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Nanopore Sequencing Confirms Zoonotic Source for Lassa Fever Outbreak in Nigeria

NEW YORK (GenomeWeb) – An international team led by investigators from Germany, Nigeria, and the UK has analyzed a Lassa fever outbreak in Nigeria using metagenomic nanopore sequencing of Lassa virus (LASV) — one of several recent efforts aimed at applying nanopore sequencing in the field during infectious disease outbreaks.

The team published the results of its analysis, which was conducted in Nigeria during the 2018 outbreak, in Science today.

"Portable metagenomic sequencing of genetically diverse RNA viruses on the MinIon, direct from patient samples without the need to export material outside of the country of origin and with no pathogen-specific enrichment, is shown to be a feasible methodology enabling a real-time characterization of potential outbreaks in the field," corresponding and co-senior author Stephan Gunther, a researcher at the Bernhard Nocht Institute for Tropical Medicine and the German Center for Infection Research, and his colleagues wrote.

The researchers used Oxford Nanopore Technologies' MinIon sequencer to perform metagenomic RNA sequencing on samples prepared with random reverse transcription and sequence-independent single-primer amplification (SISPA). They characterized three dozen LASV genomes from a 2018 hemorrhagic fever outbreak that spanned 18 Nigerian states and involved nearly 1,500 suspected and 376 confirmed Lassa fever cases over the first few months of 2018.

Following that pilot analysis, they included information on 120 Nigerian LASV samples and used Illumina re-sequencing on a subset of SISPA samples to validate the metagenomic approach.

The team's results placed the LASV isolates behind the outbreak into genotypes II and III. Based on the genetic diversity and phylogenetic comparisons with LASV isolates identified in the country in the past, the researchers concluded that the 2018 Lassa fever cases came from a zoonotic source rather than stemming from a LASV strain with more widespread human-to-human transmission capabilities.

"The conclusions drawn from the first set of genome sequences immediately eased fears of extensive human-to-human transmission and allowed public health resources to be allocated appropriately," the authors wrote, noting that this response "was focused on intensified community engagement on rodent control, environmental sanitation, and safe food storage."

The results line up with those reported in a New England Journal of Medicine study by another team, led by researchers at the Broad Institute, that sequenced new LASV isolates with Illumina short reads and performed a phylogenetic analysis involving hundreds of LASV genomes from Nigeria, Sierra Leone, Liberia, and Côte d'Ivoire.

For a corresponding perspectives article appearing in Science today, Boston University infectious diseases researcher Nahid Bhadelia noted that both studies provided "critical epidemiological clues" to the spread of LASV in Nigeria.

Even so, Bhadelia cautioned that "a sizeable portion of the world's population … is simply treated on the basis of symptomatology for common infectious diseases" due to laboratory access issues and argued that "the real test of emerging microbial detection techniques will be how accurate, affordable, and amenable to widespread use they are and whether they can test both for common endemic infectious diseases as well as rare pathogens of high concern, such as viral hemorrhagic fevers."

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