Tracking transmission in a Lassa fever outbreak

In 2018, a 10-fold rise in the number of Lassa fever cases in Nigeria raised concern that the virus causing the disease had evolved to allow easier transmission between humans — potentially the beginning of a major outbreak. It was important to understand as quickly as possible whether or not this was the case.

The Nigerian Centre of Disease Control made an urgent call for genomic sequence data on Lassa fever virus strains involved in the outbreak, which was in a geographically remote setting with poor transport accessibility. This would normally have meant that samples would need to be shipped over a long distance for sequencing in the national reference laboratory, an extremely slow process. Instead, an international team of scientists used a portable nanopore-based sequencing device to provide real-time genomic analysis of 36 viral samples, followed by a further 85 samples from other cases to confirm their findings.

The genomic analysis results were communicated immediately to the Nigerian government and to the World Health Organization. Combined with conventional epidemiological investigations, they showed that there were no signs of a new and more dangerous strain of the virus emerging. Instead, a wide variety of strains were involved, suggesting that cases were mostly caused by independent transmission events of the virus to humans from rats, allaying fears that a major outbreak driven by human-to-human transmission was imminent¹. You can check out Liana Kafetzopoulou's talk from London Calling on this topic here.

This knowledge also meant that limited public health resources could be focused most effectively on community engagement about rodent control, environmental sanitation, and safe food storage.