Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing.
Emma Louise WiseSully MárquezJack MellorsVerónica PazBarry AtkinsonBernardo GutierrezSonia ZapataJosefina ColomaOliver G PybusSimon K JacksonGabriel TruebaGyorgy FejerChristopher H LogueSteven T PullanPublished in: PLoS neglected tropical diseases (2020)
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.
Keyphrases
- single cell
- case report
- end stage renal disease
- high throughput
- antibiotic resistance genes
- ejection fraction
- chronic kidney disease
- newly diagnosed
- peritoneal dialysis
- gene expression
- prognostic factors
- chemotherapy induced
- big data
- electronic health record
- dna methylation
- healthcare
- multidrug resistant
- machine learning
- microbial community
- genome wide
- artificial intelligence
- gram negative
- antimicrobial resistance
- deep learning
- high throughput sequencing