Genetic profile of African swine fever virus responsible for the 2019 outbreak in northern Malawi

Abstract

Background: African swine fever (ASF) is an infectious transboundary animal disease which causes high mortality, approaching 100% in domestic pigs and it is currently considered as the most serious constraint to domestic pig industry and food security globally. Despite regular ASF outbreaks within Malawi, few studies have genetically characterized the causative ASF virus (ASFV). This study aimed at genetic characterization of ASFV responsible for the 2019 outbreak in northern Malawi. The disease confirmation was done by polymerase chain reaction (PCR) followed by molecular characterization of the causative ASFV by partial genome sequencing and phylogenetic reconstruction of the B646L (p72) gene, nucleotide alignment of the intergenic region (IGR) between I73R and I329L genes and translation of the central variable region (CVR) coded by B602L gene. Results: All thirteen samples collected during this study in Karonga district in September 2019 were ASFV-positive and after partial genome sequencing and phylogenetic reconstruction of the B646L (p72) gene, the viruses clustered into ASFV p72 genotype II. The viruses characterized in this study lacked a GAATATATAG fragment between the I173R and the I329L genes and were classified as IGR I variants. Furthermore, the tetrameric amino acid repeats within the CVR of the B602L gene of the 2019 Malawian ASFV reported in this study had the signature BNDBNDBNAA, 100% similar to ASFV responsible for the 2013 and 2017 ASF outbreaks in Zambia and Tanzania, respectively. Conclusions: The results of this study confirm an ASF outbreak in Karonga district in northern Malawi in September 2019. The virus was closely related to other p72 genotype II ASFV that caused outbreaks in neighboring eastern and southern African countries, emphasizing the possible regional transboundary transmission of this ASFV genotype. These findings call for a concerted regional and international effort to control the spread of ASF in order to improve nutritional and food security.

African Swine Fever Virus Circulation between Tanzania and Neighboring Countries: A Systematic Review and Meta-Analysis

“…Transmissions from Uganda to DRC, from Tanzania to Burundi were also observed as shown in Figure 3 . These observations are consistent with studies using traditional phylogenetic methods where transboundary spread of ASFV between DRC and Uganda [ 50 , 53 ], Tanzania and Malawi [ 59 , 63 ], DRC and Zambia [ 53 ], Kenya and Uganda [ 21 ] were speculated. Our findings highlight the role of neighboring countries in the epidemiology of ASFV and a regional approach would be more effective for the control of ASF.…”

“…In addition, homology between ASFV strains from ticks collected at pig shelters and those from warthog burrows was observed, suggesting the possibility of ASFV transmission at the wild and domestic pigs interface [ 20 ]. Among countries included in this review, the ASFV p72 genotype II was described in Zambia [ 17 , 40 ], Mozambique [ 20 , 22 , 49 ], Tanzania [ 56 , 59 , 62 ], and in Malawi [ 63 ]. In 2007, the ASFV p72 genotype II escaped from its African geographical distribution to Georgia and subsequently spread to countries of the European Union and Russia before it reached Asia in August 2018 [ 13 , 25 ].…”

“…In 2007, the ASFV p72 genotype II escaped from its African geographical distribution to Georgia and subsequently spread to countries of the European Union and Russia before it reached Asia in August 2018 [ 13 , 25 ]. Additionally, the transboundary spread of the highly virulent ASFV p72 genotype II similar to the Georgia 2007/1 strain is highlighted by the introduction of this genotype into Tanzania probably from Malawi [ 59 , 62 , 63 ] and the emergence of this ASFV genotype in Zimbabwe in 2015 after several years of ASF absence probably from the neighboring Mozambique [ 68 ]. Furthermore, the genotype VIII was found to circulate in Zambia, Mozambique and Malawi [ 21 , 22 , 23 ], genotype XII was described in Zambia and Malawi [ 22 ], whilst genotype XV seems to be confined to Tanzania where both domestic and sylvatic cycles have been described for this genotype [ 22 , 57 , 58 ].…”

Genetic Analysis of African Swine Fever Virus From the 2018 Outbreak in South-Eastern Burundi

“…The strain described in this study showed high genetic similarities with ASFV strains previously reported in Burundi and those circulating in the region, indicating regional distribution and circulation of this ASFV genotype. These findings are in agreement with previous studies in the region that have also reported transboundary distribution of different ASFV genotypes including genotype X between the Democratic Republic of the Congo (DRC) and Burundi (44) and genotype II between Malawi, Tanzania, and Zambia (45)(46)(47)(48). In these studies, uncontrolled movements of domestic pigs and pork products have been cited as a major factor contributing to the transboundary spread of ASFV strains.…”

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

“…Based on partial nucleotide sequence analysis of the B646L gene that encodes for the major capsid protein p72, 24 (I–XXIV) ASFV genotypes have been identified and all of these have been reported to circulate in Africa, South of the Sahara (Achenbach et al 2017 ; Lubisi et al 2007 ; Quembo et al 2018 ). Previous studies have reported ASFV p72 genotypes II, V, VIII and XII in Malawi while only ASFV p72 genotype X was reported in Burundi (Hakizimana et al 2020a , b ; Lubisi et al 2005 ). Currently, only 3 complete and fully annotated ASFV strains belonging to p72 genotype X are available in the GenBank, including two strains from Kenya and one from Democratic Republic of the Congo (DRC) (Bisimwa et al 2021 ; de Villiers et al 2010 ).…”