A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups
Author:
Spinard Edward123ORCID, Dinhobl Mark123, Tesler Nicolas14ORCID, Birtley Hillary14, Signore Anthony V.35ORCID, Ambagala Aruna35ORCID, Masembe Charles36ORCID, Borca Manuel V.123, Gladue Douglas P.123ORCID
Affiliation:
1. Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA 2. National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA 3. Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA 4. Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA 5. National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada 6. College of Natural Resources (CoNAS), Makerere University, Kampala P.O. Box 7062, Uganda
Abstract
The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.
Funder
National Pork Board Project Foundation for Food and Agriculture Rapid Outcomes from Agriculture Research
Subject
Virology,Infectious Diseases
Reference20 articles.
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