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Genome Replication and Regulation of Viral Gene Expression: Internal Disequilibria and Phenotypic Diversification during Replication of Hepatitis C Virus in a Noncoevolving Cellular Environment
  • Elena Moreno,
  • Isabel Gallego,
  • Josep Gregori,
  • Adriana Lucía-Sanz,
  • María Eugenia Soria,
  • Victoria Castro,
  • Nathan M. Beach,
  • Susanna Manrubia,
  • Josep Quer,
  • Juan Ignacio Esteban,
  • Charles M. Rice,
  • Jordi Gómez,
  • Pablo Gastaminza,
  • Esteban Domingo,
  • and Celia Perales
J. Virol. May 2017 91:10 19 e02505-16; Accepted manuscript posted online 8 March 2017, doi:10.1128/JVI.02505-16
Pathogenesis and Immunity: Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy
  • Mary F. Kearney,
  • Ann Wiegand,
  • Wei Shao,
  • John M. Coffin,
  • John W. Mellors,
  • Michael Lederman,
  • Rajesh T. Gandhi,
  • Brandon F. Keele,
  • and Jonathan Z. Li
J. Virol. February 2016 90:3 8 1369-1376; Accepted manuscript posted online 18 November 2015, doi:10.1128/JVI.02139-15
Genetic Diversity and Evolution: Increased Replicative Fitness Can Lead to Decreased Drug Sensitivity of Hepatitis C Virus
  • Julie Sheldon,
  • Nathan M. Beach,
  • Elena Moreno,
  • Isabel Gallego,
  • David Piñeiro,
  • Encarnación Martínez-Salas,
  • Josep Gregori,
  • Josep Quer,
  • Juan Ignacio Esteban,
  • Charles M. Rice,
  • Esteban Domingo,
  • and Celia Perales
J. Virol. October 2014 88:20 12098-12111; Accepted manuscript posted online 13 August 2014, doi:10.1128/JVI.01860-14
Pathogenesis and Immunity: Linking Pig-Tailed Macaque Major Histocompatibility Complex Class I Haplotypes and Cytotoxic T Lymphocyte Escape Mutations in Simian Immunodeficiency Virus Infection
  • Shayarana L. Gooneratne,
  • Hamid Alinejad-Rokny,
  • Diako Ebrahimi,
  • Patrick S. Bohn,
  • Roger W. Wiseman,
  • David H. O'Connor,
  • Miles P. Davenport,
  • and Stephen J. Kent
J. Virol. December 2014 88:24 14310-14325; Accepted manuscript posted online 1 October 2014, doi:10.1128/JVI.02428-14
Genetic Diversity and Evolution: Deep Sequencing and Phylogenetic Analysis of Variants Resistant to Interferon-Based Protease Inhibitor Therapy in Chronic Hepatitis Induced by Genotype 1b Hepatitis C Virus
  • Mitsuaki Sato,
  • Shinya Maekawa,
  • Nobutoshi Komatsu,
  • Akihisa Tatsumi,
  • Mika Miura,
  • Masaru Muraoka,
  • Yuichiro Suzuki,
  • Fumitake Amemiya,
  • Shinichi Takano,
  • Mitsuharu Fukasawa,
  • Yasuhiro Nakayama,
  • Tatsuya Yamaguchi,
  • Tomoyoshi Uetake,
  • Taisuke Inoue,
  • Tadashi Sato,
  • Minoru Sakamoto,
  • Atsuya Yamashita,
  • Kohji Moriishi,
  • and Nobuyuki Enomoto
J. Virol. June 2015 89:11 12 6105-6116; Accepted manuscript posted online 25 March 2015, doi:10.1128/JVI.03127-14
Pathogenesis and Immunity: Association between Latent Proviral Characteristics and Immune Activation in Antiretrovirus-Treated Human Immunodeficiency Virus Type 1-Infected Adults
  • Emily C. Liang,
  • Lindsay Sceats,
  • Nicholas L. Bayless,
  • Dara M. Strauss-Albee,
  • Jessica Kubo,
  • Philip M. Grant,
  • David Furman,
  • Manisha Desai,
  • David A. Katzenstein,
  • Mark M. Davis,
  • Andrew R. Zolopa,
  • and Catherine A. Blish
J. Virol. August 2014 88:15 8629-8639; Accepted manuscript posted online 21 May 2014, doi:10.1128/JVI.01257-14
Genetic Diversity and Evolution: Fifteen to Twenty Percent of HIV Substitution Mutations Are Associated with Recombination
  • Timothy E. Schlub,
  • Andrew J. Grimm,
  • Redmond P. Smyth,
  • Deborah Cromer,
  • Abha Chopra,
  • Simon Mallal,
  • Vanessa Venturi,
  • Caryll Waugh,
  • Johnson Mak,
  • and Miles P. Davenport
J. Virol. April 2014 88:7 3837-3849; Accepted manuscript posted online 22 January 2014, doi:10.1128/JVI.03136-13
Genetic Diversity and Evolution: Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification
  • Hui Li,
  • Mark B. Stoddard,
  • Shuyi Wang,
  • Elena E. Giorgi,
  • Lily M. Blair,
  • Gerald H. Learn,
  • Beatrice H. Hahn,
  • Harvey J. Alter,
  • Michael P. Busch,
  • Daniel S. Fierer,
  • Ruy M. Ribeiro,
  • Alan S. Perelson,
  • Tanmoy Bhattacharya,
  • and George M. Shaw
J. Virol. January 2016 90:1 15 152-166; Accepted manuscript posted online 14 October 2015, doi:10.1128/JVI.02156-15
OPEN ACCESS ARTICLE
Genetic Diversity and Evolution: Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution
  • Fabio Zanini and
  • Richard A. Neher
J. Virol. November 2013 87:21 11843-11850; Accepted manuscript posted online 28 August 2013, doi:10.1128/JVI.01529-13
OPEN ACCESS ARTICLE
RECOMBINATION AND EVOLUTION: Population Genetic Analysis of the Protease Locus of Human Immunodeficiency Virus Type 1 Quasispecies Undergoing Drug Selection, Using a Denaturing Gradient-Heteroduplex Tracking Assay
  • Laurence Doukhan and
  • Eric Delwart
J. Virol. July 2001 75:14 6729-6736; doi:10.1128/JVI.75.14.6729-6736.2001

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