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Viral genome sequencing in the heart of a Lassa outbreak

January 03, 2019

The first researchers to deploy a mobile nanopore sequencing technology to evaluate viral genomics at the height of a Lassa virus outbreak in 2018 now report their results. According to their new study, the emerging technology enables real-time characterization of potential outbreaks in the field, to answer time-sensitive questions about strain type and transmission pathway. Lassa fever, a viral hemorrhagic illness endemic to West Africa, is chiefly passed to people who eat food contaminated by infected rodents. Throughout West Africa, cases of the Lassa virus have been rising steadily, albeit more slowly over the past few years; generally, only a handful of new cases are reported each year. However, a dramatic upsurge of cases in Nigeria during early 2018 signaled an incipient outbreak and raised fears about the potential emergence of a new, more virulent strain of the illness - one with a much higher transmission rate. Responding to these concerns, Liana Eleni Kafetzopoulou and colleagues employed a new genomic technology - metagenomic nanopore sequencing using the small and portable Oxford Nanopore MinION device - which allowed for rapid, mobile viral genome sequencing directly from clinical samples as the outbreak was progressing. Kafetzopoulou et al. trialed the device by sequencing a total of 120 Lassa positive samples over a period of seven weeks. The detailed results didn't conclusively suggest a novel virus strain was to blame, nor did they reveal the emergence of person-to-person transition. They did implicate rodent contamination as the main driver of the outbreak. According to the authors, the ability of the technology to rapidly provide a detailed and real-time characterization of the pathogen early on during the outbreak assuaged concerns of novel strains and unknown vectors. It also allowed public health officials to respond and allocate resources appropriately. In a Perspective, Nahid Bhadelia suggests that the true test of novel techniques like mobile Nanopore sequencing will be how accessible and widespread it becomes; large portions of areas prone to dangerous viruses like Lassa lack any sort of diagnostic technology, laboratory or otherwise.
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American Association for the Advancement of Science

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