Rapid sequence-based characterisation of African swine fever virus using the Oxford Nanopore MinION sequence sensing device and a companion analysis software tool

African swine fever virus (ASFV) is the causative agent of a severe and highly contagious viral disease of pigs that poses serious economic consequences to the swine industry due to the high mortality rate and impact on international trade. There is no effective vaccine to control African swine fever (ASF), and therefore, efficient disease control is dependent on early detection and diagnosis of ASFV. The large size of the ASFV genome (∼180 kB) has historically hindered efforts to rapidly obtain full-genome sequence.

Rapid acquisition of data is critical for characterization of the isolate and to support epidemiological efforts.

Here we investigated the capacity of the Oxford Nanopore MinION sequence sensing device to act as a rapid sequencing tool. When coupled with our novel companion software script, African Swine Fever Fast Analysis Sequencing Tool (ASF-FAST), the analysis of output data was performed in real-time.

Complete ASFV genome sequences were generated from cell culture isolates and blood samples obtained from experimentally infected pigs.

Removal of the host methylated DNA from extracted nucleic acid facilitated rapid ASFV sequence identification, with reads specific to ASFV detected within 6 minutes after initiation of sequencing.

Regardless of starting material, sufficient sequence was available for complete genome resolution (up to 100%) within 10 minutes.

Overall, this manuscript highlights the use of nanopore sequencing technology in combination with the ASF-FAST software for the purpose of rapid and real-time resolution of the full ASFV genome from a diagnostic sample.