US researchers: Only 6 unique ASFv genotypes

The research team, attached to the Agricultural Research Service (ARS) of the US Department of Agriculture, the Canadian Food Inspection Agency and Makarere University in Uganda, shared their proposal to reclassify the genotypes in a publication in the peer-reviewed journal Viruses. In a news article it was described as a “scientific innovation” which may help redefine how ASF researchers across the globe classify ASF virus (ASFv) isolates and may make it easier for scientists to develop vaccines that match the different strains circulating in ASF endemic areas across the globe.”

Currently, predominantly genotype I and genotype II (in the “old” classification) are known throughout the world as these both “left” the African continent. Genotype I emerged in Europe and Latin America in the 1960s-1970s, but currently this genotype is only known from an endemic situation at the Italian island Sardinia and recent outbreaks in China. Genotype II, however, emerged also in the Caucasian area in 2007 and spread to Europe, Asia and the Caribbean, creating large pig health issues in many countries.

This information is important as it may reduce the number of vaccines previously thought to be needed to protect against all ASFv genotypes

Re-evaluating available DNA sequence of ASF virus

Senior scientist Dr Douglas Gladue of ARS was quoted when saying, “Previously, 25 different virus genotypes were identified across the globe. Our research team recently re-evaluated all the publicly available virus DNA sequences and found that the majority of genotypes (genetic makeup) originally identified as novel were not correctly identified nor compared to already existing ASFv virus genotypes. Based on this analysis, there are actually fewer unique genotypes than the ASF research community believed, and that means that there is less diversity of ASFv affecting communities across the globe. This information is important as it may reduce the number of vaccines previously thought to be needed to protect against all ASFv genotypes.”

Accurate classification of viruses is paramount for epidemiological investigations and the development of cost-effective countermeasures, including designing vaccines for unique strains of ASFv.

12,000 historical and current virus isolates

The large-scale effort involved ARS researchers re-analysing over 12,000 historical and current virus isolates that were produced from ASFv labs worldwide. The effort was made possible using the computing power of SciNet, which is ARS’ super computer cluster for solving agricultural big data problems.

Sequencing a fragment within a gene

In the article in Viruses, the authors explain: “The predominant method for genotyping ASFv relies on the sequencing of a fragment within the gene encoding the structural p72 protein. […] To evaluate its appropriateness for the classification of genotypes by p72, we reanalysed 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.”

The team concluded, “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 6 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.”

Authors of the publication in Viruses are Edward Spinard, Mark Dinhobl, Nicolas Tesler, Hillary Birtley, Manuel V. Borca and Douglas P. Gladue, all attached to ARS, USDA, United States; Anthony V. Signore and Aruna Ambagala, Canadian Food Inspection Agency, Winnipeg, MB, Canada; Charles Masembe, Makarere University, Kampala, Uganda. The majority of the authors is also connected to the Center of Excellence for African Swine Fever Genomics, Guildford, CT, United States.