Evaluation of intra-host variants of the entire hepatitis B virus genome

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Ramachandran, Sumathi ^a   Zhai, Xiangjun ^b   Thai, Hong ^a   Campo, Davis S ^a   Xia, Guoliang ^a   Ganova Raeva, Lilia M ^a   Drobeniuc, Jan ^a   Khudyakov, Yury E ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b Jiangsu Centers for Disease Control   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LAMIVUDINE; VIRUS DNA;

ARTICLE; BLOOD SAMPLING; CLINICAL ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; END POINT LIMITING DILUTION REAL TIME POLYMERASE CHAIN REACTION; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HEPATITIS B; HEPATITIS B VIRUS; HUMAN; NONHUMAN; NUCLEIC ACID ANALYSIS; PHYLOGENETIC TREE; PHYLOGENY; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS LOAD; CLASSIFICATION; DISEASE TRANSMISSION; DNA SEQUENCE; EVALUATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; VIROLOGY;

HEPATITIS B VIRUS;

BASE SEQUENCE; DNA, VIRAL; GENOME, VIRAL; GENOTYPE; HEPATITIS B; HEPATITIS B VIRUS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 80052939676     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025232     Document Type: Article

References (44)

1. Mizokami M, Orito E, Ohba K, Ikeo K, Lau JY, et al. (1997) Constrained evolution with respect to gene overlap of hepatitis B virus. J Mol Evol 44 (Suppl 1): S83-90.
2. Zhou Y, Holmes EC, (2007) Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J Mol Evol 65: 197-205.
3. Cassino L, Laufer N, Salomon H, Campos R, Quarleri J, (2009) Hepatitis B precore/core promoter mutations in isolates from HBV-monoinfected and HBV-HIV coinfected patients: a 3-yr prospective study. J Clin Virol 46: 354-359.
4. Wang F, Wang H, Shen H, Meng C, Weng X, et al. (2009) Evolution of hepatitis B virus polymerase mutations in a patient with HBeAg-positive chronic hepatitis B virus treated with sequential monotherapy and add-on nucleoside/nucleotide analogues. Clin Ther 31: 360-366.
5. Khudyakov Y, (2010) Coevolution and HBV drug resistance. Antivir Ther 15: 505-515.
6. Sheldon J, Rodes B, Zoulim F, Bartholomeusz A, Soriano V, (2006) Mutations affecting the replication capacity of the hepatitis B virus. J Viral Hepat 13: 427-434.
7. Pawlotsky JM, (2005) The concept of hepatitis B virus mutant escape. J Clin Virol 34 (Suppl 1): S125-129.
8. Angus P, Vaughan R, Xiong S, Yang H, Delaney W, et al. (2003) Resistance to adefovir dipivoxil therapy associated with the selection of a novel mutation in the HBV polymerase. Gastroenterology 125: 292-297.
9. Osiowy C, Giles E, (2003) Evaluation of the INNO-LiPA HBV genotyping assay for determination of hepatitis B virus genotype. J Clin Microbiol 41: 5473-5477.
10. Zoulim F, (2006) New nucleic acid diagnostic tests in viral hepatitis. Semin Liver Dis 26: 309-317.
11. Bai YJ, Zhao JR, Lv GT, Zhang WH, Wang Y, et al. (2003) Rapid and high throughput detection of HBV YMDD mutants with fluorescence polarization. World J Gastroenterol 9: 2344-2347.
12. Hussain M, Chu CJ, Sablon E, Lok AS, (2003) Rapid and sensitive assays for determination of hepatitis B virus (HBV) genotypes and detection of HBV precore and core promoter variants. J Clin Microbiol 41: 3699-3705.
13. Chen CH, Lee CM, Tung WC, Wang JH, Hung CH, et al. Evolution of full-length HBV sequences in chronic hepatitis B patients with sequential lamivudine and adefovir dipivoxil resistance. J Hepatol 52: 478-485.
14. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
15. Harismendy O, Frazer K, (2009) Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques 46: 229-231.
16. Lao KQ, Tang F, Barbacioru C, Wang Y, Nordman E, et al. (2009) mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system. J Biomol Tech 20: 266-271.
17. Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, et al. (2007) DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 35: e91.
18. Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW, (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17: 1195-1201.
19. Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, et al. (2009) Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 199: 1275-1285.
20. Solmone M, Vincenti D, Prosperi MC, Bruselles A, Ippolito G, et al. (2009) Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen. J Virol 83: 1718-1726.
21. Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S, (2007) Whole-genome sequencing and assembly with high-throughput, short-read technologies. Plos ONE 2: e484.
22. Ramachandran S, Guoliang X, Ganova-Raeva L, Williams I, Khudyakov Y, et al. (2008) End point limiting dilution real time PCR assay for evaluation of HCV quasispecies in serum. J Virol Meth 151: 217-224.
23. Forbi JC, Vaughan G, Purdy MA, Campo DS, Xia GL, et al. (2010) Epidemic history and evolutionary dynamics of hepatitis B virus infection in two remote communities in rural Nigeria. Plos ONE 5: e11615.
24. Nainan OV, Khristova ML, Byun K, Xia G, Taylor PE, et al. (2002) Genetic variation of hepatitis B surface antigen coding region among infants with chronic hepatitis B virus infection. J Med Virol 68: 319-327.
25. Ganova-Raeva L, Ramachandran S, Honisch C, Forbi JC, Zhai X, et al. (2010) Robust hepatitis B virus genotyping by mass spectrometry. J Clin Microbiol 48: 4161-4168.
26. Kraytsberg Y, Khrapko K, (2005) Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations. Expert Rev Mol Diagn 5: 809-815.
27. Blaak H, (2005) Isolation of human immunodeficiency virus type 2 biological clones from peripheral blood lymphocytes. Methods Mol Biol 304: 95-112.
28. Pallier C, Castera L, Soulier A, Hezode C, Nordmann P, et al. (2006) Dynamics of hepatitis B virus resistance to lamivudine. J Virol 80: 643-653.
29. Jourdain G, Ngo-Giang-Huong N, Le Coeur S, Bowonwatanuwong C, Kantipong P, et al. (2004) Intrapartum exposure to nevirapine and subsequent maternal responses to nevirapine-based antiretroviral therapy. N Engl J Med 351: 229-240.
30. Palmer S, Kearney M, Maldarelli F, Halvas EK, Bixby CJ, et al. (2005) Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol 43: 406-413.
31. Lampertico P, Vigano M, Manenti E, Iavarone M, Lunghi G, et al. (2005) Adefovir rapidly suppresses hepatitis B in HBeAg-negative patients developing genotypic resistance to lamivudine. Hepatology 42: 1414-1419.
32. Campo D, Dimitrova Z, Mitchell R, Lara J, Khudyakov Y, (2008) Coordinated evolution of the hepatitis C virus. Proc Natl Acad Sci USA 105: 9685-9690.
33. Aurora R, Donlin MJ, Cannon NA, Tavis JE, (2009) Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans. J Clin Invest 119: 225-236.
34. Bollyky PL, Rambaut A, Harvey PH, Holmes EC, (1996) Recombination between sequences of hepatitis B virus from different genotypes. J Mol Evol 42: 97-102.
35. Morozov V, Pisareva M, Groudinin M, (2000) Homologous recombination between different genotypes of hepatitis B virus. Gene 260: 55-65.
36. Garmiri P, Loua A, Haba N, Candotti D, Allain JP, (2009) Deletions and recombinations in the core region of hepatitis B virus genotype E strains from asymptomatic blood donors in Guinea, west Africa. J Gen Virol 90: 2442-2451.
37. Swenson PD, Riess JT, Krueger LE, (1991) Determination of HBsAg subtypes in different high risk populations using monoclonal antibodies. J Virol Methods 33: 27-38.
38. Nei M, (1987) Molecular evolutionary genetics. New York Columbia University Press.
39. Schneider S, Roessli D, Excoffier L, (2000) ARLEQUIN version 2000: Software for population genetic data analysis.
40. Posada D, Crandall K, (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
41. Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
42. Kosakovsky S, Frost S, Muse S, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
43. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
44. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, et al. (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73: 152-160.