Saving your bacon: Tackling the other global outbreak

Note: this event was previously scheduled to take place Friday 25 November 2022.

African Swine Fever virus (ASFV) is the causative agent of a deadly, panzootic disease, infecting wild and domesticated suid populations. Contained for a long time to the African continent, an outbreak of a particularly infectious variant in Georgia in 2007 initiated the spread of the virus around the globe, severely impacting pork production and local economies.

Of the world's three largest producers of pork, China and Germany have ongoing outbreaks, and the virus has recently reached the Caribbean, knocking on the door of the USA. The virus is highly contagious and has a mortality of up to 100% in domestic pigs.

It is critical to track the spread of the virus, detect variants associated with pathology, and implement biosecurity measures in the most effective way to limit its spread. Due to its size and other limitations, the 170-190kbp large DNA virus has not been well sequenced with fewer than 200 genome sequences available in public repositories.

When the virus reached the Philippines in September 2019, we were on our way there to do research on another virus, in this talk I will discuss how we quickly changed focus to tackle this new threat.

Here, I will describe an efficient, low-cost method of sequencing ASFV at scale. The method uses large tiled PCR amplification of the virus to achieve greater coverage, multiplexability and accuracy on a portable sequencer than achievable using shotgun sequencing.

I will also introduce Lilo, a pipeline for assembling tiled amplicon data from viral or microbial genomes without relying on polishing against a reference, allowing for structural variation and hypervariable region assembly other methods struggle with.

The resulting ASFV genomes are near complete, lacking only parts of the highly repetitive 3’- and 5’telomeric regions, and have a high level of accuracy. These methods will allow sequencing of ASFV at optimal efficiency and high throughput to monitor and act on the spread of the virus.