A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

Abstract

In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.org.za/tools.php.

Fig 1. The typing tools’ web interface.

The web interface provides users a portal to run classifications on their sequences and to visualize the classification results (A). The typing report presents information about the sequence name of the query sequence, the nucleotide length of the sequence, an illustration of the position of the sequence in the virus’ genome, the species assignment and the genotype assignment. A detailed report is provided for the phylogenetic analysis that resulted into this classification. All results can be exported to a variety of file formats (XML, CSV, Excel or FASTA format). The detailed HTML report (B) contains information on the sequence name, length, assigned virus and genotype, an illustration of the position of the sequence in the virus’ genome and the phylogenetic analysis section. The phylogenetic analysis section shows the alignment and constructed phylogeny: the query sequence is always shown at the top of the phylogenetic tree.

Fig 2. Outline of the classification procedure.

Firstly (A), the viral species is determined using BLAST. When the submitted sequence is a Zika virus, a Neighbor joining tree is constructed to determine the Zika genotype (B). When the submitted sequence is a Chikungunya virus, a Neighbor joining tree is constructed to determine the Chikungunya genotype (C). When the submitted sequence is a Dengue virus, the serotype is determined using another BLAST invocation (D). Based on the inferred serotype, a serotype specific Neighbor joining tree is constructed to determine the Dengue genotype (E, F, G, H).

Fig 3. Investigating the suitability of sub-genomic regions for genotyping through boot-scanning.

This plot was constructed using bootstrap results from Neighbor Joining trees (1000 bootstrap replicates), performed on the dataset of the indicated reference strains. The boot-scanning method uses a sliding window of a 1500 base pair segment that moves with steps of 100 base pairs along the genome. The X-axis represents the nucleotide position in the genome, and the Y-axis represents bootstrap support in percentages. The light-grey rectangular area marks the location of the envelope gene in each graph. The inset color code shows the genotypes defined in each virus species. For ZIKV (A), this is African and Asian. For CHIKV (B), this is Asian Caribbean (A-C), West African (WA) and East-Central-South African (ECSA). For DENV (C-F), the genotype is visualized by a Roman numeral. Only genotypes which showed less than 100% bootstrap support across the genome are shown.