Detection and genetic characterization of African swine fever virus (ASFV) in clinically infected pigs in two districts in South Kivu province, Democratic Republic Congo

Abstract African swine fever (ASF) is a notifiable contagious disease caused by the African swine fever virus (ASFV), leading to a serious socio-economic impact, constraining pig industry, and affecting food security worldwide. This study aimed to detect and characterize ASFV strains from suspected infected domestic pigs in two South-Kivu province districts of the Democratic Republic of the Congo (DRC). A total of 155 pig samples were screened for viral DNA and sequencing at multiple loci. An infection rate of 5.2% (8/155) was recorded from a total of 155 blood samples with the highest ASFV infection rate of 8% for Uvira (6/75) and mostly in female pigs 5 (7.6%). Most ASF associated clinical signs were redness on the skin and snout at 49% (95% CI: 21–34), followed by the unwillingness of pigs to stand at 29 % (95%, CI: 19–35). Phylogenetic analysis of partial B646L (p72) and the full-length E183 (p54) gene sequences revealed the circulation of genotypes IX and X, which clustered with previously reported viruses in the same region, Uganda, Kenya, and Tanzania. Intragenotypic resolution of the CVR region clustered the viruses into two subgroups: the genotype X strain subgroup (10 repeats, AAAABNAABA) and the genotype IX strain subgroup (11 repeats, AAAAAAAAAAF). This finding provides additional evidence that genetically similar ASFV strains may be circulating within South Kivu province and highlights the need for improved coordination to prevent the spread of the disease in non-infected areas.