Complete genomic sequences for hepatitis C virus subtypes 6e and 6g isolated from Chinese patients with injection drug use and HIV-1 co-infection

Journal of Medical Virology

Volumn 78, Issue 8, 2006, Pages 1061-1069

  Li, Chunhua ^a,b,c   Fu, Yongshui ^d   Lu, Ling ^a   Ji, Weizhi ^b   Yu, Jian ^e   Hagedorn, Curt H ^a   Zhang, Linqi ^e,f  

^a UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d Guangzhou Blood Center   (China)

^e ROCKEFELLER UNIVERSITY   (United States)

^f PEKING UNION MEDICAL COLLEGE   (China)

Author keywords

Genotype; HCV; Injection drug use; Sequence

Indexed keywords

POLYURIDYLIC ACID;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CASE REPORT; CHINESE; EPIDEMIC; GENE SEQUENCE; GENETIC VARIABILITY; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INJECTION; INTRAVENOUS DRUG ABUSE; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SUPERINFECTION; UNINDEXED SEQUENCE; VIET NAM; VIRUS GENOME; VIRUS ISOLATION; VIRUS TRANSMISSION;

CHINA; GENES, VIRAL; HEPACIVIRUS; HEPATITIS C; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SUBSTANCE ABUSE, INTRAVENOUS;

HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33745713019     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.20663     Document Type: Article

References (40)

1. Alberti A, Clumeck N, Collins S, Gerlich W, Lundgren J, Palu G, Reiss P, Thiebaut R, Weiland O, Yazdanpanah Y, Zeuzem S, ECC Jury. 2005. Short statement of the first European Consensus Conference on the treatment of chronic hepatitis B and C in HIV co-infected patients. J Hepatol 42:615-624.
2. Alter HJ, Seeff LB. 2000. Recovery, persistence, and sequelae in hepatitis C virus infection: A perspective on long-term outcome. Semin Liver Dis 20:17-35.
3. Anonymous. 1997. Hepatitis C: Global prevalence. Wkly Epidemiol Rec 72:341-344.
4. Apichartpiyakul C, Chittivudikarn C, Miyajima H, Homma M, Hotta H. 1994. Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai, Thailand. J Clin Microbiol 32:2276-2279.
5. Bernier L, Willems B, Delage G, Murphy DG. 1996. Identification of numerous hepatitis C virus genotypes in Montreal, Canada. J Clin Microbiol 34:2815-2818.
6. Bonacini M, Govindarajan S, Blatt LM, Schmid P, Conrad A, Lindsay KL. 1999. Patients co-infected with human immunodeficiency virus and hepatitis C virus demonstrate higher levels of hepatic HCV RNA. J Viral Hepat 6:203-208.
7. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244:359-362.
8. Doi H, Apichartpiyakul C, Ohba KI, Mizokami M, Hotta H. 1996. Hepatitis C virus (HCV) subtype prevalence in Chiang Mai, Thailand, and identification of novel subtypes of HCV major type 6. J Clin Microbiol 34:569-574.
9. Garten RJ, Zhang J, Lai S, Liu W, Chen J, Yu XF. 2005. Coinfection with HIV-1 and hepatitis C virus among injection drug users in southern China. Clin Infect Dis 41:S18-S24.
10. Graham CS, Baden LR, Yu E, Mrus JM, Carnie J, Heeren T, Koziel MJ. 2001. Influence of human immunodeficiency virus infection on the course of hepatitis C virus infection: A meta-analysis. Clin Infect Dis 33:562-569.
11. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
12. Inoue Y, Sulaiman HA, Matsubayashi K, Julitasari IK, Ansari A, Laras K, Corwin AL. 2000. Genotypic analysis of hepatitis C virus in blood donors in Indonesia. Am J Trop Med Hyg 62:92-98.
13. Kumar S, Tamura K, Nei M. 1994. MEGA: Molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci 10:189-191.
14. Lu L, Nakano T, He Y, Fu Y, Hagedorn CH, Robertson BH. 2005a. Hepatitis C virus genotype distribution in China: Predominance of closely related subtype 1b isolates and existence of new genotype 6 variants. J Med Virol 75:538-549.
15. Lu L, Nakano T, Smallwood GA, Heffron TG, Robertson BH, Hagedorn CH. 2005b. A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: Application to a novel hepatitis C virus variant of genotype 6. J Virol Methods 126:139-148.
16. Lu L, Nakano T, Li C, Fu Y, Miller S, Kuiken C, Robertson BH, Hagedorn CH. 2006. Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6. J Gen Virol 87:629-634.
17. Major ME, Feinstone SM. 1997. The molecular virology of hepatitis C. Hepatology 25:1527-1538.
18. Mellor J, Holmes EC, Jarvis LM, Yap PL, Simmonds P. 1995. Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: Implications for virus classification. The International HCV Collaborative Study Group. J Gen Virol 76:2493-2507.
19. Mellor J, Walsh EA, Prescott LE, Jarvis LM, Davidson F, Yap PL, Simmonds P. 1996. Survey of type 6 group variants of hepatitis C virus in Southeast Asia by using a core-based genotyping assay. J Clin Microbiol 34:417-423.
20. Murphy D, Willems B, Deschenes M, Hilzenrat N, Mousseau R. 2003. Use of nucleotide sequence analysis of the NS5B region for routine genotyping of hepatitis C virus: Identification of numerous variants not classifiable among the known HCV genotypes. Hepatology 38:423A.
21. Piyasirisilp S, McCutchan FE, Carr JK, Sanders-Buell E, Liu W, Chen J, Wagner R, Wolf H, Shao Y, Lai S, Beyrer C, Yu XF. 2000. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. J Virol 74:11286-11295.
22. Ragni MV, Belle SH. 2001. Impact of human immunodeficiency virus infection on progression to end-stage liver disease in individuals with hemophilia and hepatitis C virus infection. J Infect Dis 183:1112-1115.
23. Robertson B, Myers G, Howard C, Brettin T, Bukh J, Gaschen B, Gojobori T, Maertens G, Mizokami M, Nainan O, Netesov S, Nishioka K, Shin T, Simmonds P, Smith D, Stuyver L, Weiner A. 1998. Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: Proposals for standardization. International committee on virus taxonomy. Arch Virol 143:2493-2503.
24. Shinji T, Kyaw YY, Gokan K, Tanaka Y, Ochi K, Kusano N, Mizushima T, Fujioka S, Shiraha H, Lwin AA, Shiratori Y, Mizokami M, Khin M, Miyahara M, Okada S, Koide N. 2004. Analysis of HCV genotypes from blood donors shows three new HCV type 6 subgroups exist in Myanmar. Acta Med Okayama 58:135-142.
25. Simmonds P. 2004. Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 85:3173-3188.
26. Simmonds P, Alberti A, Alter HJ, Bonino F, Bradley DW, Brechot C, Brouwer JT, Chan SW, Chayama K, Chen DS. 1994. A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 19:1321-1324.
27. Simmonds P, Mellor J, Sakuldamrongpanich T, Nuchaprayoon C, Tanprasert S, Holmes EC, Smith DB. 1996. Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: Comparison with classifications based upon sequence similarity. J Gen Virol 77:3013-3014.
28. Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, Feinstone S, Halfon P, Inchauspe G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shinji T, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A. 2005. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42:962-973.
29. Soto B, Sanchez-Quijano A, Rodrigo L, del Olmo JA, Garcia-Bengoechea M, Hernandez-Quero J, Rey C, Abad MA, Rodriguez M, Sales Gilabevt M, Gonzalez F, Miron P, Caruz A, Relimpio F, Torronteras R, Leal M, Lissen E. 1997. Human immunodeficiency virus infection modifies the natural history of chronic parenterally-acquired hepatitis C with an unusually rapid progression to cirrhosis. J Hepatol 26:1-5.
30. Stuyver L, Wyseur A, van Arnhem W, Lunel F, Laurent-Puig P, Pawlotsky JM, Kleter B, Bassit L, Nkengasong J, van Doorn LJ, Maertens G. 1995. Hepatitis C virus genotyping by means of 5′-UR/core line probe assays and molecular analysis of untypeable samples. Virus Res 38:137-157.
31. Thaikruea L, Thongsawat S, Maneekarn N, Netski D, Thomas DL, Nelson KE. 2004. Risk factors for hepatitis C virus infection among blood donors in northern Thailand. Transfusion 44:1433-1440.
32. Theamboonlers A, Chinchai T, Bedi K, Jantarasamee P, Sripontong M, Poovorawan Y. 2002. Molecular characterization of Hepatitis C virus (HCV) core region in HCV-infected Thai blood donors. Acta Virol 46:169-173.
33. Theodore D, Fried MW. 2000. Natural history and disease manifestations of hepatitis C infection. Curr Top Microbiol Immunol 242:43-54.
34. Thomas DL, Astemborski J, Rai RM, Anania FA, Schaeffer M, Galai N, Nolt K, Nelson KE, Strathdee SA, Johnson L, Laeyendecker O, Boitnott J, Wilson LE, Vlahov D. 2000. The natural history of hepatitis C virus infection: Host, viral, and environmental factors. JAMA 284:450-456.
35. Thorpe LE, Ouellet LJ, Hershow R, Bailey SL, Williams IT, Williamson J, Monterroso ER, Garfein RS. 2002. Risk of hepatitis C virus infection among young adult injection drug users who share injection equipment. Am J Epidemiol 155:645-653.
36. Tokita H, Okamoto H, Tsuda F, Song P, Nakata S, Chosa T, Iizuka H, Mishiro S, Miyakawa Y, Mayumi M. 1994. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc Natl Acad Sci USA 91:11022-11026.
37. Tokita H, Okamoto H, Iizuka H, Kishimoto J, Tsuda F, Miyakawa Y, Mayumi M. 1998. The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7-9 and comparison with those in the other eight genetic groups. J Gen Virol 79:1847-1857.
38. Verucchi G, Calza L, Manfredi R, Chiodo F. 2004. Human immunodeficiency virus and hepatitis C virus coinfection: Epidemiology, natural history, therapeutic options and clinical management. Infection 32:33-46.
39. Zhang C, Yang R, Xia X, Qin S, Dai J, Zhang Z, Peng Z, Wei T, Liu H, Pu D, Luo J, Takebe Y, Ben K. 2002. High prevalence of HIV-1 and hepatitis C virus coinfection among injection drug users in the southeastern region of Yunnan, China. J Acquir Immune Defic Syndr 29:191-196.
40. Zhang L, Chen Z, Cao Y, Yu J, Li G, Yu W, Yin N, Mei S, Li L, Balfe P, He T, Ba L, Zhang F, Lin HH, Yuen MF, Lai CL, Ho DD. 2004. Molecular characterization of human immunodeficiency virus type 1 and hepatitis C virus in paid blood donors and injection drug users in china. J Virol 78:13591-13599.