Monitoring Viral Genetic Variation as a Tool To Improve Molecular Diagnostics for Mumps Virus

J Clin Microbiol. 2018 Sep 25;56(10):e00405-18. doi: 10.1128/JCM.00405-18. Print 2018 Oct.

Abstract

Here, we report how the analysis of viral genetic variation using next-generation sequencing (NGS) can be used as a tool to improve mumps virus diagnostics. Analysis of NGS data from recently circulating mumps virus isolates allowed optimization of the current mumps virus real-time reverse transcription-PCR (RT-PCR) by primer and probe modifications due to nucleotide variations. The modified assay showed a higher efficiency and sensitivity than the previously used CDC protocol for the detection of currently circulating mumps virus strains and could therefore offer better support for outbreak control. The NGS sequence data were also used to make predictions of changes in the hemagglutinin-neuraminidase protein structure that could explain possible immune escape mechanisms.

Keywords: genotype; molecular homology modelling; mumps virus; next-generation sequencing; real-time RT-PCR; vaccines.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genetic Variation*
  • Genome, Viral / genetics
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Models, Molecular
  • Molecular Diagnostic Techniques / methods*
  • Mumps / diagnosis
  • Mumps / virology*
  • Mumps virus / genetics*
  • Mumps virus / isolation & purification
  • Phylogeny
  • RNA, Viral / genetics
  • Sequence Analysis, RNA
  • Viral Proteins / chemistry
  • Viral Proteins / genetics

Substances

  • RNA, Viral
  • Viral Proteins