Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage

Xu, Y.; Lewandowski, K.; Lumley, S.; Sanderson, N. D.; Vaughan, A.; Vipond, R. T.; Carroll, M. W.; Jeffery, K.; Foster, D.; Walker, A. S.; Peto, T. E. A.; Crook, D. W.; Pullan, S. T.; Matthews, P. C.

doi:10.1101/496687

bioRxiv · 10.1101/496687

Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage

Xu, Y.·Lewandowski, K.·Lumley, S.·Sanderson, N. D.·Vaughan, A.·Vipond, R. T.·Carroll, M. W.·Jeffery, K.·Foster, D.·Walker, A. S.·Peto, T. E. A.·Crook, D. W.·Pullan, S. T.·Matthews, P. C.

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Abstract

Human metapneumovirus (HMPV) has been recognized as an important pathogen which can cause a spectrum of respiratory tract disease. Here, we report Nanopore metagenomic sequencing of the first full length HMPV genome directly from a throat swab from a UK patient with complex lung disease and immunocompromise. We found a predominance (26.4%) of HMPV reads in the metagenomic sequencing data and consequently assembled the full genome at a high depth of coverage (mean 4,786). Through phylogenetic analyses, we identified this HMPV strain to originate from a unique genetic group in A2b, showing the presence of this group in the UK. Our study demonstrated the effectiveness of Nanopore metagenomic sequencing for diagnosing infectious diseases and recovering complete sequences for genomic characterization, highlighting the applicability of Nanopore sequencing in clinical settings.\n\nImportanceNanopore metagenomic sequencing has the potential to evolve as a point-of-care test for a range of infectious diseases. Here, we report the first full length human metapneumovirus (HMPV) genome in the UK sequenced by Nanopore from a non-invasive sample from an immunocompromised patient. We demonstrate the presence of HMPV from a unique genetic group not previously reported from the UK. Our study demonstrates the effectiveness of Nanopore sequencing for diagnosing an infection that was not detected by routine first-line tests in the clinical microbiology laboratory. We report sufficient genomic data to provide insight into the epidemiology of infection and with the potential to inform treatment decisions.

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Xu, Y., Lewandowski, K., Lumley, S., Sanderson, N. D., Vaughan, A., Vipond, R. T., Carroll, M. W., Jeffery, K., Foster, D., Walker, A. S., Peto, T. E. A., Crook, D. W., Pullan, S. T., Matthews, P. C.. 2018-12-17. Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage. https://doi.org/10.1101/496687

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