Next-generation sequencing diagnostics to identify etiologies of acute undifferentiated fever in the Peruvian Amazon

In the tropics, ~50% of patients with acute undifferentiated febrile illnesses (AUFI) remain undiagnosed. Differential diagnosis, important to guide treatment and case management, is challenged by several factors including a broad variety of (un)known pathogens causing AUFI, large range of overlapping symptoms making clinical diagnoses unreliable, epidemiological synergy between shared vectors and geographic distribution of etiologies, and limited laboratory capacity. To date, approaches used for the identification of AUFI etiologies mostly rely on targeted tests for few pathogens, while pathogen coinfections remain understudied because once a pathogen is detected, others are rarely sought. Our objective is to implement metagenomic sequencing on Oxford Nanopore’s minION platform and evaluate the potential impact of this technology on standard clinical diagnostics and care, pathogen surveillance, and public health. Using retrospective serum samples collected from AUFI patients between 2018-2021 in Yurimaguas and Iquitos, our project aims to (1) evaluate the utility of nanopore metagenomics in absence of a diagnosis employing samples that tested negative to DENV, ZIKV, YFV, CHIKV, malaria and Leptospirosis, (2) evaluate the added value of nanopore metagenomics for samples with an existing diagnosis on samples positive to DENV and (3) evaluate the cost-effectiveness of metagenomic nanopore diagnostics and surveillance in Peru. This pilot study would build up the necessary know-how and infrastructure to perform metagenomic sequencing and also to conduct follow up studies using full genome sequences of those pathogens to answer specific epidemiological questions (spread, origin, source) and the possible implication of viral evolution in disease severity, resistance, and transmissibility.