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Targeted metagenomics using strand-specific libraries with target enrichment is a sensitive, generalized approach to pathogen sequencing and transcriptome profiling. Using this method, we recovered 13 (76%) complete human respiratory syncytial virus (RSV) genomes from 17 clinical respiratory samples, reconstructed the phylogeny of the infecting viruses, and detected differential gene expression between two RSV subgroups, specifically, a lower expression of the P gene and a higher expression of the M2 gene in RSV-A than in RSV-B. This methodology can help to relate viral genetics to clinical phenotype and facilitate ongoing population-level RSV surveillance and vaccine development.

Original publication

DOI

10.1093/infdis/jiaa448

Type

Journal article

Journal

J Infect Dis

Publication Date

23/07/2020

Keywords

RNA sequencing, differential gene expression, respiratory syncytial virus, transcriptome profiling, whole-genome sequencing