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Genomic Analysis Offers Insight Into 2018 Nigeria Lassa Fever Outbreak

October 22, 2018

Tropical Medicine

Lassa fever, also known as Lassa hemorrhagic fever (LHF), is a type of viral hemorrhagic fever caused by the Lassa virus. Lassa fever is endemic to West Africa, where Mastomys natalensis rodents, a primary animal reservoir of Lassa virus, are common. The rodent is often found in or around human habitats, and people become infected with Lassa virus through direct contact with rodent urine and stool. People with Lassa fever also can transmit the virus to other people through close contact, although experts believe this is rare. Many of those infected by the virus do not develop symptoms, but when symptoms do occur, they typically include fever, weakness, headaches, vomiting, and muscle pains. Less commonly there may be bleeding from the mouth or gastrointestinal tract. The Nigeria Centre for Disease Control (NCDC) reported an unusually large increase in Lassa fever cases in 2018, with 523 laboratory-confirmed cases and 135 deaths from January 1 through October 7. While about 15-20% of people hospitalized with Lassa fever die from the disease, only 1% of all Lassa virus infections result in death, as many infections are symptomatic. Among those who survive, about a quarter have hearing loss, which improves over time in about half.

According to an article published in The New England Journal of Medicine (18 October 2018), a surge in Lassa fever cases in Nigeria in 2018 does not appear to be linked to a single virus strain or increased human-to-human transmission. Since public health officials were concerned that the Lassa fever outbreak in Nigeria in 2018 might be driven by a previously unknown factor, such as a new or more virulent Lassa virus strain, the authors analyzed Lassa virus genomes from patient samples to determine if genomic data signatures could explain the surge in cases.

For the study, when Lassa virus genomes were analyzed from 129 patients from the 2017-2018 outbreak, and from 91 patients from the 2015-2017 seasons, results showed that Lassa genomes from 2018 were drawn from a diverse range of viruses previously observed in Nigeria, rather than from a single dominant strain. This indicated that a single virus strain was not driving the surge in cases in 2018. Additionally, dating of the most recent ancestors of samples from 2018 showed limited support for human-to-human transmission. Rather, the dataset had features consistent with many, independent zoonotic transmissions (humans becoming infected through contact with rodent feces or urine). The research team reported their findings in real time to the NCDC and local health authorities to support the public health response to the outbreak.

According to the authors, this research serves as a model for investigating infectious disease emergencies by combining genomic information with traditional epidemiological data to inform response strategies.

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