Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants

J Infect Dis. 2020 Oct 7;222(Suppl 7):S666-S671. doi: 10.1093/infdis/jiaa448.

Abstract

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 2 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. Clinical Trials Registration. NCT03627572 and NCT03756766.

Keywords: RNA sequencing; differential gene expression; respiratory syncytial virus; transcriptome profiling; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression
  • Gene Expression Profiling
  • Genome, Viral*
  • Humans
  • Infant
  • Phylogeny
  • Respiratory Syncytial Virus Infections / metabolism
  • Respiratory Syncytial Virus Infections / virology*
  • Respiratory Syncytial Virus, Human / classification
  • Respiratory Syncytial Virus, Human / genetics*
  • Respiratory Syncytial Virus, Human / metabolism
  • Sequence Analysis
  • Sequence Analysis, RNA
  • Whole Genome Sequencing

Associated data

  • ClinicalTrials.gov/NCT03627572
  • ClinicalTrials.gov/NCT03756766