An outbreak of African swine fever in small-scale pigs, Gauteng, South Africa, July 2020

Abstract

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Detection of African Swine Fever Virus in Ornithodoros Tick Species Associated with Indigenous and Extralimital Warthog Populations in South Africa

“…All 50 of the qPCR-positive tick pools also tested positive in the p72 PCR and phylogenetic analysis revealed that the ASFV nucleic acid detected in the ticks represented five p72 genotypes of the virus ( Figure 4 ; Table 1 ), with SNPs that distinguished 4 variants of genotype I supported by marked size differences in the CVR compatible with subtypes recorded in recent outbreaks of the disease in domestic pigs outside the controlled area [ 13 ]; see Discussion below. Only 20 sequences from the present study were included in the analysis, comprising one unique partial p72 sequence per tick species per collection site plus one sequence (GenBank accession number OL415194) from a warthog [ 20 ], along with 29 representative sequences of the genotypes known to occur in South Africa including isolate Spencer that has not been assigned to a p72 genotype; see Discussion below.…”

“…Viruses from the present study will be fully characterized as circumstances permit. Meanwhile, it is notable that SNPs observed among partial p72 sequences of genotype I isolates in South Africa were stable within recent series of outbreaks of disease in pigs connected by the spread of infection [ 13 ] and were supported by differences in product sizes of the CVR of the 9RL open reading frame of ASFV (L. Heath, unpublished). It is clear in retrospect that variants of genotype I had been isolated decades earlier from outbreaks of disease in pigs and from ticks, putatively O.…”

“…(O.) phacochoerus , collected in GKNP in 1981 ( Figure 4 ) [ 13 , 34 ]. Preliminary designation of some of the variants as subtypes Ia, b and c [ 13 ] should not be confused with the same designations applied to ASFV genotypes defined by p54 gene sequences [ 126 ], and the ambiguity will be addressed in a fuller description of the phenomenon.…”

“…phacochoerus , collected in GKNP in 1981 ( Figure 4 ) [ 13 , 34 ]. Preliminary designation of some of the variants as subtypes Ia, b and c [ 13 ] should not be confused with the same designations applied to ASFV genotypes defined by p54 gene sequences [ 126 ], and the ambiguity will be addressed in a fuller description of the phenomenon. The present recovery of multiple subtypes of genotype I ASFV from ticks collected at single locations ( Table 1 ), even from the same burrows, appears to be a novel observation.…”

“…The genotype of ASFV involved, genotype I, had been isolated decades earlier from outbreaks of disease in pigs, and from ticks in South Africa. The same genotype had long been associated with the disease in domestic pigs in countries of western Africa from where it is believed to have been accidentally introduced into Europe in 1957 and 1960 [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ]. In South Africa, there has been widespread translocation of warthogs since 1963 to game farms and nature reserves in the south of the country, originally from a source considered to be free of ticks and virus.…”