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. 2009 Jul;37(Web Server issue):W634-42.
doi: 10.1093/nar/gkp455. Epub 2009 May 29.

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

Luiz Carlos Junior Alcantara  1 , Sharon Cassol, Pieter Libin, Koen Deforche, Oliver G Pybus, Marc Van Ranst, Bernardo Galvão-Castro, Anne-Mieke Vandamme, Tulio de Oliveira
Affiliations

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

Luiz Carlos Junior Alcantara et al. Nucleic Acids Res. 2009 Jul.

Abstract

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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Figures

Figure 1.
Figure 1.
(A) Bootscanning results of an HBV complete genome recombinant sequence (acc. Number AM4947161). The X-axis represents the length of the sequence that is being analysed. The Y-axis represents the bootstrap support o the query sequence with subtype reference datasets. The color represents the different symbols. (B) Recombination profile not considering bootstrap confidence. (C) Recombination profile with >70% bootstrap confidence.
Figure 2.
Figure 2.
(A) Phylogenetic tree showing the location of the AJ851228 sequence. (B) Recombination profile without bootstrap confidence (top panel); recombination profile with >70% bootstrap confidence.
See this image and copyright information in PMC

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