Detection of African Swine Fever Virus Genotype II in West Africa (2020) and Its Co-Circulation With Endemic Genotype I: Implications for Pig Production

Abstract

African swine fever (ASF) is a highly devastating disease of domestic pigs caused by the ASF virus (ASFV). Historically, only ASFV Genotype I was known to circulate in West Africa. However, Genotype II has recently emerged in Nigeria, Ghana, and Benin for the first time. Between 2017 and 2023, suspected ASF outbreaks were reported in Burkina Faso, Côte d'Ivoire, Nigeria, and Mali. The source, extent, and spread of these ASF outbreaks remain unknown. Samples collected from 2017 to 2023 were analyzed using real-time qPCR and characterized using five ASFV gene segments: partial gene of the B464L (p72), full length E183L (p54), central variable region (CVR) within B602L, EP402R (CD2v), and intergenic region (IGR) between I73R and I329L genes. ASF was confirmed in 12 Nigerian states and in seven, eight, and two provinces of Burkina Faso, Côte d'Ivoire, and Mali, respectively. Phylogenetic analysis of B646L (p72), E183 (p54), and CD2v genes of ASFV revealed that Genotype I, Serogroup 4, caused the initial outbreaks in these countries, followed by Genotype II, Serogroup 8. CVR profile analysis showed ASFV Genotype I with different variants, while Genotype II presented only one CVR variant. This is the first report of ASFV Genotype II in Burkina Faso, Cote d'Ivoire, and Mali. The introduction of ASFV Genotype II and its co-circulation with Genotype I in pig populations in these West African countries threatens food security and complicates control measures. Therefore, increased surveillance at international ports of entry, restrictions on live pig movements within the countries, and improved farm-level biosecurity measures are needed to control the further spread of the disease.

Keywords: CVR variants; food security; p72; phylogenetic analysis; serogroup; surveillance.

Figure 1

Map of West Africa highlighting the regions within the four countries with ASFV Genotype I (sky blue) and II (dark blue) outbreaks between 2017 and 2023.

Figure 2

Phylogenetic tree of (A) partial B646L (p72) gene nucleotide sequences inferred using the neighbor-joining method and (B) the full-length p54 gene sequences based on the minimum evolution method, with the evolutionary distances computed using the Kimura two-parameter method. The ASFV isolates analyzed in this study from 2017 to 2023 are shown in red (Burkina Faso), green (Côte d'Ivoire), blue (Nigeria), and purple (Mali), with the number of sequences generated in various years from each country indicated in brackets. Only the bootstrap values greater than 70% are shown.

Figure 3

Maximum likelihood phylogenetic tree based on the partial amino acid sequence of the CD2v protein, showing the relationships between the ASFV isolates analyzed in this study, in red (Burkina Faso), green (Côte d'Ivoire), blue (Nigeria), and purple (Mali) and representatives of known ASFV serogroups as well as ASFVs clustering outside the eight established serogroups. The number of sequences generated from samples collected from various years from each country is indicated in brackets. The general reversible chloroplast model with gamma distribution was used. Only the bootstrap values greater than 70% are shown.

Figure 4

(A and B) Central variable region (CVR) profiles of ASFV Genotype I in light gray and Genotype II in dark gray from Burkina Faso (red), Nigeria (blue), Côte d'Ivoire (green), Mali (purple), and selected ASFV isolates from previous studies. The unique CVR profiles identified in this study are marked by asterisk (⁣^∗). Note: CVR codes as previously described: CAST/CVST/CTST/CASI = A, CADT/CTDT/CADI/CAGT = B, GAST/GANT = C, CASM = D, CANT/CAAT = F, CTNT = G, NEDT = M, NVDT/NVGT/NVDI/NCDT = N, NANI/NADI/NASI = O, RAST = H, SAST = S, NVNT = T, NAST/NADT/NANT/NAVT = V, and SADT/SVDT = W.

Figure 5

Multiple sequence alignments of the intergenic region (IGR) between I73R and I329L genes of the ASFV Genotype II isolates including those from Burkina Faso (red), Côte d'Ivoire (green), Nigeria (blue), and Mali (purple). The number of sequences generated from each country is indicated in brackets. The highlighted areas show the 10 bp tandem repeats and the nucleotide substitution between the isolates. The dots indicate the identical nucleotides in the alignment.