Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

(2013) Wei Shao et al.   Retrovirology

Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications

(2012) Ina Vandenbroucke et al.   BIOTECHNIQUES

Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes

(2012) A. Gall et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

Systematic exploration of error sources in pyrosequencing flowgram data

(2011) S. Balzer et al.   BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) Diversity and Tropism in 145 Patients With Primary HIV-1 Infection

(2011) P. Rieder et al.   CLINICAL INFECTIOUS DISEASES

Ambiguous Nucleotide Calls From Population-based Sequencing of HIV-1 are a Marker for Viral Diversity and the Age of Infection

(2011) Roger D. Kouyos et al.   CLINICAL INFECTIOUS DISEASES

Low-Frequency HIV-1 Drug Resistance Mutations and Risk of NNRTI-Based Antiretroviral Treatment Failure

(2011) Jonathan Z. Li   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Performance of Ultra-Deep Pyrosequencing in Analysis of HIV-1 pol Gene Variation

(2011) Mattias Mild et al.   PLoS One

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim

(2010) S. Balzer et al.   BIOINFORMATICS

Reducing chimera formation during PCR amplification to ensure accurate genotyping

(2010) R.P. Smyth et al.   GENE

Efficient Suppression of Minority Drug‐Resistant HIV Type 1 (HIV‐1) Variants Present at Primary HIV‐1 Infection by Ritonavir‐Boosted Protease Inhibitor–Containing Antiretroviral Therapy

(2010) Karin J. Metzner et al.   JOURNAL OF INFECTIOUS DISEASES

The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing

(2010) Irene Görzer et al.   JOURNAL OF VIROLOGICAL METHODS

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog et al.   PLoS One

Accurately Measuring Recombination between Closely Related HIV-1 Genomes

(2010) Timothy E. Schlub et al.   PLoS Computational Biology

Quasispecies Theory and the Behavior of RNA Viruses

(2010) Adam S. Lauring et al.   PLoS Pathogens

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

The Remarkable Frequency of Human Immunodeficiency Virus Type 1 Genetic Recombination

(2009) A. Onafuwa-Nuga et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

(2009) Athe M. N. Tsibris et al.   PLoS One

Minority Quasispecies of Drug‐Resistant HIV‐1 That Lead to Early Therapy Failure in Treatment‐Naive and ‐Adherent Patients

(2008) Karin J. Metzner et al.   CLINICAL INFECTIOUS DISEASES

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

(2008) J. F. Salazar-Gonzalez et al.   JOURNAL OF VIROLOGY

Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

(2008) Jeffrey A Johnson et al.   PLOS MEDICINE