Identification and typing of human enterovirus: a genomic barcode approach.
Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. He...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3194813?pdf=render |
| _version_ | 1811327951985180672 |
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| author | Chengguo Wei Guoqing Wang Xin Chen Honglan Huang Bin Liu Ying Xu Fan Li |
| author_facet | Chengguo Wei Guoqing Wang Xin Chen Honglan Huang Bin Liu Ying Xu Fan Li |
| author_sort | Chengguo Wei |
| collection | DOAJ |
| description | Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV or other human viruses, for a fixed k, 1<k<7, where a genome barcode is defined in terms of the k-mer frequency distribution across the whole genome for all combinations of k-mers. A phylogenetic tree is constructed using a barcode-based distance and a neighbor-joining method among a set of 443 representative non-HEV human viruses and 395 HEV sequences. The tree shows a clear separation of the HEV viruses from all the non-HEV viruses with 100% accuracy and a separation of the HEVs into four distinct clads with 93.4% consistency with a multiple sequence alignment-based phylogeny. Our detailed analyses of the HEVs having different typing results by the two methods indicate that our results are in better agreement with known information about the HEVs. |
| first_indexed | 2024-04-13T15:16:54Z |
| format | Article |
| id | doaj.art-892f65e5b346478985e7b8572c7872d7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T15:16:54Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-892f65e5b346478985e7b8572c7872d72022-12-22T02:41:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-01610e2629610.1371/journal.pone.0026296Identification and typing of human enterovirus: a genomic barcode approach.Chengguo WeiGuoqing WangXin ChenHonglan HuangBin LiuYing XuFan LiIdentification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV or other human viruses, for a fixed k, 1<k<7, where a genome barcode is defined in terms of the k-mer frequency distribution across the whole genome for all combinations of k-mers. A phylogenetic tree is constructed using a barcode-based distance and a neighbor-joining method among a set of 443 representative non-HEV human viruses and 395 HEV sequences. The tree shows a clear separation of the HEV viruses from all the non-HEV viruses with 100% accuracy and a separation of the HEVs into four distinct clads with 93.4% consistency with a multiple sequence alignment-based phylogeny. Our detailed analyses of the HEVs having different typing results by the two methods indicate that our results are in better agreement with known information about the HEVs.http://europepmc.org/articles/PMC3194813?pdf=render |
| spellingShingle | Chengguo Wei Guoqing Wang Xin Chen Honglan Huang Bin Liu Ying Xu Fan Li Identification and typing of human enterovirus: a genomic barcode approach. PLoS ONE |
| title | Identification and typing of human enterovirus: a genomic barcode approach. |
| title_full | Identification and typing of human enterovirus: a genomic barcode approach. |
| title_fullStr | Identification and typing of human enterovirus: a genomic barcode approach. |
| title_full_unstemmed | Identification and typing of human enterovirus: a genomic barcode approach. |
| title_short | Identification and typing of human enterovirus: a genomic barcode approach. |
| title_sort | identification and typing of human enterovirus a genomic barcode approach |
| url | http://europepmc.org/articles/PMC3194813?pdf=render |
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