Phylogeographic analysis of African swine fever virus based on the p72 gene sequence

Abstract

African swine fever virus (ASFV) outbreak has been considered as an emerging and re-emerging disease for almost a century. Diagnostically, simple polymerase chain reaction and sequencing-based molecular detection could be employed for both viral identification and genotyping. This study established a novel phylogenetic analysis and epidemiology comparison based on 205 bp of p72 gene sequences. Based on this partial p72 fragment, an updated list of 44 different genotypes from a total of 516 ASFV sequences compiled from GenBank was generated. Nucleotide diversity was 0.04325 ± 0.00231. The analysis of spatial genetic variation divided the ASFV populations of the African continent into four clades (clade A: central and upper eastern Africa; clade B: eastern Africa; clade C: eastern and southern Africa; and clade D: southern Africa). These results and the developed protocol could serve as useful molecular tools for ASFV diagnosis from degraded DNA or putrefied samples, and also provide the phylogeographic perspective to identify the origin of viral outbreaks, facilitating the decision planning to limit their spread.