Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

CD8+ T-Cell Response Promotes Evolution of Hepatitis C Virus Nonstructural Proteins

(2011) Marianne Ruhl et al.   GASTROENTEROLOGY

Progress in the development of preventive and therapeutic vaccines for hepatitis C virus

(2011) Joseph Torresi et al.   JOURNAL OF HEPATOLOGY

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

(2010) Elena E Giorgi et al.   BMC BIOINFORMATICS

Incidence of primary hepatitis C infection and risk factors for transmission in an Australian prisoner cohort

(2010) Suzy Teutsch et al.   BMC PUBLIC HEALTH

Incidence and risk for acute hepatitis C infection during imprisonment in Australia

(2010) Kate Dolan et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

Frequent multiple hepatitis C virus infections among injection drug users in a prison setting

(2010) Son T. Pham et al.   HEPATOLOGY

Effect of immune pressure on hepatitis C virus evolution: Insights from a single-source outbreak

(2010) Shahzma Merani et al.   HEPATOLOGY

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Viral entry and escape from antibody-mediated neutralization influence hepatitis C virus reinfection in liver transplantation

(2010) Samira Fafi-Kremer et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Viral Evolution and Escape during Acute HIV‐1 Infection

(2010) Christian L. Boutwell et al.   JOURNAL OF INFECTIOUS DISEASES

Genetic recombination of the hepatitis C virus: clinical implications

(2010) V. Morel et al.   JOURNAL OF VIRAL HEPATITIS

A perspective on modelling hepatitis C virus infection

(2010) J. Guedj et al.   JOURNAL OF VIRAL HEPATITIS

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Beyond the Consensus: Dissecting Within-Host Viral Population Diversity of Foot-and-Mouth Disease Virus by Using Next-Generation Genome Sequencing

(2010) C. F. Wright et al.   JOURNAL OF VIROLOGY

Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing

(2010) G. P. Wang et al.   JOURNAL OF VIROLOGY

Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug Users

(2010) K. J. Bar et al.   JOURNAL OF VIROLOGY

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

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

Candidate hepatitis C vaccine trials and people who inject drugs: Challenges and opportunities

(2010) Lisa Maher et al.   VACCINE

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

(2009) Nilu Goonetilleke et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

(2009) Jesus F. Salazar-Gonzalez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Ultra‐Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse‐Transcriptase Inhibitor (NRTI)–Treated Patients and NRTI‐Naive Patients

(2009) Severine Margeridon‐Thermet et al.   JOURNAL OF INFECTIOUS DISEASES

Modeling sequence evolution in acute HIV-1 infection

(2009) Ha Youn Lee et al.   JOURNAL OF THEORETICAL BIOLOGY

Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use

(2009) Thuy Le et al.   PLoS One

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

Focal Distribution of Hepatitis C Virus RNA in Infected Livers

(2009) J. David Stiffler et al.   PLoS One

Depletion of interfering antibodies in chronic hepatitis C patients and vaccinated chimpanzees reveals broad cross-genotype neutralizing activity

(2009) P. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

(2009) Richard E. Haaland et al.   PLoS Pathogens

Immunological determinants of the outcomes from primary hepatitis C infection

(2008) J. Post et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

NS3 Helicase Domains Involved in Infectious Intracellular Hepatitis C Virus Particle Assembly

(2008) Y. Ma et al.   JOURNAL OF VIROLOGY

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen

(2008) M. Solmone et al.   JOURNAL OF VIROLOGY

Hepatitis C vaccine: supply and demand

(2008) G Thomas Strickland et al.   LANCET INFECTIOUS DISEASES

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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