Real Time Classification of Viruses in 12 Dimensions

Abstract

The International Committee on Taxonomy of Viruses authorizes and organizes the taxonomic classification of viruses. Thus far, the detailed classifications for all viruses are neither complete nor free from dispute. For example, the current missing label rates in GenBank are 12.1% for family label and 30.0% for genus label. Using the proposed Natural Vector representation, all 2,044 single-segment referenced viral genomes in GenBank can be embedded in . Unlike other approaches, this allows us to determine phylogenetic relations for all viruses at any level (e.g., Baltimore class, family, subfamily, genus, and species) in real time. Additionally, the proposed graphical representation for virus phylogeny provides a visualization of the distribution of viruses in . Unlike the commonly used tree visualization methods which suffer from uniqueness and existence problems, our representation always exists and is unique. This approach is successfully used to predict and correct viral classification information, as well as to identify viral origins; e.g. a recent public health threat, the West Nile virus, is closer to the Japanese encephalitis antigenic complex based on our visualization. Based on cross-validation results, the accuracy rates of our predictions are as high as 98.2% for Baltimore class labels, 96.6% for family labels, 99.7% for subfamily labels and 97.2% for genus labels.

Ebolavirus Classification Based on Natural Vectors

“…To accurately and quickly classify ebolavirus genomes and genes, we employed our alignment-free natural vector method (Yu et al, 2013). The natural vector represents a virus nucleotide sequence by a 12-dimensional vector.…”

“…The advantage of the method is that it does not rely on any model assumption. The natural vector method has been successfully used to classify and predict not only single-segmented viruses, such as HIV (Deng et al, 2011) and West Nile viruses (Yu et al, 2013), but also multiple-segmented viruses, such as influenza (Huang et al, 2014). The viral genome space can be embedded into a 12-dimensional space using the natural vector method.…”

“…To classify new ebolaviruses and associate proteins with the virus virulence, we used the reliable alignment-free natural vector method (Yu et al, 2013). Our phylogenetic analysis of the ebolaviruses is not only based on coding-complete genomes but also the seven protein genes in the genomes.…”

Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification

“…Its application to virus classification has been investigated [6], and high prediction accuracies have been achieved at the genus level and above. Its ability to classify viruses at the species level needs to be improved.…”

2D graphical representation of dna sequence based on horizon lines from a probabilistic view

“…In order to overcome these two problems and analyze genes, many other representations were studied. For example, 2D or 3D representations were discussed (GUO et al, 2001;RANDIC et al, 2003b;a;YAU et al, 2003;YAO et al, 2005;ZHANG et al, 2005;FAN, 2007;CAO et al, 2008;YU et al, 2009;ZHANG, 2009;CAO et al, 2010;XIE;MO, 2011;WANG, 2012;YU et al, 2013;YU et al, 2014;ZHANG et al, 2014;ZOU et al, 2014;.…”