title: Genotyping field strains of African swine fever virus by partial p72 gene characterisation.
abstract: A PCR-based sequencing method was developed which permits detection and characterization of African swine fever virus (ASFV) variants within 5 and 48 h, respectively, of receipt of a clinical specimen. Amplification of a 478 bp fragment corresponding to the C-terminal end of the p72 gene, confirms virus presence with genetic characterization being achieved by nucleotide sequence determination and phylogenetic analysis. The method was applied to 55 viruses including those representative of the major ASF lineages identified previously by restriction fragment length polymorphism (RFLP) analysis. Results confirmed that the p72 genotyping method identifies the same major viral groupings. Characterization of additional viruses of diverse geographical, species and temporal origin using the PCR-based method indicated the presence of ten major ASF genotypes on the African continent, the largest of which comprised a group of genetically homogeneous viruses recovered from outbreaks in Europe, South America, the Caribbean and West Africa (the ESAC-WA genotype). In contrast, viruses from southern and East African countries were heterogeneous, with multiple genotypes being present within individual countries. This study provides a rapid and accurate means of determining the genotype of field and outbreak strains of ASF and is therefore useful for molecular epidemiological clarification of ASF.
authors.affiliation: ARC-Onderstepoort Veterinary Institute, Onderstepoort, South Africa. ADBastos@zoology.up.ac.za
authors.forename: A D S
authors.initials: AD
authors.lastname: Bastos
authors.forename: M-L
authors.initials: ML
authors.lastname: Penrith
authors.forename: C
authors.initials: C
authors.lastname: Crucière
authors.forename: J L
authors.initials: JL
authors.lastname: Edrich
authors.forename: G
authors.initials: G
authors.lastname: Hutchings
authors.forename: F
authors.initials: F
authors.lastname: Roger
authors.forename: E
authors.initials: E
authors.lastname: Couacy-Hymann
authors.forename: G
authors.initials: G
authors.lastname: R Thomson
mesh_terms: D000349:Africa / Q000453:epidemiology; D000357:African Swine Fever / Q000453:epidemiology / Q000821:virology; D000358:African Swine Fever Virus / Q000145:classification* / Q000235:genetics; D000595:Amino Acid Sequence; D000818:Animals; D036022:Capsid Proteins / Q000145:classification / Q000235:genetics*; D005814:Genes, Viral; D005838:Genotype; D014943:Global Health; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D016415:Sequence Alignment; D013552:Swine
chemical_list: D036022:Capsid Proteins; C063745:capsid protein p72, African swine fever virus