Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

Abstract

Several African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

Complete genome analysis of the African swine fever virus isolated from a wild boar responsible for the first viral outbreak in Korea, 2019

“…′ -ITR region is 956 bp, 3 ITR regions (44). Inverted terminal repeats were missing from both ends of the Korea/YC1/2019 genome sequence, presumably because of the complexity of the ASFV material or region in the limited number of sequenced DNA samples and/or the difficulty of sequencing/assembly.…”

One hundred years of African swine fever in Africa: Where have we been, where are we now, where are we going?

“…Genotypes I and II are the most striking examples of pig‐related ASF viruses, although both have also been isolated from ticks and/or African wild suids (Lubisi et al., 2005; Quembo et al., 2018). Genotypes VIII, IX and X, although they have a more restricted distribution, spanning several countries in eastern and Central Africa (Atuhaire, Afayoa et al., 2013; Atuhaire, Ochwo et al., 2013; Bishop et al., 2015; Bisimwa, Ongus et al., 2020; Bisimwa, Ongus et al., 2021; Chang'a et al., 2019; Gallardo, Anchuelo et al., 2011; Hakizimana, Nyabongo et al., 2020; Hakizimana et al., 2021; Misinzo, Jumapili et al., 2012; Misinzo et al., 2014; Mulumba‐Mfumu et al., 2017) are also well adapted to pigs (Lubisi et al., 2005). These viruses may also be candidates for extra‐African ventures.…”

Whole genome sequencing and molecular epidemiology of the 2021 African swine fever virus outbreak in the Dominican Republic

“…Sequences that were of questionable quality based on the locations of mutations and degree of relatedness via comparison using multiple pairwise alignment were removed. A total of 54 ASFV genomes from public databases were included in the final analysis (Supplementary File 1) (Farlow et al, 2018;Gallardo et al, 2015;Olesen et al, 2009;Kovalenko et al, 2019;Mazur-Panasiuk et al, 2020;Gilliaux et al 2018;Xuexia et al, 2019;Olasz et al, 2019;Hakizimana et al, 2021;Mazloum et al, 2021;Jia et al, 2020;Xiong et al, 2019). NCBI SRA raw data retrieved from NCBI was aligned to the ASFV Georgia 2007/1 reference genome (GenBank accession NC 044959.2) using either the Burrows-Wheeler Aligner (v0.7.17, short-read data) or Minimap2 (v2.18-r1015, long-read data) and variant-called as described above.…”