title: A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations.
abstract: Determining the composition of viral populations is becoming increasingly important in the field of medical virology. While recently developed computational tools for viral haplotype analysis allow for correcting sequencing errors, they do not always allow for the removal of errors occurring in the upstream experimental protocol, such as PCR errors. Primer IDs (pIDs) are one method to address this problem by harnessing redundant template resampling for error correction. By using a reference mixture of five HIV-1 strains, we show how pIDs can be useful for estimating key experimental parameters, such as the substitution rate of the PCR process and the reverse transcription (RT) error rate. In addition, we introduce a hidden Markov model for determining the recombination rate of the RT PCR process. We found no strong sequence-specific bias in pID abundances (the same RT efficiencies as compared to commonly used short, specific RT primers) and no effects of pIDs on the estimated distribution of the references viruses.
authors.affiliation: Department of Biosystems Sciences and Engineering, ETH Zurich, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Seifert
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Di Giallonardo
authors.affiliation: Department of Biosystems Sciences and Engineering, ETH Zurich, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: Armin
authors.initials: A
authors.lastname: Töpfer
authors.affiliation: Department of Biosystems Sciences and Engineering, ETH Zurich, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: Jochen
authors.initials: J
authors.lastname: Singer
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schmutz
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland.
authors.forename: Huldrych F
authors.initials: HF
authors.lastname: Günthard
authors.affiliation: Department of Biosystems Sciences and Engineering, ETH Zurich, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland. Electronic address: niko.beerenwinkel@bsse.ethz.ch.
authors.forename: Niko
authors.initials: N
authors.lastname: Beerenwinkel
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland; Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland. Electronic address: karin.metzner@usz.ch.
authors.forename: Karin J
authors.initials: KJ
authors.lastname: Metzner
mesh_terms: D017931:DNA Primers / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D008967:Molecular Biology / Q000379:methods*; D011786:Quality Control
chemical_list: D017931:DNA Primers
keywords: HIV-1; PCR; RT; next-generation sequencing; primer ID