Full-Length ASFV B646L Gene Sequencing by Nanopore Offers a Simple and Rapid Approach for Identifying ASFV Genotypes
Vivian O’Donnell,
Edward Spinard,
Lizhe Xu,
Amy Berninger,
Roger W. Barrette,
Douglas P. Gladue,
Bonto Faburay
Affiliations
Vivian O’Donnell
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Orient, NY 11944, USA
Edward Spinard
Agricultural Research Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Orient, NY 11944, USA
Lizhe Xu
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Orient, NY 11944, USA
Amy Berninger
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37831, USA
Roger W. Barrette
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Orient, NY 11944, USA
Douglas P. Gladue
Agricultural Research Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Orient, NY 11944, USA
Bonto Faburay
Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Orient, NY 11944, USA
African swine fever (ASF) is an acute, highly hemorrhagic viral disease in domestic pigs and wild boars. The disease is caused by African swine fever virus, a double stranded DNA virus of the Asfarviridae family. ASF can be classified into 25 different genotypes, based on a 478 bp fragment corresponding to the C-terminal sequence of the B646L gene, which is highly conserved among strains and encodes the major capsid protein p72. The C-terminal end of p72 has been used as a PCR target for quick diagnosis of ASF, and its characterization remains the first approach for epidemiological tracking and identification of the origin of ASF in outbreak investigations. Recently, a new classification of ASF, based on the complete sequence of p72, reduced the 25 genotypes into only six genotypes; therefore, it is necessary to have the capability to sequence the full-length B646L gene (p72) in a rapid manner for quick genotype characterization. Here, we evaluate the use of an amplicon approach targeting the whole B646L gene, coupled with nanopore sequencing in a multiplex format using Flongle flow cells, as an easy, low cost, and rapid method for the characterization and genotyping of ASF in real-time.
