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.
Highlights
The aetiology of Africa swine fever (ASF) is ASF virus (ASFV), a linear double-stranded DNA arbovirus with a genome size ranging between 170 and 194 kilobase pairs, and the only member of the genus Asfivirus, family Asfarviridae (Alonso et al 2018)
Characteristics of the complete genomes of Burundian and Malawian ASFV strains Complete genome sequences of the ASFV strains responsible for the 2018 outbreak in Rutana region, South-eastern Burundi (BUR/18/Rutana), and the 2019 outbreak in Karonga district, northern Malawi (MAL/19/Karonga), were determined in this study
The strains BUR/18/Rutana and MAL/19/Karonga belong to ASFV p72 genotypes X and II, respectively, as previously described through partial genome amplification and sequencing targeting specific genomic regions (Hakizimana et al 2020a, b)
Summary
The aetiology of Africa swine fever (ASF) is ASF virus (ASFV), a linear double-stranded DNA arbovirus with a genome size ranging between 170 and 194 kilobase pairs (kbp), and the only member of the genus Asfivirus, family Asfarviridae (Alonso et al 2018). Transmission of ASF is through direct contact between infected and susceptible domestic pigs or wild boars, ingestion of contaminated pork products, contact with infected fomites, indirect transmission through carcasses in the habitat in the case of wild boars, or bites by infected soft ticks of the Ornithodoros moubata complex (Chenais et al 2018; Penrith and Vosloo 2009). Soft ticks of the O. moubata complex act as vectors of the ASFV while in eastern and southern Africa, asymptomatically infected wild suids mainly warthogs (Phacochoerus africanus) play an important role as ASFV reservoirs (Jori et al 2013). The ASFV infection of other wild suids species such as bush pig (Potamochoerus larvatus) and giant forest hogs (Hylochoerus meinertzhageni) has been previously reported but their role in the epidemiology of the virus is not well known (Penrith et al 2019)
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