Cuypers L, Ceccherini Silberstein F, Van Laethem K, et al. Impact of HCV genotype on treatment regimens and drug resistance: a snapshot in time. Rev Med Virol. 2016. doi:10.1002/rmv.1895.
PubMed
Google Scholar
Schneider MD, Sarrazin C. Antiviral therapy of hepatitis C in 2014: do we need resistance testing? Antiviral Res. 2014;105:64–71. doi:10.1016/j.antiviral.2014.02.011.
Article
CAS
PubMed
Google Scholar
EASL recommendations on treatment of hepatitis C, 2015. http://www.easl.eu/medias/cpg/HEPC-2015/Full-report.pdf
Cuypers L, Li G, Libin P, et al. Genetic diversity and selective pressure in hepatitis C virus genotypes 1–6: significance for direct-acting antiviral treatment and drug resistance. Viruses. 2015;7:5018–39. doi:10.3390/v7092857.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawitz E, Matusow G, DeJesus E, et al. Simeprevir plus sofosbuvir in patients with chronic hepatitis C virus genotype 1 infection and cirrhosis: a phase 3 study (OPTIMIST-2). Hepatology. 2016;64:360–9. doi:10.1002/hep.28422.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sarrazin C, Lathouwers E, Peeters M, et al. Prevalence of the hepatitis C virus NS3 polymorphism Q80K in genotype 1 patients in the European region. Antiviral Res. 2015;116:10–6. doi:10.1016/j.antiviral.2015.01.003.
Article
CAS
PubMed
Google Scholar
Cuypers L, Li G, Neumann-Haefelin C, et al. Mapping the genomic diversity of HCV subtypes 1a and 1b: implications of structural and immunological constraints for vaccine and drug development. Virus Evolution. 2016;2. doi:10.1093/ve/vew024.
Magiorkinis G, Magiorkinis E, Paraskevis D, et al. The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med. 2009;6:e1000198. doi:10.1371/journal.pmed.1000198.
Article
PubMed
PubMed Central
Google Scholar
Nakano T, Lu L, Liu P, Pybus OG. Viral gene sequences reveal the variable history of hepatitis C virus infection among countries. J Infect Dis. 2004;190:1098–108. doi:10.1086/422606.
Article
CAS
PubMed
Google Scholar
Pybus OG, Charleston MA, Gupta S, et al. The epidemic behavior of the hepatitis C virus. Science. 2001;292:2323–5. doi:10.1126/science.1058321.
Article
CAS
PubMed
Google Scholar
Tanaka Y, Hanada K, Mizokami M, et al. A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United Status will increase over the next two decades. Proc Natl Acad Sci U S A. 2002;99:15584–9. doi:10.1073/pnas.242608099.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bagaglio S, Uberti-Foppa C, Messina E, et al. Distribution of natural resistance to NS3 protease inhibitors in hepatitis C genotype 1a separated into clades 1 and 2 and in genotype 1b of HIV-infected patients. Clin Microbiol Infect. 2016;22:386. doi:10.1016/j.cmi.2015.12.007.
Article
PubMed
Google Scholar
Beloukas A, King S, Childs K, et al. Detection of the NS3 Q80K polymorphism by Sanger and deep sequencing in hepatitis C virus genotype 1a strains in the UK. Clin Microbiol Infect. 2015;21:1033–9. doi:10.1016/j.cmi.2015.07.017.
Article
CAS
PubMed
Google Scholar
De Luca A, Di Giambenedetto S, Lo Presti A, et al. Two distinct hepatitis C virus genotype 1a clades have different geographica distribution and association with natural resistance to NS3 protease inhibitors. Open Forum Infect Dis. 2015;2:ofv043. doi:10.1093/ofid/ofv043.
Article
PubMed
PubMed Central
Google Scholar
Pickett BE, Striker R, Lefkowitz EJ. Evidence for separation of HCV subtype 1a into two distinct clades. J Viral Hepat. 2011;9:608–18. doi:10.1111/j.1365-2893.2010.01342.x.
Article
Google Scholar
Santos AF, Bello G, Vidal LL, et al. In-depth phylogenetic analysis of hepatitis C virus subtype 1a and occurrence of 80 K and associated polymorphisms in the NS3 protease. Sci Rep. 2016;6:31780. doi:10.1038/sreo31780.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCloskey RM, Liang RH, Joy JB, et al. Global origin and transmission of hepatitis C virus nonstructural protein 3 Q80K polymorphism. J Infect Dis. 2015;211:1288–95. doi:10.1093/infdis/jiu613.
PubMed
Google Scholar
Aghemo AM, Cologni G, Maggiolo F, et al. Safety and efficacy of directly acting antivirals in 2432 HCV patients with advanced fibrosis: an interim analysis of the Lombardia regional network for viral hepatitis. Barcelona, Spain: 51st EASL; 2016. Abstract LBP500.
Google Scholar
Mauss S, Buggisch P, Böker KHW, et al. Treatment outcomes for hepatitis C genotype 1 infection with direct acting antivirals: data from the German hepatitis C-registry. Barcelona, Spain: 51st EASL; 2016. Abstract SAT-263.
Google Scholar
EASL recommendations on treatment of hepatitis C, 2016. http://www.easl.eu/medias/cpg/HCV2016/English-report.pdf.
Craxì A, Perno CF, Viganò M, et al. From current status to optimization of HCV treatment: Recommendations from an expert panel. Dig Liver Dis. 2016;48:995–1005. doi:10.1016/j.did.2016.06.004.
Article
PubMed
Google Scholar
González-Candelas F, López-Labrador FX, Bracho MA. Recombination in hepatitis C virus. Viruses. 2011;3:2006–24. doi:10.3390/v3102006.
Article
PubMed
PubMed Central
Google Scholar
Cento V, Mirabelli C, Salpini R, et al. HCV genotypes are differently prone to the development of resistance to linear and macrocyclic protease inhibitors. PLoS One. 2012;7:e39652. doi:10.1371/journal.pone.0039652.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Oliveira T, Deforche K, Cassol S, et al. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics. 2005;21:3797–800. doi:10.1093/bioinformatics/bti607.
Article
PubMed
Google Scholar
Struck D, Lawyer G, Ternes AM, et al. COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res. 2014;42:e144. doi:10.1093/nar/gku739.
Article
PubMed
PubMed Central
Google Scholar
Vrancken B, Rambaut A, Suchard MA, et al. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol. 2014;10:e1003505. doi:10.1371/journal.pcbi.1003505.
Article
PubMed
PubMed Central
Google Scholar
Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. Methods Ecol Evol. 2015;6:83–91. doi:10.1111/2041-210X.12299.
Article
PubMed
Google Scholar
Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969–73. doi:10.1093/molbev/mss075.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenies. Bioinformatics. 2009;25:1370–6. doi:10.1093/bioinformatics/btp244.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rambaut A, Lam TT, Carvalho M, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evolution. 2016;2. doi:10.1093/ve/vew007.
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4:e88. doi:10.1371/journal.pbio.0040088.
Article
PubMed
PubMed Central
Google Scholar
Gray RR, Parker J, Lemey P, et al. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol Biol. 2011;11:131. doi:10.1186/1471-2148-11-131.
Article
PubMed
PubMed Central
Google Scholar
Edwards CJ, Suchard MA, Lemey P, et al. Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol. 2011;21:1251–8. doi:10.1016/j.cub.2011.05.058.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009;5:e1000520. doi:10.1371/journal.pcbi.1000520.
Article
PubMed
PubMed Central
Google Scholar
Kass RE, Raftery AE. Bayes factors. J Am Stat Assoc. 1995;90:773–95. doi:10.1080/01621459.1995.10476572.
Article
Google Scholar
Bielejec F, Baele G, Vrancken B, et al. SpreaD3 : interactive visualization of spatiotemporal history and trait evolutionary processes. Mol Biol Evol. 2016. doi: 10.1093/molbev/msw082.
Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol. 2008;56:391–412. doi:10.1007/s00285-007-0120-8.
Article
PubMed
Google Scholar
Gower E, Estes C, Blach S, et al. Global epidemiology and genotype distribution of the hepatitis C virus infection. J Hepatol. 2014;61:S45–57. doi:10.1016/j.jhep.2014.07.027.
Article
PubMed
Google Scholar
Yoder AD, Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol. 2000;17:1081–90.
Article
CAS
PubMed
Google Scholar
Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all. BMC Biol. 2010;8:114. doi:10.1186/1741-7007-8-114.
Article
PubMed
PubMed Central
Google Scholar
Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Biol. 1978;27:401–10. doi:10.1093/sysbio/27.4.401.
Article
Google Scholar
Worobey M, Han GZ, Rambaut A. A synchronized global sweep of the internal genes of modern avian influenza virus. Nature. 2014;508:254–7. doi:10.1038/nature13016.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cochrane A, Searle B, Hardie A, et al. A genetic analysis of hepatitis C virus transmission between injection drug users. J Infect Dis. 2002;186:1212–21. doi:10.1086/344314.
Article
CAS
PubMed
Google Scholar
Silini E, Bono F, Cividini A, et al. Molecular epidemiology of hepatitis C virus infection among intravenous drug users. J Hepatol. 1995;22:691–5. doi:10.1016/0168-8278(95)80225-8.
Article
CAS
PubMed
Google Scholar
Wepman D. Immigration: from the founding of Virginia to the closing of Ellis Island. New York: Facts on File Book; 2002. p. 430.
Monticelli GL. Italian emigration: basic characteristic and trends with special reference to the last twenty years. International Migration Review. 1967;1:10–24. doi:10.2307/3002737.
Article
Google Scholar
Cometti E. Trends in Italian Emigration. The Western Political Quarterly. 1958;11:820–34. doi:10.2307/443655.
Article
Google Scholar
Brockmann D, Hufnagel L, Geisel T. The scaling laws of human travel. Nature. 2005;439:462–5. doi:10.1038/nature04292.
Article
Google Scholar
Pybus OG, Tatem AJ, Lemey P. Virus evolution and transmission in an ever more connected world. Proc Biol Sci. 2015;282:20142878. doi:10.1098/rspb.2014.2878.
Article
PubMed
PubMed Central
Google Scholar
Jacka B, Applegate T, Poon AF, et al. Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver. Canada J Hepatol. 2016;64:1247–55. doi:10.1016/j.jhep.2016.02.031.
Article
PubMed
Google Scholar
Paolucci S, Fiorina A, Piralla R, et al. Naturally occurring mutations to HCV protease inhibitors in treatment-naive patients. Virol J. 2012;9:245.
Article
CAS
PubMed
PubMed Central
Google Scholar