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Metagenomic next-generation sequencing of the 2014 Ebola virus disease outbreak in the Democratic Republic of the Congo
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Edité par CCSD ; American Society for Microbiology -
International audience. We applied metagenomic next-generation sequencing (mNGS) to detect Zaire Ebola virus (EBOV) and other potential pathogens from whole blood samples from 70 patients with suspected Ebola hemorrhagic fever during a 2014 outbreak in Boende, Democratic Republic of the Congo (DRC) and correlated these findings with clinical symptoms. 20 of 31 patients (64.5%) tested in Kinshasa, DRC, were EBOV positive by quantitative RT-PCR (qRT-PCR). Despite partial degradation of sample RNA during shipping and handling, mNGS followed by EBOV-specific capture probe enrichment in a US genomics laboratory identified EBOV reads in 22 of 70 samples (31.4%), versus 21 of 70 (30.0%) EBOV-positive samples by repeat qRT-PCR (overall concordance = 87.1%). Reads from P. falciparum (malaria) were detected in 21 patients, of which at least 9 (42.9%) were co-infected with EBOV. Other positive viral detections include hepatitis B virus (n=2), human pegivirus 1 (n=2), Epstein-Barr virus (n=9), and Orungo virus (n=1), a virus in the Reoviridae family. The patient with Orungo virus infection presented with an acute febrile illness and died rapidly from massive hemorrhage and dehydration. Although the patient blood sample was negative by EBOV qRT-PCR testing, identification of viral reads by mNGS confirmed the presence of EBOV co-infection. In total, 9 new EBOV genomes (3 complete genomes, and an additional 6 ≥50% complete) were assembled. Relaxed molecular clock phylogenetic analysis demonstrated a molecular evolutionary rate for the Boende strain 4-10X slower than that of other Ebola lineages. These results demonstrate the utility of mNGS in broad-based pathogen detection and outbreak surveillance.
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