Complete Genome Sequence of a Virulent African Swine Fever Virus from a Domestic Pig in Ukraine

Abstract

Here, we report the complete genome sequence of an African swine fever (ASF) virus (ASFV/Kyiv/2016/131) isolated from the spleen of a domestic pig in Ukraine with a lethal case of African swine fever. Using only long-read Nanopore sequences, we assembled a full-length genome of 191,911 base pairs in a single contig.

The Spillover of African Swine Fever in Western Poland Revealed Its Estimated Origin on the Basis of O174L, K145R, MGF 505-5R and IGR I73R/I329L Genomic Sequences

“…Another tandem repeat sequence variation located between MGF 505-9R/10R genes has also been described as a molecular marker [ 24 ]. Nowadays, wide use of NGS caused it to become more affordable, therefore the technique is commonly applied to ASFV genomic sequencing, especially in light of its considerable size of almost 200 kb [ 2 , 3 , 4 , 5 , 6 , 8 , 25 , 26 , 27 ]. Its usefulness for variation detection is invaluable; nonetheless, it is inadequate in terms of population studies.…”

“…Besides previously investigated O174L gene variation, the IGR I73R/I329L region, which is routinely used to perform molecular characteristics of worldwide distributed ASFV genotype II isolates, was employed. Furthermore, two SNPs: within K145R and MGF 505-5R , which, according to NGS results, were specific to Poland and Ukraine [ 2 , 6 ], were also evaluated as useful molecular tools for tracing disease spreading. Obtained results allowed for discrimination of four distinct genetic groups of ASFV circulating in Poland.…”

“…In order to determine the geographical origin of new ASFV cluster in western Poland, which was distanced about 270 km westwards from the nearest confirmed cases, next generation sequencing (NGS) of four selected ASFV isolates collected between 2017–2019 in Poland, including samples originated from western cluster was performed. Based on the obtained result, supported by other investigations [ 2 , 6 , 9 , 10 ], the O174L , K145R , MGF 505-5R genes and intergenic region (IGR) I73R/I329L region were selected as molecular “fingerprints”. The conducted conventional sequencing of these ASFV genomic regions allowed for the enhanced discrimination between closely related viruses circulating within the country since 2014.…”

“…Several next- as well third- generation sequencing platforms, including Roche 454, Illumina, IonTorrent, Pacbio and MinIon technologies have repeatedly been applied to generate whole genome sequences of numerous ASFV strains [ 2 , 3 , 4 , 5 , 6 , 7 , 8 ]. In order to determine the geographical origin of new ASFV cluster in western Poland, which was distanced about 270 km westwards from the nearest confirmed cases, next generation sequencing (NGS) of four selected ASFV isolates collected between 2017–2019 in Poland, including samples originated from western cluster was performed.…”

“…According to the recently published ASFV whole genomic sequences originated from Poland, K145R and MGF 505-5R genes contain single nucleotide polymorphisms (SNPs) specific to all Polish isolates in comparison to the referenced Georgia 2007/1 strain [ 2 ]. The mutations are absent in the other viruses currently circulating in Europe and China, except the Ukraine/Kyiv/2016 strain [ 6 ]. This may suggest that these regions may become the potential molecular markers, which could provide tracking of the disease spreading.…”