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A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses...

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Autores principales: Alcantara, Luiz Carlos Junior, Cassol, Sharon, Libin, Pieter, Deforche, Koen, Pybus, Oliver G., Van Ranst, Marc, Galvão-Castro, Bernardo, Vandamme, Anne-Mieke, de Oliveira, Tulio
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703899/
https://www.ncbi.nlm.nih.gov/pubmed/19483099
http://dx.doi.org/10.1093/nar/gkp455
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author Alcantara, Luiz Carlos Junior
Cassol, Sharon
Libin, Pieter
Deforche, Koen
Pybus, Oliver G.
Van Ranst, Marc
Galvão-Castro, Bernardo
Vandamme, Anne-Mieke
de Oliveira, Tulio
author_facet Alcantara, Luiz Carlos Junior
Cassol, Sharon
Libin, Pieter
Deforche, Koen
Pybus, Oliver G.
Van Ranst, Marc
Galvão-Castro, Bernardo
Vandamme, Anne-Mieke
de Oliveira, Tulio
author_sort Alcantara, Luiz Carlos Junior
collection PubMed
description Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/ http://lasp.cpqgm.fiocruz.br/virus-genotype/html/ http://jose.med.kuleuven.be/genotypetool/html/.
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spelling pubmed-27038992009-07-01 A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences Alcantara, Luiz Carlos Junior Cassol, Sharon Libin, Pieter Deforche, Koen Pybus, Oliver G. Van Ranst, Marc Galvão-Castro, Bernardo Vandamme, Anne-Mieke de Oliveira, Tulio Nucleic Acids Res Articles Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/ http://lasp.cpqgm.fiocruz.br/virus-genotype/html/ http://jose.med.kuleuven.be/genotypetool/html/. Oxford University Press 2009-07-01 2009-05-29 /pmc/articles/PMC2703899/ /pubmed/19483099 http://dx.doi.org/10.1093/nar/gkp455 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Alcantara, Luiz Carlos Junior
Cassol, Sharon
Libin, Pieter
Deforche, Koen
Pybus, Oliver G.
Van Ranst, Marc
Galvão-Castro, Bernardo
Vandamme, Anne-Mieke
de Oliveira, Tulio
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
title A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
title_full A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
title_fullStr A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
title_full_unstemmed A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
title_short A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
title_sort standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703899/
https://www.ncbi.nlm.nih.gov/pubmed/19483099
http://dx.doi.org/10.1093/nar/gkp455
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