Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing

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Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing is …
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scholarly articleQ13442814

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P356DOI10.1371/JOURNAL.PPAT.1002880
P932PMC publication ID3426529
P698PubMed publication ID22927816
P5875ResearchGate publication ID230749357

P50authorBarton HaynesQ4865631
Michael SaagQ6834090
Paul A GoepfertQ87472808
Lily M BlairQ114423038
Erica H ParrishQ114423041
Elena E GiorgiQ122828494
Ruy M. RibeiroQ30504775
Bette KorberQ30505218
Thomas DennyQ42939171
Gerald H LearnQ54541884
Beatrice H. HahnQ55293537
Tanmoy BhattacharyaQ55414889
Alan S. PerelsonQ55719625
George M. ShawQ78514357
Peter T. HraberQ37366689
P2093author name stringHui Li
Shuyi Wang
Mark B Stoddard
P2860cites workGenetic variation in IL28B and spontaneous clearance of hepatitis C virusQ24596340
Viral mutation ratesQ24611162
Assessment of hepatitis C virus sequence complexity by electrophoretic mobilities of both single-and double-stranded DNAsQ27469409
"Lifespan" of liver cells. Autoradio-graphic study using tritiated thymidine in normal, cirrhotic, and partially hepatectomized ratsQ79064331
Wide range of quasispecies diversity during primary hepatitis C virus infectionQ27469430
Quantitative Analysis of the Hepatitis C Virus Replication ComplexQ27472670
Identification of a Naturally Occurring Recombinant Genotype 2/6 Hepatitis C VirusQ27477460
Viral Sequence Evolution in Acute Hepatitis C Virus InfectionQ27484985
CD8 Epitope Escape and Reversion in Acute HCV InfectionQ27485189
Cellular immune selection with hepatitis C virus persistence in humansQ27485219
Immune evasion versus recovery after acute hepatitis C virus infection from a shared sourceQ27485222
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patientsQ27487949
Effect of Ribavirin on the Mutation Rate and Spectrum of Hepatitis C Virus In VivoQ27488394
Hepatitis C virus versus innate and adaptive immune responses: a tale of coevolution and coexistenceQ27488844
A trans-Complementing Recombination Trap Demonstrates a Low Propensity of Flaviviruses for Intermolecular RecombinationQ27490533
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsQ27860746
Replication of hepatitis C virusQ27860957
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodQ27861000
Determinants of viral clearance and persistence during acute hepatitis C virus infectionQ28131757
Hepatitis C virus phylogenetic clustering is associated with the social-injecting network in a cohort of people who inject drugsQ28484576
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation timeQ29547822
Genetic diversity and evolution of hepatitis C virus--15 years onQ29547888
Rates of evolutionary change in viruses: patterns and determinantsQ29616174
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infectionQ29619510
Adaptive immune responses in acute and chronic hepatitis C virus infectionQ29619722
The outcome of acute hepatitis C predicted by the evolution of the viral quasispeciesQ29619723
Telaprevir for previously untreated chronic hepatitis C virus infectionQ29619800
Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptaseQ29619994
Boceprevir for untreated chronic HCV genotype 1 infectionQ29620617
Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infectionQ30407004
Modeling sequence evolution in acute HIV-1 infectionQ37384535
Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase ampliconsQ37511426
IL28B and the control of hepatitis C virus infectionQ37800518
Treatment failure and resistance with direct-acting antiviral drugs against hepatitis C virusQ37849720
Turning hepatitis C into a real virusQ37891074
HIV-1 transmission, by stage of infectionQ38875941
Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, UgandaQ38881073
High rates of forward transmission events after acute/early HIV-1 infectionQ39788342
Acceleration of hepatitis C virus envelope evolution in humans is consistent with progressive humoral immune selection during the transition from acute to chronic infectionQ40341996
DNA recombination during PCR.Q40515497
Virus 'quasispecies': making a mountain out of a molehill?Q41532832
Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: proposed mechanism for its formationQ42630119
HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infectionQ42986755
A step forward in therapy for hepatitis C.Q42987221
Dynamics of viremia in early hepatitis C virus infectionQ42992916
Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.Q42993927
Acute hepatitis C virus infection: a dynamic-and challenging-concept.Q43001397
Absence of HCV viral recombination following superinfectionQ43030464
A new era of hepatitis C therapy beginsQ43035622
Sexual transmission of hepatitis C virus among HIV-infected men who have sex with men--New York City, 2005-2010.Q43038865
From RNA to quasispecies: a DNA polymerase with proofreading activity is highly recommended for accurate assessment of viral diversityQ43048808
HIV Quasispecies and ResamplingQ58002652
Novel CD4+ and CD8+ T-cell determinants within the NS3 protein in subjects with spontaneously resolved HCV infectionQ62735434
Sexual transmission during the incubation period of primary HIV infectionQ74608008
Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1Q33402461
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men.Q33582135
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysisQ33592278
Acute hepatitis C virus infection in young adult injection drug users: a prospective study of incident infection, resolution, and reinfectionQ33650138
Estimating time since infection in early homogeneous HIV-1 samples using a poisson modelQ33727328
Wide variation in the multiplicity of HIV-1 infection among injection drug usersQ33877419
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.Q33877425
Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virusQ33955998
Acute hepatitis C.Q34013032
Cross-border paid plasma donation among injection drug users in two Mexico-U.S. border citiesQ34202259
Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rateQ34395271
Pervasive genomic recombination of HIV-1 in vivoQ34645720
Evidence of a large, international network of HCV transmission in HIV-positive men who have sex with menQ34663297
Predicting spontaneous clearance of acute hepatitis C virus in a large cohort of HIV-1-infected men.Q34983860
Dynamic coinfection with multiple viral subtypes in acute hepatitis C.Q35022787
Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteinsQ35192915
Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistanceQ35650866
Generation of transmitted/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophagesQ35826158
Delayed induction, not impaired recruitment, of specific CD8⁺ T cells causes the late onset of acute hepatitis CQ35986301
Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escapeQ36000736
Infectivity in chimpanzees (Pan troglodytes) of plasma collected before HCV RNA detectability by FDA-licensed assays: implications for transfusion safety and HCV infection outcomesQ36058580
Prospects for a vaccine against the hepatitis C virusQ36233831
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencingQ36540055
Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1Q36795889
High specific infectivity of plasma virus from the pre-ramp-up and ramp-up stages of acute simian immunodeficiency virus infectionQ37127899
Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variantsQ37145228
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1.Q37273086
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infectionQ37273158
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infectionQ37273195
Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C.Q37381208
P275copyright licenseCreative Commons CC0 LicenseQ6938433
P6216copyright statuscopyrighted, dedicated to the public domain by copyright holderQ88088423
P433issue8
P407language of work or nameEnglishQ1860
P921main subjecthepatitis CQ154869
pathogen transmissionQ525512
Hepatitis C virusQ708693
viral transmissionQ123924092
P304page(s)e1002880
P577publication date2012-01-01
P1433published inPLOS PathogensQ283209
P1476titleElucidation of hepatitis C virus transmission and early diversification by single genome sequencing
P478volume8

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cites work (P2860)
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