Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing
By
Emma 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 T Pullan
Posted 27 Jun 2019
bioRxiv DOI: 10.1101/683953
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 rRT-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 rRT-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.
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