Identification, Molecular Cloning, and Analysis of Full-Length Hepatitis C Virus Transmitted/Founder Genotypes 1, 3, and 4
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Hui Li | Charles M. Rice | Wenge Ding | Gerald H. Learn | Linda Andrus | George M. Shaw | Paul A. Goepfert | G. Learn | C. Rice | G. Shaw | B. Hahn | P. Goepfert | Hui Li | Shuyi Wang | J. Wen | Mohsan Saeed | A. Ploss | Shuyi Wang | Beatrice H. Hahn | Alexander Ploss | M. Stoddard | Markus von Schaewen | Wenge Ding | Markus von Schaewen | Mark B. Stoddard | Mohsan Saeed | Xinpei Jiang | Jessica Wen | L. Andrus | Xinpei Jiang
[1] Alan S. Perelson,et al. Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing , 2012, PLoS pathogens.
[2] J. Jiricny,et al. RNA-dependent RNA polymerase of hepatitis C virus. , 1996, Methods in enzymology.
[3] Ling Lu,et al. Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant. , 2013, The Journal of general virology.
[4] C. Rice,et al. Identification of a highly conserved sequence element at the 3' terminus of hepatitis C virus genome RNA , 1996, Journal of virology.
[5] C. Rice,et al. 3′ RNA Elements in Hepatitis C Virus Replication: Kissing Partners and Long Poly(U) , 2007, Journal of Virology.
[6] Frederic D. Bushman,et al. Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing , 2010, Journal of Virology.
[7] A. Tarr,et al. Identification of Conserved Residues in the E2 Envelope Glycoprotein of the Hepatitis C Virus That Are Critical for CD81 Binding , 2006, Journal of Virology.
[8] S. Lemon,et al. Production of infectious genotype 1a hepatitis C virus (Hutchinson strain) in cultured human hepatoma cells , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[9] J. Kench,et al. Genotype‐specific mechanisms for hepatic steatosis in chronic hepatitis C infection , 2002, Journal of gastroenterology and hepatology.
[10] Mario Roederer,et al. Immunological and Virological Mechanisms of Vaccine-Mediated Protection Against SIV and HIV , 2013, Nature.
[11] Todd M. Allen,et al. Viral Sequence Evolution in Acute Hepatitis C Virus Infection , 2007, Journal of Virology.
[12] M. Otto,et al. Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA , 2012, Journal of Virology.
[13] Todd M. Allen,et al. Characterization of full‐length hepatitis C virus genotype 4 sequences , 2007, Journal of viral hepatitis.
[14] R. Bartenschlager,et al. Genetic Analysis of Sequences in the 3′ Nontranslated Region of Hepatitis C Virus That Are Important for RNA Replication , 2002, Journal of Virology.
[15] E. Delwart,et al. Infectivity in chimpanzees (Pan troglodytes) of plasma collected before HCV RNA detectability by FDA-licensed assays: implications for transfusion safety and HCV infection outcomes. , 2012, Blood.
[16] A. Telesnitsky,et al. Altering the Intracellular Environment Increases the Frequency of Tandem Repeat Deletion during Moloney Murine Leukemia Virus Reverse Transcription , 1999, Journal of Virology.
[17] R. Bartenschlager,et al. Production of infectious hepatitis C virus in tissue culture from a cloned viral genome , 2005, Nature Medicine.
[18] F. Mahoney,et al. Evolution of infection control in Egypt: achievements and challenges. , 2006, American journal of infection control.
[19] Lawrence C Kuo,et al. Inhibition of Hepatitis C Virus RNA Replication by 2′-Modified Nucleoside Analogs* , 2003, The Journal of Biological Chemistry.
[20] H. Thomas,et al. Sequence, expression and reconstitution of an HCV genome from a British isolate derived from a single blood donation , 2000, Journal of viral hepatitis.
[21] Christopher T. Jones,et al. Hepatitis C virus induces interferon‐λ and interferon‐stimulated genes in primary liver cultures , 2011, Hepatology.
[22] A. Perelson,et al. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection , 2009, The Journal of experimental medicine.
[23] Bette T. Korber,et al. Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission , 2004, Science.
[24] A. Folgori,et al. Novel Adenovirus-Based Vaccines Induce Broad and Sustained T Cell Responses to HCV in Man , 2012, Science Translational Medicine.
[25] Hui Li,et al. Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug Users , 2010, Journal of Virology.
[26] R. Bartenschlager,et al. Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity , 1997, Journal of virology.
[27] S. Lemon,et al. Regulating Intracellular Antiviral Defense and Permissiveness to Hepatitis C Virus RNA Replication through a Cellular RNA Helicase, RIG-I , 2005, Journal of Virology.
[28] Sangeeta N. Bhatia,et al. Real-time imaging of hepatitis C virus infection using a fluorescent cell-based reporter system , 2010, Nature Biotechnology.
[29] G. Shaw,et al. Transmitted/Founder Hepatitis C Viruses Induce Cell-Type- and Genotype-Specific Differences in Innate Signaling within the Liver , 2015, mBio.
[30] M. Georgiadis,et al. The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus. , 2004, Structure.
[31] Thomas Lengauer,et al. Recco: recombination analysis using cost optimization , 2006, Bioinform..
[32] Ralf Bartenschlager,et al. Quantitative Analysis of the Hepatitis C Virus Replication Complex , 2005, Journal of Virology.
[33] P. Roingeard,et al. Role of N-Linked Glycans in the Functions of Hepatitis C Virus Envelope Proteins Incorporated into Infectious Virions , 2010, Journal of Virology.
[34] T. Date,et al. Full-length sequence of the genome of hepatitis C virus type 3a: comparative study with different genotypes. , 1994, The Journal of general virology.
[35] Rebecca R. Gray,et al. The mode and tempo of hepatitis C virus evolution within and among hosts , 2011, BMC Evolutionary Biology.
[36] B. Korber,et al. Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing , 2008, Journal of Virology.
[37] V. Pathak,et al. Retroviral mutation rates and reverse transcriptase fidelity. , 2003, Frontiers in bioscience : a journal and virtual library.
[38] P. Sarnow,et al. Modulation of Hepatitis C Virus RNA Abundance by a Liver-Specific MicroRNA , 2005, Science.
[39] Alan S. Perelson,et al. Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate , 2012, PLoS pathogens.
[40] Martin A. Nowak,et al. Antibody neutralization and escape by HIV-1 , 2003, Nature.
[41] R. Purcell,et al. Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and In Vivo Pathogenesis Studies , 2010, Journal of Virology.
[42] R. Colina,et al. Evidence of structural genomic region recombination in Hepatitis C virus , 2006, Virology Journal.
[43] S. Lemon,et al. 3′ Nontranslated RNA Signals Required for Replication of Hepatitis C Virus RNA , 2003, Journal of Virology.
[44] M. Gale,et al. Uridine Composition of the Poly-U/UC Tract of HCV RNA Defines Non-Self Recognition by RIG-I , 2012, PLoS pathogens.
[45] C. Tural,et al. Hepatitis C virus NS3/4A quasispecies diversity in acute hepatitis C infection in HIV‐1 co‐infected patients , 2014, Journal of viral hepatitis.
[46] A. Lever,et al. Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5' and 3' of the catalytic site. , 1998, Nucleic acids research.
[47] A. Tuplin,et al. Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. , 2004, The Journal of general virology.
[48] Fengzhu Sun,et al. Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. , 2003, Nucleic acids research.
[49] A. Moya,et al. Evidence of Recombination in Intrapatient Populations of Hepatitis C Virus , 2008, PloS one.
[50] H. Drummer,et al. Expression and Characterization of a Minimal Hepatitis C Virus Glycoprotein E2 Core Domain That Retains CD81 Binding , 2007, Journal of Virology.
[51] C. Rice,et al. Studying Hepatitis C Virus: Making the Best of a Bad Virus , 2007, Journal of Virology.
[52] T. Wakita,et al. Replication of hepatitis C virus genotype 3a in cultured cells. , 2013, Gastroenterology.
[53] G. Klarmann,et al. Template-directed pausing of DNA synthesis by HIV-1 reverse transcriptase during polymerization of HIV-1 sequences in vitro. , 1993, The Journal of biological chemistry.
[54] J. Bukh,et al. Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus. , 2014, Trends in microbiology.
[55] S. Glynn,et al. Dynamics of viremia in early hepatitis C virus infection , 2005, Transfusion.
[56] P. Farci. New insights into the HCV quasispecies and compartmentalization. , 2011, Seminars in liver disease.
[57] F. Negro,et al. Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e. , 2014, The Journal of general virology.
[58] Alan S. Perelson,et al. High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men , 2010, PLoS pathogens.
[59] Eric J. Arts,et al. In Vitro Intersubtype Recombinants of Human Immunodeficiency Virus Type 1: Comparison to Recent and Circulating In Vivo Recombinant Forms , 2002, Journal of Virology.
[60] E. L. Potter,et al. Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design , 2013, Journal of Virology.
[61] Tanmoy Bhattacharya,et al. Modeling sequence evolution in acute HIV-1 infection. , 2009, Journal of theoretical biology.
[62] M. Lai,et al. Determination of the secondary structure of and cellular protein binding to the 3'-untranslated region of the hepatitis C virus RNA genome , 1997, Journal of virology.
[63] S. Réhman,et al. Hepatitis C Virus Envelope Glycoprotein Fitness Defines Virus Population Composition following Transmission to a New Host , 2012, Journal of Virology.
[64] M. Yanagi,et al. Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[65] R. Francesco,et al. Identification and properties of the RNA‐dependent RNA polymerase of hepatitis C virus. , 1996, The EMBO journal.
[66] Sergei L. Kosakovsky Pond,et al. GARD: a genetic algorithm for recombination detection , 2006, Bioinform..
[67] J. Silver,et al. Replication of Subgenomic Hepatitis C Virus Rnas in a Hepatoma Cell Line , 1999 .
[68] Christopher T. Jones,et al. Expression of Paramyxovirus V Proteins Promotes Replication and Spread of Hepatitis C Virus in Cultures of Primary Human Fetal Liver Cells , 2011, Hepatology.
[69] Gabriel Waksman,et al. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation , 1998, The EMBO journal.
[70] S. Lemon,et al. Distinct Poly(I-C) and Virus-activated Signaling Pathways Leading to Interferon-β Production in Hepatocytes* , 2005, Journal of Biological Chemistry.
[71] Birke Bartosch,et al. Role of N-Linked Glycans in the Functions of Hepatitis C Virus Envelope Glycoproteins , 2005, Journal of Virology.
[72] N. Kato,et al. Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus. , 1992, Biochemical and biophysical research communications.
[73] Alan S. Perelson,et al. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection , 2009, The Journal of experimental medicine.
[74] M. Yanagi,et al. In vivo analysis of the 3' untranslated region of the hepatitis C virus after in vitro mutagenesis of an infectious cDNA clone. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[75] H. Ding,et al. Relative resistance of HIV-1 founder viruses to control by interferon-alpha , 2013, Retrovirology.
[76] C. Rice,et al. Efficient Replication of Genotype 3a and 4a Hepatitis C Virus Replicons in Human Hepatoma Cells , 2012, Antimicrobial Agents and Chemotherapy.
[77] M. Dowton,et al. Poly(T) Variation in Heteroderid Nematode Mitochondrial Genomes is Predominantly an Artefact of Amplification , 2011, Journal of Molecular Evolution.
[78] C. Rice,et al. Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA. , 1997, Science.
[79] R. Bartenschlager,et al. Production of Infectious Genotype 1b Virus Particles in Cell Culture and Impairment by Replication Enhancing Mutations , 2009, PLoS pathogens.
[80] S. Ehrlich,et al. In vitro replication slippage by DNA polymerases from thermophilic organisms. , 2001, Journal of molecular biology.
[81] H. Ding,et al. Generation of Transmitted/Founder HIV-1 Infectious Molecular Clones and Characterization of Their Replication Capacity in CD4 T Lymphocytes and Monocyte-Derived Macrophages , 2011, Journal of Virology.
[82] D. Montefiori,et al. Protection Afforded by an HIV Vaccine Candidate in Macaques Depends on the Dose of SIVmac251 at Challenge Exposure , 2013, Journal of Virology.
[83] C. Rice,et al. Expanded Classification of Hepatitis C Virus Into 7 Genotypes and 67 Subtypes: Updated Criteria and Genotype Assignment Web Resource , 2013, Hepatology.
[84] Alan S. Perelson,et al. Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1 , 2009, The Journal of experimental medicine.
[85] Nancy Glass,et al. Global burden of hepatitis C: considerations for healthcare providers in the United States. , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[86] N. Habuka,et al. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. , 1999, Structure.
[87] R. Lanford,et al. Infectious cDNA clone of the hepatitis C virus genotype 1 prototype sequence. , 2001, The Journal of general virology.
[88] M. Bracho,et al. Recombination in Hepatitis C Virus , 2011, Viruses.
[89] G. Learn,et al. Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users , 2014, Open forum infectious diseases.
[90] Charles M. Rice,et al. Flaviviridae :T he Viruses and Their Replication , 2007 .
[91] Tomer Hertz,et al. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env-V2 , 2012, Nature.
[92] C. Guillemette,et al. Three-dimensional culture and cAMP signaling promote the maturation of human pluripotent stem cell-derived hepatocytes , 2013, Development.
[93] Lynn Morris,et al. Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape , 2012, Nature Medicine.
[94] Jean Dubuisson,et al. Glycosylation of hepatitis C virus envelope proteins. , 2003, Biochimie.
[95] G. Shaw,et al. Hepatitis C virus infection induces autocrine interferon signaling by human liver endothelial cells and release of exosomes, which inhibits viral replication. , 2015, Gastroenterology.
[96] Christophe Combet,et al. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes , 2005, Hepatology.
[97] N. Kato,et al. Structure of the 3' terminus of the hepatitis C virus genome , 1996, Journal of virology.
[98] Peter B. Gilbert,et al. Genetic impact of vaccination on breakthrough HIV-1 sequences from the Step trial , 2011, Nature Medicine.
[99] Jiayou Zhang,et al. Determination of the Frequency of Retroviral Recombination between Two Identical Sequences within a Provirus , 2000, Journal of Virology.
[100] S. Odelberg,et al. Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I. , 1995, Nucleic acids research.
[101] B. Haynes,et al. Low-Dose Mucosal Simian Immunodeficiency Virus Infection Restricts Early Replication Kinetics and Transmitted Virus Variants in Rhesus Monkeys , 2010, Journal of Virology.
[102] Y. Hirata,et al. A serine palmitoyltransferase inhibitor blocks hepatitis C virus replication in human hepatocytes. , 2013, Gastroenterology.
[103] Michael Gale,et al. Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA , 2008, Nature.
[104] F. Hu,et al. Evolution of a Cell Culture-Derived Genotype 1a Hepatitis C Virus (H77S.2) during Persistent Infection with Chronic Hepatitis in a Chimpanzee , 2014, Journal of Virology.
[105] Feng Gao,et al. Phenotypic properties of transmitted founder HIV-1 , 2013, Proceedings of the National Academy of Sciences.
[106] L. Menéndez-Arias. Mutation Rates and Intrinsic Fidelity of Retroviral Reverse Transcriptases , 2009, Viruses.
[107] P. Klenerman,et al. Dynamic coinfection with multiple viral subtypes in acute hepatitis C. , 2010, The Journal of infectious diseases.
[108] James J. Champoux,et al. Pausing during Reverse Transcription Increases the Rate of Retroviral Recombination , 2006, Journal of Virology.
[109] J. Dubuisson,et al. Permissivity of Primary Human Hepatocytes and Different Hepatoma Cell Lines to Cell Culture Adapted Hepatitis C Virus , 2013, PloS one.
[110] T. Kunkel,et al. Unequal human immunodeficiency virus type 1 reverse transcriptase error rates with RNA and DNA templates. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[111] Rowena A. Bull,et al. Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection , 2011, PLoS pathogens.
[112] R Sedivy,et al. Reverse transcriptase template switching during reverse transcriptase-polymerase chain reaction: artificial generation of deletions in ribonucleotide reductase mRNA. , 2001, The Journal of laboratory and clinical medicine.
[113] H J Alter,et al. The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. , 2000, Science.
[114] Hui Li,et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection , 2008, Proceedings of the National Academy of Sciences.