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

Autor: 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 T Pullan
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Zdroj: PLoS Neglected Tropical Diseases, Vol 14, Iss 1, p e0007897 (2020)
Druh dokumentu: article
ISSN: 1935-2727
1935-2735
DOI: 10.1371/journal.pntd.0007897
Popis: 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.
Databáze: Directory of Open Access Journals
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