A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-05-01
|
| Series: | PLoS Neglected Tropical Diseases |
| Online Access: | https://doi.org/10.1371/journal.pntd.0007231 |
| _version_ | 1818737602947186688 |
|---|---|
| author | Vagner Fonseca Pieter J K Libin Kristof Theys Nuno R Faria Marcio R T Nunes Maria I Restovic Murilo Freire Marta Giovanetti Lize Cuypers Ann Nowé Ana Abecasis Koen Deforche Gilberto A Santiago Isadora C de Siqueira Emmanuel J San Kaliane C B Machado Vasco Azevedo Ana Maria Bispo-de Filippis Rivaldo Venâncio da Cunha Oliver G Pybus Anne-Mieke Vandamme Luiz C J Alcantara Tulio de Oliveira |
| author_facet | Vagner Fonseca Pieter J K Libin Kristof Theys Nuno R Faria Marcio R T Nunes Maria I Restovic Murilo Freire Marta Giovanetti Lize Cuypers Ann Nowé Ana Abecasis Koen Deforche Gilberto A Santiago Isadora C de Siqueira Emmanuel J San Kaliane C B Machado Vasco Azevedo Ana Maria Bispo-de Filippis Rivaldo Venâncio da Cunha Oliver G Pybus Anne-Mieke Vandamme Luiz C J Alcantara Tulio de Oliveira |
| author_sort | Vagner Fonseca |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-18T00:55:40Z |
| format | Article |
| id | doaj.art-4e43129addbc4996b003291af82e3d82 |
| institution | Directory Open Access Journal |
| issn | 1935-2727 1935-2735 |
| language | English |
| last_indexed | 2024-12-18T00:55:40Z |
| publishDate | 2019-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Neglected Tropical Diseases |
| spelling | doaj.art-4e43129addbc4996b003291af82e3d822022-12-21T21:26:32ZengPublic Library of Science (PLoS)PLoS Neglected Tropical Diseases1935-27271935-27352019-05-01135e000723110.1371/journal.pntd.0007231A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.Vagner FonsecaPieter J K LibinKristof TheysNuno R FariaMarcio R T NunesMaria I RestovicMurilo FreireMarta GiovanettiLize CuypersAnn NowéAna AbecasisKoen DeforcheGilberto A SantiagoIsadora C de SiqueiraEmmanuel J SanKaliane C B MachadoVasco AzevedoAna Maria Bispo-de FilippisRivaldo Venâncio da CunhaOliver G PybusAnne-Mieke VandammeLuiz C J AlcantaraTulio de OliveiraIn 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.https://doi.org/10.1371/journal.pntd.0007231 |
| spellingShingle | Vagner Fonseca Pieter J K Libin Kristof Theys Nuno R Faria Marcio R T Nunes Maria I Restovic Murilo Freire Marta Giovanetti Lize Cuypers Ann Nowé Ana Abecasis Koen Deforche Gilberto A Santiago Isadora C de Siqueira Emmanuel J San Kaliane C B Machado Vasco Azevedo Ana Maria Bispo-de Filippis Rivaldo Venâncio da Cunha Oliver G Pybus Anne-Mieke Vandamme Luiz C J Alcantara Tulio de Oliveira A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLoS Neglected Tropical Diseases |
| title | A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. |
| title_full | A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. |
| title_fullStr | A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. |
| title_full_unstemmed | A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. |
| title_short | A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. |
| title_sort | computational method for the identification of dengue zika and chikungunya virus species and genotypes |
| url | https://doi.org/10.1371/journal.pntd.0007231 |
| work_keys_str_mv | AT vagnerfonseca acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT pieterjklibin acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT kristoftheys acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT nunorfaria acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT marciortnunes acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT mariairestovic acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT murilofreire acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT martagiovanetti acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT lizecuypers acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT annnowe acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT anaabecasis acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT koendeforche acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT gilbertoasantiago acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT isadoracdesiqueira acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT emmanueljsan acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT kalianecbmachado acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT vascoazevedo acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT anamariabispodefilippis acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT rivaldovenanciodacunha acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT olivergpybus acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT annemiekevandamme acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT luizcjalcantara acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT tuliodeoliveira acomputationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT vagnerfonseca computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT pieterjklibin computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT kristoftheys computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT nunorfaria computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT marciortnunes computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT mariairestovic computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT murilofreire computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT martagiovanetti computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT lizecuypers computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT annnowe computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT anaabecasis computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT koendeforche computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT gilbertoasantiago computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT isadoracdesiqueira computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT emmanueljsan computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT kalianecbmachado computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT vascoazevedo computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT anamariabispodefilippis computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT rivaldovenanciodacunha computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT olivergpybus computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT annemiekevandamme computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT luizcjalcantara computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes AT tuliodeoliveira computationalmethodfortheidentificationofdenguezikaandchikungunyavirusspeciesandgenotypes |