Probing of viral diversity by global haplotype prediction

Author

Topfer, Armin ; Di Giallonardo, Francesca ; Metzner, Karin J. ; Gunthard, Huldrych F. ; Beerenwinkel, Niko

Author_Institution

Dept. of Biosyst. Sci. & Eng., ETH Zurich, Basel, Switzerland

fYear

2013

fDate

12-14 June 2013

Firstpage

1

Lastpage

1

Abstract

The focus in clinical virology shifts from well-established identification of single nucleotide variants (SNV) to probing of individual viral RNA strains, called haplotypes. The success of antiretroviral treatment of HIV infection heavily depends on the knowledge of an intra-patient´s viral population heterogeneity, because diversity and in particular, low frequency variants affect virulence, immune escape, and drug resistance.

Keywords

DNA; diseases; drugs; genetics; microorganisms; molecular biophysics; molecular configurations; patient treatment; HIV infection; antiretroviral treatment; clinical virology shifts; drug resistance; global haplotype prediction; immune escape; individual viral RNA strains; intrapatient viral population heterogeneity; low-frequency variants; single nucleotide variant identification; viral diversity probing; virulence; Bioinformatics; Computational modeling; Educational institutions; Electronic mail; Hidden Markov models; Human immunodeficiency virus; Sequential analysis; HMM; Haplotype reconstruction; next-generation sequencing; viral quasispecies;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Advances in Bio and Medical Sciences (ICCABS), 2013 IEEE 3rd International Conference on

Conference_Location

New Orleans, LA

Type

conf

DOI

10.1109/ICCABS.2013.6629231

Filename

6629231