Abstract
Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution.
Highlights
The Enterovirus (EV) genus contains twelve species, including Enterovirus A to H and J, and Rhinovirus A to C
Many clinicians have turned to sequence-based molecular typing methods, which assign viral genotypes based on nucleotide sequences; such techniques are more successful at resolving EV isolates to the corresponding genotype, and provide rapid diagnosis [3]
We developed a web tool, EVIDENCE (EnteroVirus In DEep coNCEption), a workbench for phylogenetic-based genotyping and recombination detection in EV genomes
Summary
The Enterovirus (EV) genus (family Picornaviridae) contains twelve species, including Enterovirus A to H and J, and Rhinovirus A to C. These viruses cause a wide range of diseases in humans and mammals. The genetic diversity of EVs arises from the accumulation of single-base changes during viral propagation, as well as Different enterovirus genotypes cause different clinical symptoms [1]. Classical serotyping methods, such as serum neutralizing test and immunofluorescent assay, are not sufficient to specify all genotypes. The VP1 capsid-coding region has been suggested to be the most suitable region for EV genome genotyping [4,5]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
