Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

Abstract

In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150-200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.

Keywords: ASFV; African swine fever; biotype; classification; genotype.

Figure 1

Summary of the analysis pipeline described in Materials and Methods.

Figure 2

Process for going from pairwise percent identity gene-gene identity matrices to DBSCAN. (A) Gene-level identity matrices are multiplied by their weights and averaged resulting in the (B) genome-genome identity matrix. The average genome-genome identity matrix is then analyzed via DBSCAN to identify clusters based on similarity. The weight equation is described in Section 2.4.

Figure 3

Results of DBSCAN demonstrate the number of clusters at the indicated epsilon value. Brackets indicate the convergence of clusters. Dark blue boxes indicate a sequence from a single isolate, and medium blue boxes indicate a group of isolates with similar sequences.