Molecular characterization of African swine fever viruses from Burkina Faso, 2018

Abstract

Background: African swine fever (ASF) is a viral hemorrhagic disease of domestic and wild swine. ASF has been endemic in Burkina Faso since 2003. In October 2018, substantial pig deaths occurred in Ouagadougou and two neighboring municipalities in central Burkina Faso. Following these mortalities, the veterinary extension services carried out investigations to begin control measures and collect samples.

Methods: We performed real-time PCR for diagnostic confirmation and molecular characterization of the virus based on the partial P72, the complete p54, the partial CD2v, and partial B602L genes.

Results: The field study revealed that mortalities started two weeks before our investigations. The real-time PCR results confirmed ASFV DNA in twenty samples out of sixty-two blood samples collected in four different locations. The sequencing and phylogenetic analysis showed that ASFVs causing these outbreaks belong to genotype I and serogroup 4. The study of the CVR showed 4 TRS variants, and that of the CD2v amino acid sequence revealed five variants based on the number of deleted KCPPPK motifs in the C-terminal proline-reach region of the protein.

Conclusions: The existence of multiple variants in these outbreaks shows the importance of molecular characterization to understand the evolution of ASFV isolates and the link between epidemics.

Keywords: African swine fever; B602L; B646L; Burkina Faso; Central variable region; E183L.

Fig.1

Map showing the ASF outbreak suspicion areas in Ouagadougou and surroundings (Kadiogo province) in central Burkina Faso. The red zones circle indicates the confirmed outbreaks, and the green the non-confirmed ones

Fig. 2

Neighbor-joining tree of the partial p72 gene, depicting genetic relationships of the 2018 ASFV isolates from Burkina Faso (highlighted with red diamonds) with representatives of the 24 known ASFV genotypes. The evolutionary distances were computed using the Maximum Composite Likelihood method. Bootstrap values > 70% are shown

Fig. 3

Minimum Evolution tree, based on the full-length p54 gene sequences, depicting the genetic relationships between the 2018 ASFV isolates from Burkina Faso (are highlighted with red diamonds) with representatives of the 18 out of 24 known ASFV genotypes. The evolutionary distances were computed using the p‐distance method. Bootstrap values > 70% are shown

Fig. 4

Comparison of the 2018 ASFV isolates from Burkina Faso using the amino acid sequences of the p54 protein. The partial representation of the multiple sequence alignment shows the amino acid sequences variation among the isolates (inside the red box)

Fig. 5

Maximum Likelihood tree based on the partial amino acid sequences of the CD2v protein. The tree shows the relationship between the 2018 ASFV isolates from Burkina Faso (highlighted with red diamonds) and the representatives of the eight known ASFV serogroups and ASFVs clustering outside the eight established serogroups. The General Reversible Chloroplast Model with Gamma distribution (cpREV + G) was used. Bootstrap values higher than 70% are shown

Fig. 6

Comparison of the 2018 ASFV isolates from Burkina Faso using the C-terminal of the CD2v protein. The partial representation of the multiple sequence alignment shows the amino acid sequences variation in the C-terminal of the CD2v protein (inside the red box)