Phylogenomic analysis of African swine fever virus from the Philippines.

Abstract

African swine fever (ASF) is a viral pandemic in domestic pigs and wild boars that has recently caused outbreaks across Asia, Europe, and the Caribbean. The Philippines has 90% of its provinces affected, but there is limited information on the current circulating strain. Here, we present a comprehensive genomic profile of two ASF virus (ASFV) genomes from blood samples collected at the center of ongoing domestic farm outbreaks in the country in 2020. Using amplification-free whole-genome sequencing and a customized analysis pipeline, we were able to assemble 80-99% of the genome sequence, allowing us to determine the viral genotype (i.e., genotype 2), identify the subgenotype profile based on essential genetic markers, and detect potential variants relative to the current reference strain. This report provides in-depth baseline data on the molecular characteristics of ASFV in the Philippines since the outbreak in 2019.