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Mobile Genomics Device Guides Response to Lassa Fever Outbreak

A new portable metagenomic technology allowed investigators to perform real-time analysis of viral genomes during a 2018 Lassa fever outbreak in Nigeria.

Scientists used a portable DNA sequencing tool to investigate a 2018 Lassa fever outbreak in Nigeria, according to a recent study published online in the journal Science.

This allowed them to effectively guide the public health response to the outbreak as it was unfolding in real time.

“Results showed no strong evidence of a new strain emerging nor of person-to-person transmission,” Liana. E. Kafetzopoulou, from Public Health England, Porton Down, and the University of Liverpool, United Kingdom, and colleagues write.

Instead, “rodent contamination was the main source,” they note.

Rodents are reservoirs and hosts for several zoonotic diseases of significant public health significance, including leptospirosis, hantavirus pulmonary syndrome, rat-bite fever, salmonellosis, plague, and, more recently, rat hepatitis E virus.

Lassa fever is an acute and frequently fatal hemorrhagic illness that occurs in West Africa. It is caused by Lassa virus, a member of the arenavirus family, which is transmitted to humans via the urine or feces of infected rats.

The symptoms of Lassa fever are similar to those of Ebola virus disease, and include fever, weakness, muscle pain, and seizures. However, many infected people do not develop symptoms.

The 2018 Lassa fever outbreak in Nigeria was the largest on record, resulting in 376 confirmed cases as of March 18. In comparison, only 102 confirmed cases had been reported during the same period in 2017, the authors say.

Because of this sudden rise in cases, experts were concerned about the possibility of emergence of a new, highly transmissible strain of the virus.

With this in mind, Kafetzopoulou and colleagues analyzed patient samples during the outbreak to better understand the reason behind the sudden upsurge in cases.

The investigators used the Oxford Nanopore MinION device to perform viral genome sequencing while the outbreak was ongoing.

This new portable metagenomic technology allowed them to rapidly sequence the genetic code of Lassa virus samples collected from 120 affected patients. The investigators confirmed the presence of Lassa virus in all samples, and were able to perform real-time analysis of the viral genomes from 36 of these during the outbreak, and from the remaining samples after the outbreak.

Overall, the results confirmed extensive diversity among the viral strains, as well as mixing of the strains with those from previous years. According to the authors, this was most suggestive of independent zoonotic transmission events via rodents, and not indicative of a new emergent strain that was spreading quickly between people.

By obtaining these results in real time during the outbreak, experts in the region were better able to appropriately allocate public health resources, thus focusing the response on rodent control, environmental sanitation, and safe food storage.

“Further research is needed to evaluate whether improved diagnostics and disease awareness and/or ecological and climate factors promoting transmission are the drivers behind the changing epidemiology of Lassa fever in Nigeria,” the authors concluded.