Detection and genomic characterization of foot and mouth disease virus SAT2 XIV topotype using amplicon-based nanopore sequencing

Foot and mouth disease (FMD) is a highly contagious vesicular viral disease that infects cloven-hoofed animals. This disease is caused by Foot-and-mouth disease virus (FMDV) which is composed of seven serotypes (O, A, C, Asia-1, SAT1, SAT2, and SAT3), each of which lacks cross immune protection among serotypes which complicates vaccination strategies. For that, sequencing of viral protein 1 (VP1) is crucial to identify circulating serotypes in a country. Jordan is endemic for FMD, with primarily O and A serotypes circulating according to previous data. However, the epidemiological status of FMD requires updates in Jordan. In this study, out of 200 samples collected during a recent outbreak in Al-Dhlail, Jordan in early 2023, forty-nine were positive by quantitative polymerase chain reaction (qPCR). Fourteen of these positive samples were selected for PCR amplification of the viral protein 1 (VP1) gene, which were then sequenced using nanopore technology. Phylogenetic analysis highlighted the presence of SAT2 XIV topotype, with eleven samples successfully sequenced using this approach. In addition to that, Sanger sequencing validated a N137S SNP in the VP1 protein that initially identified by our approach. This study provides additional data that can be used and incorporated into the national and global efforts against this disease with new means of diagnostics methods.