Genotyping field strains of African swine fever virus by partial p72 gene characterisation

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 v...

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Bibliographic Details
Published in:Archives of virology 2003-04, Vol.148 (4), p.693-706
Main Authors: BASTES, A. D. S, PENRITH, M.-L, CRUCIERE, C, EDRICH, J. L, HUTCHINGS, G, ROGER, F, COUACY-HYMANN, E, THOMSON, G. R
Format: Article
Language:English
Subjects:
Africa - epidemiology
African Swine Fever - epidemiology
African Swine Fever - virology
African Swine Fever Virus - classification
African Swine Fever Virus - genetics
Amino Acid Sequence
Animals
Biological and medical sciences
Capsid Proteins - classification
Capsid Proteins - genetics
Epidemiology
Fundamental and applied biological sciences. Psychology
Genes, Viral
Genotype
Global Health
Life Sciences
Microbiology
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction - methods
Sequence Alignment
Swine
Virology
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Summary: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.
ISSN:0304-8608
1432-8798
DOI:10.1007/s00705-002-0946-8