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.
Highlights
Oropouche virus (OROV) is the causative agent of Oropouche fever, an arboviral illness that is usually self-limiting and mild but in rare cases infects the central nervous system and causes meningitis [1,2]
Oropouche virus (OROV) causes outbreaks of febrile illness in areas of South and Central America and we recently identified it in Ecuador for the first time, using metagenomic sequencing
The genome sequence data revealed that the Ecuadorian strain of the virus was not detected using a published qRT-PCR, as it differed genetically at the binding site of the reverse primer
Summary
Oropouche virus (OROV) is the causative agent of Oropouche fever, an arboviral illness that is usually self-limiting and mild but in rare cases infects the central nervous system and causes meningitis [1,2]. OROV is one of the most clinically important orthobunyaviruses in the Americas, with over half a million cases and more than 30 major outbreaks reported since it was first isolated in Trinidad and Tobago in 1955 [4]. These figures are likely to be underestimates, caused in part by underreporting due to the similar clinical presentation of other arboviral diseases that co-circulate in the same areas, including dengue virus (DENV), chikungunya virus (CHIKV), Mayaro virus (MAYV), yellow fever virus (YFV) and Zika virus (ZIKV) [4,5]. This led us to further investigate the presence of OROV in an additional 196 febrile patients from the same coastal area of Esmeraldas, Ecuador, sampled in 2016
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