TY - JOUR
T1 - Precise genotyping and recombination detection of Enterovirus
AU - Lin, Chieh Hua
AU - Wang, Yu Bin
AU - Chen, Shu Hwa
AU - Hsiung, Chao Agnes
AU - Lin, Chung Yen
N1 - Funding Information:
The authors wish to thank Dr. Min-Shi Lee and Dr. Pao-Yang Chen for valuable discussions on epidemiology of enterovirus and model of molecular tying, respectively. We also thank the editor and anonymous reviewers for their helpful advice. The research was funded by Ministry of Science and Technology (MOST), Taiwan, for financially supporting this research through MOST 104-2319-B-400-002 to CAH, MOST 103-2311-B-001-033-MY3 to CYL, MOST 101-2321-B-001-043-MY2 and MOST 102-2811-B-001-046 to SHC.
Funding Information:
The authors wish to thank Dr. Min-Shi Lee and Dr. Pao-Yang Chen for valuable discussions on epidemiology of enterovirus and model of molecular tying, respectively. We also thank the editor and anonymous reviewers for their helpful advice. The research was funded by Ministry of Science and Technology (MOST), Taiwan, for financially supporting this research through MOST 104-2319-B-400-002 to CAH, MOST 103-2311-B-001-033-MY3 to CYL, MOST 101-2321-B-001-043-MY2 and MOST 102-2811-B-001-046 to SHC
Publisher Copyright:
© 2015 Lin et al.
PY - 2015/12/9
Y1 - 2015/12/9
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2164-16-S12-S8
DO - 10.1186/1471-2164-16-S12-S8
M3 - Article
C2 - 26678286
AN - SCOPUS:84969277614
SN - 1471-2164
VL - 16
JO - BMC Genomics
JF - BMC Genomics
IS - 12
M1 - S8
ER -
