Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing

Emma L. Wise, Sully Márquez, Jack Mellors, Verónica Paz, Barry Atkinson, Bernardo Gutierrez, Sonia Zapata, Josefina Coloma, Oliver G. Pybus, Simon K. Jackson, Gabriel Trueba, Gyorgy Fejer, Christopher H. Logue*, Steven Pullan

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)
22 Downloads (Pure)

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.

Original languageEnglish
Article numbere0007897
Pages (from-to)1-15
Number of pages15
JournalPLoS Neglected Tropical Diseases
Volume14
Issue number1
DOIs
Publication statusPublished - 21 Jan 2020

Bibliographical note

Funding Information: This work was funded by Public Health England as part of a PHE-funded PhD studentship awarded to ELW, SKJ, GF, CHL, and STP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Open Access: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publisher Copyright: © 2020 Wise et al.

Citation: Wise EL, Ma´rquez S, Mellors J, Paz V, Atkinson B, Gutierrez B, et al. (2020) Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing. PLoS Negl Trop Dis 14(1): e0007897.

DOI: https://doi.org/10.1371/journal.pntd.0007897

Fingerprint

Dive into the research topics of 'Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing'. Together they form a unique fingerprint.

Cite this