Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing

PLoS Negl Trop Dis. 2020 Jan 21;14(1):e0007897. doi: 10.1371/journal.pntd.0007897. eCollection 2020 Jan.

Abstract

Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68-99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Bunyaviridae Infections / diagnosis
  • Bunyaviridae Infections / virology*
  • Cohort Studies
  • Ecuador
  • Genome, Viral
  • Humans
  • Metagenome
  • Orthobunyavirus / classification
  • Orthobunyavirus / genetics
  • Orthobunyavirus / isolation & purification*
  • Phylogeny
  • RNA, Viral / genetics
  • Reverse Transcriptase Polymerase Chain Reaction / methods*

Substances

  • RNA, Viral

Supplementary concepts

  • Oropouche orthobunyavirus