Rapid genome-wide sequence typing of African swine fever virus based on alleles

Abstract

Rapid and accurate molecular typing of African swine fever virus (ASFV) during outbreaks is important to reveal diversity and sourcing of ASFV. Here we present a new way to perform rapid genome-wide multi-locus sequence typing of ASFV using an allele calling based on gene by gene approach. Using open-accessed chewBBACA software, 41 publicly available ASFV genomes were analyzed to optimize the parameters to find the alleles. Alleles as many as 127 were found for building the phylogenetic trees, which covered more than 60 % of the whole genome. Then the method was used to analyze two ASFV genomes assembled from two metagenomic sequences of a swine whole blood and a swine spleen tissue collected in Wuhan, China. It reveals that the two ASFV genomes are the closest to that of Pig/HLJ/2018 strain and DB/LN/2018 strain, which were isolated earlier in China. This proved that the ASFV in Wuhan originated from the same source causing the earlier outbreaks in Heilongjiang and Liaoning province of China. This method could identify more informative genome regions that could be used for accurate typing than other genome-wide analysis, and with less demand on computing resources. It also showed tolerance to analyze ASFV draft genomes assembled directly from metagenomic sequences. Furthermore, the ASFV-specific genetic markers found by the allele calling could be translated into clinical diagnostics or can be used broadly to identify conserved putative therapeutic candidates.

Keywords: African swine fever virus; Allele calling; Gene by Gene approach; Metagenomic sequences; Sequence typing.