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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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