A re-evaluation of African swine fever genotypes based on p72 sequences reveals only 5 distinct p72 groups

Authors: Spinard Iii, Edward; Dinhobl, Mark; TESLER, NICHOLAS - Oak Ridge Institute For Science And Education (ORISE); BIRTLEY, HILLARY - Oak Ridge Institute For Science And Education (ORISE); SIGNORE, ANTHONY - Canadian Food Inspection Agency; AMBAGALA, ARUNA - Canadian Food Inspection Agency; MASEMBE, CHARLES - Makerere University; Borca, Manuel; Gladue, Douglas

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/5/2023
Publication Date: 8/11/2023
Citation: Spinard III, E.J., Dinhobl, M.W., Tesler, N., Birtley, H., Signore, A., Ambagala, A., Masembe, C., Borca, M.V., Gladue, D.P. 2023. A re-evaluation of African swine fever genotypes based on p72 sequences reveals only 5 distinct p72 groups. Viruses. 15(8). Article 1722. https://doi.org/10.3390/v15081722.
DOI: https://doi.org/10.3390/v15081722

Interpretive Summary: African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. It was previously believed that there were over 25 genotypes of ASFV, as new sequencing and analysis techniques have advanced since the first discovery of ASFV, a re-evaluation of the published sequences was performed, and revealed that only 5 genotypes have existed.

Technical Abstract: African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently an ASFV vaccine is only available in Vietnam, based on a genotype II virus strain. With 25 reported ASFV genotypes in the literature it is important to understand the basis of and usefulness of ASFV genotyping, and the true significance of genotypes in the epidemiology, transmission, evolution, control and prevention of ASFV. Genotyping of ASFV has been used historically because of the need for disease tracking and has been based on small fragments containing less than 1% of the viral genome. The most used genotyping of ASFV relies on sequencing a fragment or the entire gene encoding the structural p72 protein. However, assigning genotypes has largely gone unchecked, and is based on automated phylogenic trees or comparison to the closest match of an already sequenced and classified p72 gene. Here we reanalyzed all available sequencing data for ASFV, to evaluate its appropriateness for classification of genotypes by p72. We conclude that the majority of p72 genotypes when initially observed were neither identified under any specific criteria nor correctly compared to existing genotypes. We report based on our analysis of p72 genotypes, that based only on p72, the previously identified 25 genotypes of ASFV should be reduced to 5 genotypes. We also discuss the potential future usefulness of genotyping by p72.