Tracking HCV protease population diversity during transmission and susceptibility of founder populations to antiviral therapy

Brown, 2012, Hepatitis C virus envelope glycoprotein fitness defines virus population composition following transmission to a new host, J. Virol., 86, 11956, 10.1128/JVI.01079-12 Brown, 2014, Analysis of serine codon conservation reveals diverse phenotypic constraints on hepatitis C virus glycoprotein evolution, J. Virol., 88, 667, 10.1128/JVI.01745-13 Bukh, 2012, Animal models for the study of hepatitis C virus infection and related liver disease, Gastroenterology, 142, 1279, 10.1053/j.gastro.2012.02.016 Buti, 2016, Grazoprevir, Elbasvir, and Ribavirin for chronic hepatitis C virus genotype 1 infection after failure of pegylated interferon and Ribavirin with an Earlier-generation protease inhibitor: final 24-week results from C-SALVAGE, Clin. Infect. Dis., 62, 32, 10.1093/cid/civ722 Crooks, 2004, WebLogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004 DiversiTools: Beyond the consensus HTS (High-throughput sequencing) tools, [http://josephhughes.github.io/btctools/]. D'Arienzo, 2013, Sequence and functional analysis of the envelope glycoproteins of hepatitis C virus variants selectively transmitted to a new host, J. Virol., 87, 13609, 10.1128/JVI.02119-13 Fafi-Kremer, 2010, Viral entry and escape from antibody-mediated neutralization influence hepatitis C virus reinfection in liver transplantation, J. Exp. Med., 207, 2019, 10.1084/jem.20090766 Felmlee, 2016, New perspectives for preventing hepatitis C virus liver graft infection, Lancet. Infect. Dis., 16, 735, 10.1016/S1473-3099(16)00120-1 Fofana, 2012, Mutations that alter use of hepatitis C virus cell entry factors mediate escape from neutralizing antibodies, Gastroenterology, 143, 223, 10.1053/j.gastro.2012.04.006 Honegger, 2013, Loss of immune escape mutations during persistent HCV infection in pregnancy enhances replication of vertically transmitted viruses, Nat. Med., 19, 1529, 10.1038/nm.3351 Irving, 2010, Acute hepatitis C virus infection: a dynamic-and challenging-concept, J. Infect. Dis., 202, 1765, 10.1086/657318 Irving, 2014, Development of a high-throughput pyrosequencing assay for monitoring temporal evolution and resistance associated variant emergence in the Hepatitis C virus protease coding-region, Antivir. Res., 110, 52, 10.1016/j.antiviral.2014.07.009 Lamarre, 2003, An NS3 protease inhibitor with antiviral effects in humans infected with hepatitis C virus, Nature, 426, 186, 10.1038/nature02099 Lange, 2014, Emerging therapies for the treatment of hepatitis C, EMBO Mol. Med., 6, 4, 10.1002/emmm.201303131 Li, 2012, Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing, PLoS Pathog., 8, 31, 10.1371/journal.ppat.1002880 Li, 2016, Single-genome sequencing of hepatitis C virus in donor-recipient pairs distinguishes modes and models of virus transmission and early diversification, J. Virol., 90, 152, 10.1128/JVI.02156-15 Martell, 1992, Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution, J. Virol., 66, 3225, 10.1128/JVI.66.5.3225-3229.1992 Meuleman, 2005, Morphological and biochemical characterization of a human liver in a uPA-SCID mouse chimera, Hepatology, 41, 847, 10.1002/hep.20657 Meylan, 2005, Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus, Nature, 437, 1167, 10.1038/nature04193 Pawlotsky, 2006, Hepatitis C virus population dynamics during infection, Curr. Top. Microbiol. Immunol., 299, 261 Polenakovik, 2015, New therapies for hepatitis C virus, Pril. Makedon. Akad. na Nauk. i Umet. Oddelenie za Med. Nauk., 36, 119 Salazar-Gonzalez, 2008, Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing, J. Virol., 82, 3952, 10.1128/JVI.02660-07 Simmonds, 2004, Genetic diversity and evolution of hepatitis C virus–15 years on, J. Gen. Virol., 85, 3173, 10.1099/vir.0.80401-0 TANOTI: a rapid BLAST-guided read mapper for small, divergent genomes, (manuscript communicated) [http://www.bioinformatics.cvr.ac.uk/tanoti.php]. Tarr, 2015, Genetic diversity underlying the envelope glycoproteins of hepatitis C virus: structural and functional consequences and the implications for vaccine design, Viruses, 7, 3995, 10.3390/v7072809 Vercauteren, 2014, HCV animal models and liver disease, J. Hepatol., 61, S26, 10.1016/j.jhep.2014.07.013 Vercauteren, 2015, Targeting a host-cell entry factor barricades antiviral-resistant HCV variants from on-therapy breakthrough in human-liver mice, Gut Vercauteren, 2015, Animal models for the study of HCV, Curr. Opin. Virol., 13, 67, 10.1016/j.coviro.2015.04.009 Wang, 2010, Hepatitis C virus transmission bottlenecks analyzed by deep sequencing, J. Virol., 84, 6218, 10.1128/JVI.02271-09 Whitfield, 2016, Characterization of viral populations by using circular sequencing, J. Virol., 90, 8950, 10.1128/JVI.00804-14 Zeuzem, 2015, Grazoprevir-elbasvir combination therapy for treatment-naive cirrhotic and noncirrhotic patients with chronic hepatitis C virus genotype 1, 4, or 6 infection, A Randomized Trial. Ann. Intern. Med., 163, 1, 10.7326/M15-0785 Zhang, 2016, Chronic hepatitis C virus infection: a review of current direct-acting antiviral treatment strategies, N. Am. J. Med. Sci. Boston, 9, 47