Genetic characterisation of African swine fever virus from 2017 outbreaks in Zambia: Identification of p72 genotype II variants in domestic pigs

Abstract

African swine fever (ASF) is a contagious haemorrhagic disease associated with causing heavy economic losses to the swine industry in many African countries. In 2017, Zambia experienced ASF outbreaks in Mbala District (Northern province) and for the first time in Isoka and Chinsali districts (Muchinga province). Meanwhile, another outbreak was observed in Chipata District (Eastern province). Genetic analysis of part of the B646L gene, E183L gene, CP204L gene and the central variable region of the B602L gene of ASF virus (ASFV) associated with the outbreaks in Mbala and Chipata districts was conducted. The results revealed that the ASFV detected in Mbala District was highly similar to that of the Georgia 2007/1 isolate across all the genome regions analysed. In contrast, while showing close relationship with the Georgia 2007/1 virus in the B646L gene, the ASFV detected in Chipata District showed remarkable genetic variation in the rest of the genes analysed. These results suggest that the Georgia 2007/1-like virus could be more diverse than what was previously thought, underscoring the need of continued surveillance and monitoring of ASFVs within the south-eastern African region to better understand their epidemiology and the relationships between outbreaks and their possible origin.

Keywords: African swine fever; Zambia; domestic pigs; genotyping; molecular epidemiology.

FIGURE 1

Phylogenetic relationships of the p72 gene of African swine fever viruses detected in domestic pigs during 2017 in Zambia. The evolutionary relationships were conducted by MEGA6 software using the neighbour-joining method, with evolutionary distances being computed by the p-distance method. Numbers at branch nodes indicate bootstrap values ≥ 50%. The GenBank accession numbers of strains included in the analyses are indicated in parenthesis and the p72 genotypes are shown after the country of origin of the strains or the right bracket. Virus strains characterised in this study are in bold. Bar, number of substitutions per site.

FIGURE 2

Phylogenetic relationships of the p54 (a) and p30 (b) genes of African swine fever viruses detected in domestic pigs during 2017 in Zambia. The evolutionary relationships were conducted by MEGA6 software using the neighbour-joining method, with evolutionary distances being computed by the p-distance method. Numbers at branch nodes indicate bootstrap values ≥ 50%. The GenBank accession numbers of strains included in the analyses are indicated in parenthesis and the p54 genotypes are shown after the country of origin of the strains or the right bracket. Virus strains characterised in this study are in bold. Bar, number of substitutions per site.