Abstract
BackgroundSerotypes of the Foot-and-Mouth disease viruses (FMDVs) were generally determined by biological experiments. The computational genotyping is not well studied even with the availability of whole viral genomes, due to uneven evolution among genes as well as frequent genetic recombination. Naively using sequence comparison for genotyping is only able to achieve a limited extent of success.ResultsWe used 129 FMDV strains with known serotype as training strains to select as many as 140 most serotype-specific nucleotide strings. We then constructed a linear-kernel Support Vector Machine classifier using these 140 strings. Under the leave-one-out cross validation scheme, this classifier was able to assign correct serotype to 127 of these 129 strains, achieving 98.45% accuracy. It also assigned serotype correctly to an independent test set of 83 other FMDV strains downloaded separately from NCBI GenBank.ConclusionComputational genotyping is much faster and much cheaper than the wet-lab based biological experiments, upon the availability of the detailed molecular sequences. The high accuracy of our proposed method suggests the potential of utilizing a few signature nucleotide strings instead of whole genomes to determine the serotypes of novel FMDV strains.
Highlights
Serotypes of the Foot-and-Mouth disease viruses (FMDVs) were generally determined by biological experiments
The high accuracy of our proposed method suggests the potential of utilizing a few signature nucleotide strings instead of whole genomes to determine the serotypes of novel FMDV strains
We propose to identify a set of signature nucleotide strings which can be readily used to efficiently detect the genotypes for emerging FMDV strains
Summary
Serotypes of the Foot-and-Mouth disease viruses (FMDVs) were generally determined by biological experiments. The most recent outbreak in the United Kingdom costs tens of billions of dollars [1]. This disease causes extensive epidemics in domestic and wild clovenhooved animals, such as cattle, sheep, goats, and pigs. It can result in persistent infections in ruminants, and so the disease is in the importation banning and detection list of most countries. This disease can cause mild infection in human through skin wounds or the oral mucosa. The vaccination is the most efficient method to prevent this disease, so preparation and selection of an efficient vaccine will be the most important for FMD prevention and control
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