Working Paper Article Version 1 This version is not peer-reviewed

An Amplicon-Based Approach for the Whole Genome Sequencing of Human Metapneumovirus

Version 1 : Received: 2 February 2021 / Approved: 3 February 2021 / Online: 3 February 2021 (10:08:44 CET)

A peer-reviewed article of this Preprint also exists.

Tulloch, R.L.; Kok, J.; Carter, I.; Dwyer, D.E.; Eden, J.-S. An Amplicon-Based Approach for the Whole-Genome Sequencing of Human Metapneumovirus. Viruses 2021, 13, 499. Tulloch, R.L.; Kok, J.; Carter, I.; Dwyer, D.E.; Eden, J.-S. An Amplicon-Based Approach for the Whole-Genome Sequencing of Human Metapneumovirus. Viruses 2021, 13, 499.

Journal reference: Viruses 2021, 13, 499
DOI: 10.3390/v13030499

Abstract

Human metapneumovirus (HMPV) is an important cause of upper and lower respiratory tract disease in individuals of all ages. It is estimated that most individuals will be infected by HMPV by the age of 5 years old. Despite this burden of disease, there remains caveats in our knowledge of virus global genetic diversity due to a lack of HMPV sequencing, particularly at whole genome scale. The purpose of this study was to create a simple and robust approach for HMPV whole genome sequencing to be used for genomic epidemiological studies. To design our assay, all available HMPV full length genome sequences were downloaded from the NCBI GenBank database and used to design four primer sets to amplify long, overlapping amplicons spanning the viral genome and, importantly, specific to all known HMPV subtypes. These amplicons were then pooled and sequenced on an Illumina iSeq; however the approach is suitable to other common NGS platforms. We demonstrate the utility of this method using a representative subset of clinical samples and examine these sequences using a phylogenetic approach. Here we present an amplicon-based method for the whole genome sequencing of HMPV from clinical extracts that can be used to better inform genomic studies of HMPV epidemiology and evolution.

Subject Areas

human metapneumovirus; whole genome sequencing; genomic epidemiology

Comments (0)

We encourage comments and feedback from a broad range of readers. See criteria for comments and our diversity statement.

Leave a public comment
Send a private comment to the author(s)
Views 0
Downloads 0
Comments 0
Metrics 0


×
Alerts
Notify me about updates to this article or when a peer-reviewed version is published.
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.