Saving your bacon: nanopore sequencing of deadly porcine viruses in the Philippines

Last year, it is estimated that ¼ of the world’s pigs either died of African Swine Fever Virus (ASFV) or were culled to contain it.

Sequencing of ASFV samples performed in the Philippines and the UK, aiming to help track the spread of the virus.

The lab in the Philippines experienced powercuts, but sequencing via MinION was able to continue as it ran off laptop power.

Despite not performing target enrichment (sequencing ASFV & pig DNA), the 180 kb viral genome was assembled into single contigs in several samples.

Next: tiled amplification to enrich for ASFV-PRRSV: the 15 kb RNA genome can be sequenced in single reads with nanopore.

Method for amplification of full PRRSV genome in single piece developed by Ingrida Vendelė; sequencing produced tens of thousands-fold coverage of genome.

Direct RNA sequencing of PRRSV enabled ‘a really nice profile of sub-genomic RNA’.