Molecular epidemiology of African swine fever in East Africa

Genetic characterisation of African swine fever viruses from outbreaks in southern Africa (1973–1999)

“…Despite this, the 42 viruses clustered within 22 discrete lineages, representative of distinct genotypes. Of these, 16 coincided with genotypes identified by distance methods in previous studies (Bastos et al, 2003 andLubisi et al, 2005), with six being novel and confined to the southern African region. The phylogeny further revealed that the 22 genotypes clustered within 3 discrete evolutionary lineages, labelled I-III ( Of the 22 genotypes recovered, 14 were associated with domestic pig outbreaks in southern Africa and 8 appear to be country-specific ( The results revealed the involvement of a genotype I (ESACWA) virus in the 1989 outbreaks occurring in Windhoek, Namibia.…”

“…These results contrast markedly with the recovery of identical genotype XIX viruses from the temporally unrelated (1987, 1992 and 1996) outbreaks in South Africa, indicating a prolonged field presence for this virus. As the C-terminal end of the p72 gene of viruses from domestic pig cycles in West and East Africa (genotypes I and VIII, respectively) are genetically homogeneous (Bastos et al, 2003 andLubisi et al, 2005), it raises the possibility the genotype XIX homogeneity observed here may imply the existence of a pig-restricted cycle in South Africa, in addition to the recognised sylvatic cycle, which would have serious implications for disease control (Penrith et al, in press). However, this requires further investigation as only five genotype XIX have been characterised thus far whilst in excess of 40 viruses each have been sequenced for genotypes I and VIII (Bastos et al, 2003 andLubisi et al, 2005).…”

“…Thirteen of the 14 southern African genotypes clustered within evolutionary lineage I which has the widest geographical distribution, mainly due to the incorporation of genotype I (or the ESACWA genotype) which comprises viruses of European, South American, Caribbean and West African origin (Bastos et al, 2003). In contrast lineages II and III have a more restricted distribution, with each being confined to four East African countries (Bastos et al, 2003 andLubisi et al, 2005), namely Zambia, Mozambique, Malawi and Tanzania (for lineage II), and Tanzania, Kenya, Burundi and Uganda (for lineage III).…”

“…The virus occurs naturally in both vertebrate and invertebrate sylvatic hosts throughout sub-Saharan Africa and is transmitted to domestic pigs when infected soft-shelled, eyeless ticks of the Ornithodoros moubata complex feed on them (reviewed by Penrith et al, 2004). A domestic pig cycle, which is apparently not reliant on the presence of the tick vector, is believed to occur in both West and East Africa (reviewed by Penrith et al, 2004) and is characterised by the openUP presence of viruses that are genetically homogeneous across the C-terminal end of the p72 gene (Bastos et al, 2003 andLubisi et al, 2005). ASF, initially termed 'East African swine fever' was first described from Kenya in 1921 (Montgomery, 1921), with the earliest record of the disease in South Africa dating back to 1926 (Steyn, 1932) from the northern area of this country (former Transvaal province) where contact between warthogs (Phacochoerus africanus) and domestic pigs was known to occur.…”

Role of Wild Suids in the Epidemiology of African Swine Fever

“…Variation in clinical disease and virus genome length and composition is known to occur, with infections in domestic swine ranging from sub-clinical to lethal and field strains having genomes up to 20 kbp longer than laboratoryadapted strains (Tulman et al, 2009). Recent molecular epidemiological studies have also uncovered substantial field heterogeneity with at least 22 genotypes being identified to date on the basis of C-terminus p72 gene sequencing (Bastos et al, 2003;Lubisi et al, 2005;Boshoff et al, 2007). The recent incursion of ASF into Georgia (Beltran Alcrudo et al, 2008;Rowlands et al, 2008) has highlighted the potential of the virus to expand its range towards Asia through the Caucasus and the Indian Ocean (Costard et al, 2009) as it encounters new populations of wild and domestic pigs, yet important gaps in our knowledge remain regarding the role of many wild Suidae in the maintenance of ASFV.…”