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 predefined 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 nonrecombinant 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/.
