Oxford Nanopore Technology genomics device reveals sources of Lassa outbreak

Research carried out during the 2018 Lassa fever outbreak in Nigeria used rapid, portable genomic sequencing technology to identify viruses without prior knowledge of the cause of disease. This enabled researchers to allay fears and direct the public health interventions to limit the spread of the virus and help to protect more people from disease.

The outbreak in early 2018 led to 376 confirmed cases within a few months, more than the combined total for the 3 previous years, raising concerns that a new, highly transmissible form of the virus had evolved, able to pass from person to person more effectively than previous strains.

The Nigeria Center for Disease Control with the WHO commissioned the research from a team including scientists from Public Health England, the Bernhard Nocht Institute for Tropical Medicine in Germany, and the Irrua Specialist Teaching Hospital in Nigeria.

The researchers used Oxford Nanopore Technology's portable device to rapidly sequence the genetic code of 120 virus samples. Rather than looking at one genetic marker at a time, the team tested for multiple different variations of Lassa virus genome, which is known to be highly diverse.

The researchers found that the strains in the samples weren't all closely related, suggesting multiple different instances of contraction from rodents. These early, rapid results allowed teams on the ground to continue focusing the public health response on community engagement around rodent control, environmental sanitation and safe food storage rather than shifting to solely focusing on addressing person to person spread.

The real-time, portable DNA sequencing technology has the potential to enable scientists on the ground during any disease outbreak to rapidly study the pathogen genome without necessarily knowing what it is they are looking for, and could be applied to previously unknown pathogens. This is important because international health agencies have predicted that an unknown ‘Pathogen X’ could cause the next major outbreak.