Universal primers for HBV genome DNA amplification across subtypes: A case study for designing more effective viral primers

Virology Journal

Volumn 4, Issue , 2007, Pages

  Zhang, Qingrun ^a   Wu, Guanghua ^a   Richards, Elliott ^b   Jia, Shan'gang ^a   Zeng, Changqing ^a  

^a Chinese Academy of Sciences   (China)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; VIRUS DNA;

ARTICLE; CASE STUDY; GENE AMPLIFICATION; HEPATITIS B VIRUS; NONHUMAN; POLYMERASE CHAIN REACTION; VIRUS GENOME; COMPUTER PROGRAM; GENETICS; METHODOLOGY; RETRACTED ARTICLE;

HEPATITIS B VIRUS;

DNA PRIMERS; GENOME, VIRAL; HEPATITIS B VIRUS; POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 36649015602     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-4-92     Document Type: Article

References (22)

1. Complete genomes, phylogenetic relatedness, and structural proteins of six strains of the hepatitis B virus, four of which represent two new genotypes. H Norder AM Courouce LO Magnius, Virology 1994 198 489 503 10.1006/viro.1994. 1060 8291231
2. Typing hepatitis B virus by homology in nucleotide sequence: comparison of surface antigen subtypes. H Okamoto F Tsuda H Sakugawa RI Sastrosoewignjo M Imai Y Miyakawa M Mayumi, J Gen Virol 1988 69 Pt 10 2575 2583 3171552
3. Genotypic dominance and novel recombinations in HBV genotype B and C co-infected intravenous drug users. BF Chen JH Kao CJ Liu DS Chen PJ Chen, J Med Virol 2004 73 13 22 10.1002/jmv.20051 15042642
4. Evolution of Hepatitis B virus in an acute hepatitis B patient co-infected with genotypes B and C. BF Chen CJ Liu GM Jow PJ Chen JH Kao DS Chen, J Gen Virol 2006 87 39 49 10.1099/vir.0.81357-0 16361416
5. A new intertype recombinant between genotypes C and D of hepatitis B virus identified in China. Z Wang Z Liu G Zeng S Wen Y Qi S Ma NV Naoumov J Hou, J Gen Virol 2005 86 985 990 10.1099/vir.0.80771-0 15784891
6. Genomic heterogeneity of hepatitis B virus in a 54-year-old woman who contracted the infection through materno-fetal transmission. H Okamoto M Imai M Kametani T Nakamura M Mayumi, Jpn J Exp Med 1987 57 231 236 3430800
7. Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. E Orito M Mizokami Y Ina EN Moriyama N Kameshima M Yamamoto T Gojobori, Proc Natl Acad Sci USA 1989 86 7059 7062 2780562 10.1073/pnas.86.18.7059
8. Hepatitis B virus: significance of naturally occurring mutants. HE Blum, Intervirology 1993 35 40 50 8407249
9. Genetic heterogeneity of hepatitis viruses and its clinical significance. A Alexopoulou SP Dourakis, Curr Drug Targets Inflamm Allergy 2005 4 47 55 10.2174/1568010053622867 15720236
10. Hepatitis B virus genomic heterogeneity: variation between quasispecies may confound molecular epidemiological analyses of transmission incidents. SL Ngui CG Teo, J Viral Hepat 1997 4 309 315 10.1046/j.1365-2893.1997.00066.x 9310929
11. Rare quasispecies in the YMDD motif of hepatitis B virus detected by polymerase chain reaction with peptide nucleic acid clamping. W Ohishi K Chayama, Intervirology 2003 46 355 361 10.1159/000074992 14688452
12. Evolution of multi-drug resistant hepatitis B virus during sequential therapy. HJ Yim M Hussain Y Liu SN Wong SK Fung AS Lok, Hepatology 2006 44 703 712 10.1002/hep.21290 16941700
13. A novel method for efficient amplification of whole hepatitis B virus genomes permits rapid functional analysis and reveals deletion mutants in immunosuppressed patients. S Gunther BC Li S Miska DH Kruger H Meisel H Will, J Virol 1995 69 5437 5444 7636989
14. Amplification of full-length hepatitis B virus genomes from samples from patients with low levels of viremia: frequency and functional consequences of PCR-introduced mutations. S Gunther G Sommer F Von Breunig A Iwanska T Kalinina M Sterneck H Will, J Clin Microbiol 1998 36 531 538 9466771
15. Long PCR and its application to hepatitis viruses: amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes. R Tellier J Bukh SU Emerson RH Miller RH Purcell, J Clin Microbiol 1996 34 3085 3091 8940452
16. Amplification of the full-length hepatitis A virus genome by long reverse transcription-PCR and transcription of infectious RNA directly from the amplicon. R Tellier J Bukh SU Emerson RH Purcell, Proc Natl Acad Sci USA 1996 93 4370 4373 8633073 10.1073/pnas.93.9.4370
17. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 403 410 2231712
18. http://primer3.sourceforge.net/
19. http://www.perl.org/
20. http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
21. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 25 4876 4882 9396791 10.1093/nar/25.24.4876
22. Primer3 on the WWW for general users and for biologist programmers. S Rozen H Skaletsky, Methods Mol Biol 2000 132 365 386 10547847