Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers

J Infect. 2019 Oct;79(4):383-388. doi: 10.1016/j.jinf.2019.08.003. Epub 2019 Aug 6.


Objectives: Travel-associated infections are challenging to diagnose because of the broad spectrum of potential aetiologies. As a proof-of-principle study, we used MNGS to identify viral pathogens in clinical samples from returning travellers in a single center to explore its suitability as a diagnostic tool.

Methods: Plasma samples from 40 returning travellers presenting with a fever of ≥38°C were sequenced using MNGS on the Illumina MiSeq platform and compared with standard-of-care diagnostic assays.

Results: In total, 11/40 patients were diagnosed with a viral infection. Standard of care diagnostics revealed 5 viral infections using plasma samples; dengue virus 1 (n = 2), hepatitis E (n = 1), Ebola virus (n = 1) and hepatitis A (n = 1), all of which were detected by MNGS. Three additional patients with Chikungunya virus (n = 2) and mumps virus were diagnosed by MNGS only. Respiratory infections detected by nasal/throat swabs only were not detected by MNGS of plasma. One patient had infection with malaria and mumps virus during the same admission.

Conclusions: MNGS analysis of plasma samples improves the sensitivity of diagnosis of viral infections and has potential as an all-in-one diagnostic test. It can be used to identify infections that have not been considered by the treating physician, co-infections and new or emerging pathogens.

Summary: Next generation sequencing (NGS) has potential as an all-in-one diagnostic test. In this study we used NGS to diagnose returning travellers with acute febrile illness in the UK, highlighting cases where the diagnosis was missed using standard methods.

Keywords: Diagnosis; NGS; Returning travellers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Bacterial Infections / diagnosis
  • Bacterial Infections / microbiology
  • Fever / virology*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Metagenomics
  • Parasitic Diseases / diagnosis
  • Parasitic Diseases / parasitology
  • Proof of Concept Study
  • RNA, Viral / genetics
  • Respiratory Tract Infections / blood
  • Respiratory Tract Infections / diagnosis*
  • Respiratory Tract Infections / microbiology
  • Respiratory Tract Infections / virology
  • Retrospective Studies
  • Sensitivity and Specificity
  • Travel / statistics & numerical data
  • Travel-Related Illness*
  • Virus Diseases / blood
  • Virus Diseases / diagnosis*
  • Viruses / genetics
  • Viruses / pathogenicity


  • RNA, Viral