nicholas Sanderson AU - Alison Vaughan AU - Marcus Morgan AU - Nicole Bright AU - James Kavanagh AU - Richard Vipond AU - Miles Carroll AU - Anthony C. Marriott AU - Karen E Gooch AU - Monique Andersson AU - Katie Jeffery AU - Timothy EA Peto AU - Derrick W. Crook AU - A Sarah Walker AU - Philippa C. Matthews Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/06/19/676155.abstract N2 - Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential of a diagnostic test for influenza which also provides insights on transmission, evolution and drug resistance, and simultaneously detects other viruses. We therefore set out to apply Oxford Nanopore Technology to metagenomic sequencing of respiratory samples. We generated influenza reads down to a 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 (p = 4.7×10-5). Applying our methods to clinical throat swabs, we generated influenza reads for 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. Thus Nanopore sequencing operated with 83% sensitivity (95% CI 67-93%) and 100% specificity (95% CI 69-100%) compared to the current diagnostic standard. Coverage of full length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza titres, we were able to reconstruct >99% complete sequence for all eight gene segments. We also detected Human Coronavirus and generated a near complete Human Metapneumovirus genome from clinical samples. While further optimisation is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza and other respiratory viruses. ER -