Genetic characterisation of African swine fever viruses from recent and historical outbreaks in Sardinia (1978–2009)

Abstract

Three discrete regions of the African swine fever virus (ASFV) were analysed in the genomes of a wide range of isolates collected from wild and domestic pigs in Sardinia, over a 31-year period (1978-2009). The analysis was conducted by genotyping based on sequence data from three single copy ASF genes. The E183L gene encoding the structural protein p54 and part of the gene encoding the p72 protein were used to delineate genotypes, before intra-genotypic resolution of viral relationships by analysis of tetramer amino acid repeats within the hypervariable central variable region (CVR) of the B602L gene. The data revealed that these isolates did not show significant variation in their p72 and p54 sequence when compared between different isolates showing a remarkable genetic stability of these genome regions. In particular, the phylogeny revealed that all the Sardinian isolates belong to the same largest and most homogeneous p72 genotype I together with viruses from Europe, South America, the Caribbean and West Africa, and p54 genotype Ia which comprises viruses from Europe and America. The analysis of B602L gene revealed a minor difference in the number of tetramer repeats, placing the Sardinian isolates into two clusters, accordingly to their temporal distribution, namely sub-group III and sub-group X, this latter showing a deletion of 12 tetramer repeats located in the centre of the array. The genetic variation of this fragment suggests that one sub-group could be derived from the other supporting the hypothesis of a single introduction of ASFV in Sardinia.

Thirty-Five-Year Presence of African Swine Fever in Sardinia: History, Evolution and Risk Factors for Disease Maintenance

“…Only a slight variation in the number of tretramer acid repeats within the central variable region (CVR) of the B602L gene was found, revealing the existence of two different temporarily related subgroups. However, this change is considered a very small mutation, and as no changes were found in the other main analysed regions (p72 and p54), the close relationship between isolates is confirmed and supports the hypothesis of a single introduction of ASFV in 1978 (Giammarioli et al., ).…”

Comprehensive Phylogenetic Reconstructions of African Swine Fever Virus: Proposal for a New Classification and Molecular Dating of the Virus

“…In contrast, several recombination events were detected among E183L sequences. A total of 17 isolates were subsequently removed from the E183L multiple sequence alignments: 16 were Italian isolates (24/Or/04, 26/Ss/04, 30/Ol/04, 48/Ss/08, 5/Ca/02, 04/Ol/02, 3/Og/98, 1/Nu/97, 46/Ca/08, 25/Nu/04, 43/Og/07, 42/Og/0, 22/Nu/04, 23/Or/04, 41/Og/07 and 36/Ss/05) [50] and one was a South African isolate (RSA/85/1). The recombination events were all identical for Italian isolates (Figure 1).…”

African swine fever: a global view of the current challenge

“…The current approach is based on the analysis of the C-terminal end of gene B646L encoding the major protein p72 [39], following by the sequencing of the Central Variable Region (CVR) within the B602L gene, or other several regions (e.g. E183L encoding p54 protein, CP204L encoding p30 protein), for distinguishing between geographically and temporally constrained p72 genotype viruses [28–30, 33, 34, 36, 38]. This approach has allowed identifying twenty-two different p72 genotypes among virus isolates from East and South African countries to date, whereas genotype I is predominant in West Africa [35, 37].…”