High HCV subtype heterogeneity in a chronically infected general population revealed by high-resolution hepatitis C virus subtyping

Clinical Microbiology and Infection

Volumn 23, Issue 10, 2017, Pages 775.e1-775.e6

  Rodriguez Frias, F ^a,b,c   Nieto Aponte, L ^a,d   Gregori, J ^b,e,f   Garcia Cehic, D ^b,f   Casillas, R ^a,d   Tabernero, D ^a,b   Homs, M ^a   Blasi, M ^a   Vila, M ^a   Chen, Q ^b   Vargas, V ^b,c,f   Castells, Ll ^b,c,f   Viladomiu, Ll ^c,f   Genesca, J ^b,c,f   Minguez, B ^b,c,f   Augustin, S ^b,c,f   Riveiro Barciela, M ^b,c,f   Carbonell, J ^c,f   Perales, C ^b,f   Soria, M E ^b,f   Asensio, M ^a   Llorens, M ^b   Ordeig, L ^b   Godoy, C ^a   Buti, M ^b,c,f   Esteban, R ^b,c,f   Pumarola, T ^c,d   Esteban, J I ^b,c,f   Quer, J ^b,c,f   more..

^a HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

^b INSTITUTO DE SALUD CARLOS III   (Spain)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d Microbiology Unit   (Spain)

^e Roche Diagnostics SL Diabetes Care   (Spain)

^f HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

Author keywords

HCV; Hepatitis C virus; High resolution HCV subtyping; Mixed infections; Prevalence; Subtypes

Indexed keywords

ADULT; ARTICLE; BLOOD SAMPLING; CHILD; CHRONIC HEPATITIS C; CONTROLLED STUDY; GENOTYPE; HAPLOTYPE; HEALTH CARE POLICY; HEPATITIS C VIRUS; HIGH RESOLUTION HEPATITIS C VIRUS SUBTYPING; HUMAN; MAJOR CLINICAL STUDY; MIDDLE AGED; MIXED INFECTION; NEXT GENERATION SEQUENCING; POPULATION; PRESCHOOL CHILD; PREVALENCE; PRIORITY JOURNAL; SCHOOL CHILD; YOUNG ADULT; ADOLESCENT; AGED; CLASSIFICATION; FEMALE; GENETIC VARIATION; GENETICS; GENOTYPING TECHNIQUE; HEPACIVIRUS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MALE; MOLECULAR EPIDEMIOLOGY; PROCEDURES; SPAIN; VIROLOGY;

ADOLESCENT; ADULT; AGED; COINFECTION; FEMALE; GENETIC VARIATION; GENOTYPE; GENOTYPING TECHNIQUES; HEPACIVIRUS; HEPATITIS C, CHRONIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; PREVALENCE; SPAIN; YOUNG ADULT;

EID: 85018630915     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1016/j.cmi.2017.02.007     Document Type: Article

References (40)

1. Bartenschlager, R., Lohmann, V., Penin, F., The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection. Nat Rev Microbiol 11:7 (2013 Jul), 482–496.
2. Bacon, B.R., Gordon, S.C., Lawitz, E., Marcellin, P., Vierling, J.M., Zeuzem, S., et al. Boceprevir for previously treated chronic HCV genotype 1 infection. N Engl J Med 364:13 (2011 Mar 31), 1207–1217.
3. Poordad, F., McCone, J. Jr., Bacon, B.R., Bruno, S., Manns, M.P., Sulkowski, M.S., et al. Boceprevir for untreated chronic HCV genotype 1 infection. N Engl J Med 364:13 (2011 Mar 31), 1195–1206.
4. Zeuzem, S., Soriano, V., Asselah, T., Bronowicki, J.P., Lohse, A.W., Mullhaupt, B., et al. Faldaprevir and deleobuvir for HCV genotype 1 infection. N Engl J Med 369:7 (2013 Aug 15), 630–639.
5. McNaughton, A.L., Thomson, E.C., Templeton, K., Gunson, R.N., Leitch, E.C., Mixed genotype hepatitis C infections and implications for treatment. Hepatology, 59(3), 2014 Mar, 1209.
6. Doyle, J.S., Hellard, M.E., Thompson, A.J., The role of viral and host genetics in natural history and treatment of chronic HCV infection. Best Pract Res Clin Gastroenterol 26:4 (2012 Aug), 413–427.
7. Lam, A.M., Espiritu, C., Bansal, S., Micolochick Steuer, H.M., Niu, C., Zennou, V., et al. Genotype and subtype profiling of PSI-7977 as a nucleotide inhibitor of hepatitis C virus. Antimicrob Agents Chemother 56:6 (2012 Jun), 3359–3368.
8. Mauss, S., Berg, T., Rockstroh, J., Sarrazin, C., Wedemeyer, H., Short Guide to Hepatitis C. Mauss, S., Berg, T., Rockstroh, J., Sarrazin, C., Wedemeyer, H., (eds.) 2012 edition, 2012, The Flying Publisher Group. The Flying Publisher Guide http://www.FlyingPublisher.com.
9. Smith, D.B., Bukh, J., Kuiken, C., Muerhoff, A.S., Rice, C.M., Stapleton, J.T., et al. Expanded classification of hepatitis C Virus into 7 genotypes and 67 Subtypes: updated criteria and assignment web resource. Hepatology 59:1 (2014), 318–327.
10. Navarro D, Casas P, Nieto L, Viciana I, Martinez-Sapiña AM, Rodriguez MJ, et al. Distribution of hepatitis C virus genotypes in Spain during the period 2011–2015 (GEHEP 005 Study). OR-07. AIDS reviews I National Conference of the Group for the Study of Viral Hepatitis (GEHEP) of SEIMC [Vol. 17-Suppl 1. Sept 2015. http://www.aidsreviews.com.], 7–8.
11. Gower, E., Estes, C.C., Hindman, S., Razavi-Shearer, H., Global epidemiology and genotype distribution of the hepatitis C virus. J Hepatol 61:1 (2014), S45–S57.
12. Messina, J.P., Humphreys, I., Flaxman, A., Brown, A., Cooke, G.S., Pybus, O.G., et al. Global distribution and prevalence of hepatitis C virus genotypes. Hepatology 61:1 (2015 Jan), 77–87.
13. Benedet, M., Adachi, D., Wong, A., Wong, S., Pabbaraju, K., Tellier, R., et al. The need for a sequencing-based assay to supplement the Abbott m2000 RealTime HCV Genotype II assay: a 1 year analysis. J Clin Virol 60:3 (2014 Jul), 301–304.
14. Hara, K., Rivera, M.M., Koh, C., Sakiani, S., Hoofnagle, J.H., Heller, T., Important factors in reliable determination of hepatitis C virus genotype by use of the 5’ untranslated region. J Clin Microbiol 51:5 (2013 May), 1485–1489.
15. Mallory, M.A., Lucic, D.X., Sears, M.T., Cloherty, G.A., Hillyard, D.R., Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5′UTR, core and NS5B sequencing. J Clin Virol 60:1 (2014 May), 22–26.
16. Martro, E., Gonzalez, V., Buckton, A.J., Saludes, V., Fernandez, G., Matas, L., et al. Evaluation of a new assay in comparison with reverse hybridization and sequencing methods for hepatitis C virus genotyping targeting both 5′ noncoding and nonstructural 5b genomic regions. J Clin Microbiol 46:1 (2008 Jan), 192–197.
17. Quer, J., Gregori, J., Rodriguez-Frias, F., Buti, M., Madejon, A., Perez-Del-Pulgar, S., et al. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. J Clin Microbiol 53:1 (2015 Jan), 219–226.
18. Rodriguez-Frias, F., Tabernero, D., Quer, J., Esteban, J.I., Ortega, I., Domingo, E., et al. Ultra-deep pyrosequencing detects conserved genomic sites and quantifies linkage of drug-resistant amino acid changes in the hepatitis B virus genome. PLoS One, 7(5), 2012, e37874.
19. Homs, M., Buti, M., Tabernero, D., Quer, J., Sanchez, A., Corral, N., et al. Quasispecies dynamics in main core epitopes of hepatitis B virus by ultra-deep-pyrosequencing. World J Gastroenterol 18:42 (2012 Nov 14), 6096–6105.
20. Ramirez, C., Gregori, J., Buti, M., Tabernero, D., Camos, S., Casillas, R., et al. A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model. Antiviral Res 98:2 (2013 May), 273–283.
21. Homs, M., Caballero, A., Gregori, J., Tabernero, D., Quer, J., Nieto, L., et al. Clinical application of estimating hepatitis B virus quasispecies complexity by massive sequencing: correlation between natural evolution and on-treatment evolution. PLoS One, 9(11), 2014, e112306.
22. Gregori, J., Esteban, J.I., Cubero, M., Garcia-Cehic, D., Perales, C., Casillas, R., et al. Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS One, 8(12), 2013, e83361.
23. Gregori, J., Salicru, M., Domingo, E., Sanchez, A., Esteban, J.I., Rodriguez-Frias, F., et al. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics 30:8 (2014 Apr 15), 1104–1111.
24. AASLD, Hepatitis C guidance: AASLD-IDSA recommendations for testing, managing, and treating adults infected with hepatitis C virus. Hepatology 62:3 (2015 Sep), 932–954.
25. EASL, EASL Recommendations on Treatment of Hepatitis C 2016. J Hepatol 66:1 (2017 Jan), 153–194.
26. Sarrazin, C., The importance of resistance to direct antiviral drugs in HCV infection in clinical practice. J Hepatol 64 (2016), 486–504.
27. Abergel, A., Loustaud-Ratti, V., Metivier, S., Jiang, D., Kersey, K., Knox, S., et al. Ledipasvir/Sofosbuvir treatment results in high SVR rates in patients with chronic genotype 4 and 5 HCV infection. O056. J Hepatol, 62(Supplement 2), 2014, S219.
28. Hezode, C., Asselah, T., Reddy, K.R., Hassanein, T., Berenguer, M., Fleischer-Stepniewska, K., et al. Ombitasvir plus paritaprevir plus ritonavir with or without ribavirin in treatment-naive and treatment-experienced patients with genotype 4 chronic hepatitis C virus infection (PEARL-I): a randomised, open-label trial. Lancet 385:9986 (2015 Jun 20), 2502–2509.
29. Echevarria, J.M., Leon, P., Pozo, F., Avellon, A., Follow-up of the prevalence of hepatitis C virus genotypes in Spain during a nine-year period (1996–2004). Enferm Infecc Microbiol Clin 24:1 (2006 Jan), 20–25.
30. Saludes, V., Quer, J., Gregori, J., Bascunana, E., Garcia-Cehic, D., Esteban, J.I., et al. Identification of hepatitis C virus genotype 3 by a commercial assay challenged by natural polymorphisms detected in Spain from patients with diverse origins. J Clin Virol 78 (2016 May), 14–19.
31. Crespo, M., Esteban, J.I., Ribera, E., Falco, V., Sauleda, S., Buti, M., et al. Utility of week-4 viral response to tailor treatment duration in hepatitis C virus genotype 3/HIV co-infected patients. AIDS 21:4 (2007 Feb 19), 477–481.
32. Marco, A., Esteban, J.I., Sole, C., da Silva, A., Ortiz, J., Roget, M., et al. Hepatitis C virus reinfection among prisoners with sustained virological response after treatment for chronic hepatitis C. J Hepatol 59:1 (2013 Jul), 45–51.
33. Grint, D., Peters, L., Rockstroh, J.K., Rakmanova, A., Trofimova, T., Lacombe, K., et al. Liver-related death among HIV/hepatitis C virus-co-infected individuals: implications for the era of directly acting antivirals. AIDS 29:10 (2015 Jun 19), 1205–1215.
34. Martinez-Rebollar, M., Mallolas, J., Perez, I., Gonzalez-Cordon, A., Lonca, M., Torres, B., et al. [Acute outbreak of hepatitis C in human immunodeficiency virus-infected patients]. Enferm Infecc Microbiol Clin 33:1 (2015 Jan), 3–8.
35. Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Ho, S.Y., Shapiro, B., Pybus, O.G., et al. The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med, 6(12), 2009 Dec, e1000198.
36. Smith, B.D., Morgan, R.L., Beckett, G.A., Falck-Ytter, Y., Holtzman, D., Teo, C.G., et al. Recommendations for the identification of chronic hepatitis C virus infection among persons born during 1945–1965. MMWR Recomm Rep 61:RR-4 (2012 Aug 17), 1–32.
37. JSH, JSH Guidelines for the Management of Hepatitis C Virus Infection: A 2014 Update for Genotype 1. Hepatol Res 44:Suppl S1 (2014 Jan), 59–70.
38. Markov, P.V., Pepin, J., Frost, E., Deslandes, S., Labbe, A.C., Pybus, O.G., Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa. J Gen Virol 90:Pt 9 (2009 Sep), 2086–2096.
39. Esteban, J.I., Sauleda, S., Quer, J., The changing epidemiology of hepatitis C virus infection in Europe. J Hepatol 48:1 (2008 Jan), 148–162.
40. Boesecke, C., Grint, D., Soriano, V., Lundgren, J.D., d'Arminio, M.A., Mitsura, V.M., et al. Hepatitis C seroconversions in HIV infection across Europe: which regions and patient groups are affected?. Liver Int 35:11 (2015 Nov), 2384–2391.