A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens

Mol Cell Probes. 2019 Aug:46:101412. doi: 10.1016/j.mcp.2019.06.002. Epub 2019 Jun 12.

Abstract

Lineage 2 West Nile virus (WNV) strains have been implicated in severe encephalitis outbreaks in humans and equines residing in Europe. WNV molecular characterization is important for the development of diagnostic assays, as well as for obtaining molecular information, which is necessary for epidemiological investigations of virus transmission in areas at risk. For whole genome sequencing of lineage 2 WNV strains, directly from biological specimens, a PCR-based NGS protocol was developed. The method was applied in WNV-positive specimens obtained from animal, human and mosquito hosts in Greece. The results of its application indicate that, even in cases of low virus titers, the developed PCR-based NGS approach is able to provide whole genome sequences of lineage 2 WNV strains.

Keywords: Lineage 2; Next generation sequencing; PCR-Based; West Nile virus; Whole genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Culicidae / virology
  • Disease Outbreaks
  • Europe
  • Genome, Viral / genetics*
  • Greece
  • High-Throughput Nucleotide Sequencing
  • Horses / genetics
  • Horses / virology
  • Humans
  • Phylogeny*
  • RNA, Viral / genetics
  • West Nile Fever / diagnosis
  • West Nile Fever / genetics*
  • West Nile Fever / virology
  • West Nile virus / genetics*
  • West Nile virus / pathogenicity
  • Whole Genome Sequencing

Substances

  • RNA, Viral