Molecular epidemiology and genetic diversity of hepatitis B virus genotype E in an isolated Afro-Colombian community

Journal of General Virology

Volumn 91, Issue 2, 2010, Pages 501-508

  Alvarado Mora, Mónica Viviana ^a   Romano, Camila Malta ^a   Gomes Gouvêa, Michele Soares ^a   Gutierrez, Maria Fernanda ^b   Carrilho, Flair José ^a   Pinho, João Renato Rebello ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b PONTIFICIA UNIVERSIDAD JAVERIANA   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; AFRICA; AMINO ACID SUBSTITUTION; ARTICLE; CLINICAL ARTICLE; COLOMBIA; CONTROLLED STUDY; FEMALE; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HEPATITIS B; HEPATITIS B VIRUS; HUMAN; MALE; MOLECULAR EPIDEMIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; UNINDEXED SEQUENCE; VIRAL GENETICS; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; VIROLOGY;

HEPATITIS B VIRUS;

HEPATITIS B SURFACE ANTIGEN;

ADOLESCENT; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; COLOMBIA; EVOLUTION, MOLECULAR; FEMALE; GENETIC VARIATION; GENOTYPE; HEPATITIS B; HEPATITIS B SURFACE ANTIGENS; HEPATITIS B VIRUS; HUMANS; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; YOUNG ADULT;

EID: 76249120532     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.015958-0     Document Type: Article

References (53)

1. Andernach, I. E., Hübschen, J. M. & Muller, C. P. (2009). Hepatitis B virus: the genotype E puzzle. Rev Med Virol 19, 231-240.
2. Arauz-Ruiz, P., Norder, H., Robertson, B. H. & Magnius, L. O. (2002). Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central America. J Gen Virol 83, 2059-2073.
3. Bekondi, C., Olinger, C. M., Boua, N., Talarmin, A., Muller, C. P., Le Faou, A. & Venard, V. (2007). Central African Republic is part of the West-African hepatitis B virus genotype E crescent. J Clin Virol 40, 31-37.
4. Bowyer, S. M., van Staden, L., Kew, M. C. & Sim, J. G. (1997). A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa. J Gen Virol 78, 1719-1729.
5. Candotti, D., Opare-Sem, O., Rezvan, H., Sarkodie, F. & Allain, J. P. (2006). Molecular and serological characterization of hepatitis B virus in deferred Ghanaian blood donors with and without elevated alanine aminotransferase. J Viral Hepat 13, 715-724.
6. Chomczynski, P. & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.
7. Cuéllar-Ambrosi, F., Mondragón, M. C., Figueroa, M., Préhu, C., Galactéros, F. & Ruiz-Linares, A. (2000). Sickle cell anemia and beta-globin gene cluster haplotypes in Colombia. Hemoglobin 24, 221-225.
8. Cunha, L., Plouzeau, C., Ingrand, P., Gudo, J. P., Ingrand, I., Mondlane, J., Beauchant, M. & Agius, G. (2007). Use of replacement blood donors to study the epidemiology of major blood-borne viruses in the general population of Maputo, Mozambique. J Med Virol 79, 1832-1840.
9. Drummond, A. J. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214.
10. Dumpis, U., Mendy, M., Hill, A., Thursz, M., Hall, A., Whittle, H. & Karayiannis, P. (2001). Prevalence of HBV core promoter /precore/core mutations in Gambian chronic carriers. J Med Virol 65, 664-670.
11. Ewing, B. & Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8, 186-194.
12. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8, 175-185.
13. Gomes-Gouvêa, M. S., Soares, M. C., Bensabath, G., de Carvalho-Mello, I. M., Brito, E. M., Souza, O. S., Queiroz, A. T., Carrilho, F. J. & Pinho, J. R. (2009). Hepatitis B virus and hepatitis delta virus genotypes in outbreaks of fulminant hepatitis (Labrea black fever) in the western Brazilian Amazon region. J Gen Virol 90, 2638-2643.
14. Halfon, P., Bourlière, M., Pol, S., Benhamou, Y., Ouzan, D., Rotily, M., Khiri, H., Renou, C., Pénaranda, G. & other authors (2006). Multicentre study of hepatitis B virus genotypes in France: correlation with liver fibrosis and hepatitis B e antigen status. J Viral Hepat 13, 329-335.
15. Hannoun, C., Söderström, A., Norkrans, G. & Lindh, M. (2005). Phylogeny of African complete genomes reveals a West African genotype A subtype of hepatitis B virus and relatedness between Somali and Asian A1 sequences. J Gen Virol 86, 2163-2167.
16. Hübschen, J. M., Andernach, I. E. & Muller, C. P. (2008). Hepatitis B virus genotype E variability in Africa. J Clin Virol 43, 376-380.
17. Huelsenbeck, J. P., Ronquist, F., Nielsen, R. & Bollback, J. P. (2001). Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314.
18. Kato, H.,Gish, R. G.,Bzowej, N., Newsom, M., Sugauchi, F., Tanaka, Y., Kato, T., Orito, E., Usuda, S. & other authors (2004). Eight genotypes (A-H) of hepatitis B virus infecting patients from San Francisco and their demographic, clinical, and virological characteristics. J Med Virol 73, 516-521.
19. Kramvis, A. & Kew, M. C. (2007). Epidemiology of hepatitis B virus in Africa, its genotypes and clinical associations of genotypes. Hepatol Res 37, S9-S19.
20. Kramvis, A., Restorp, K., Norder, H., Botha, J. F., Magnius, L. O. & Kew, M. C. (2005). Full genome analysis of hepatitis B virus genotype E strains from South-Western Africa and Madagascar reveals low genetic variability. J Med Virol 77, 47-52.
21. Kwok, S. & Higuchi, R. (1989). Avoiding false positives with PCR. Nature 339, 237-238.
22. Lemos Cardoso, G. & Farias Guerreiro, J. (2006). African gene flow to north Brazil as revealed by HBB*S gene haplotype analysis. Am J Hum Biol 18, 93-98.
23. Liu, H. F., Sokal, E. & Goubau, P. (2001). Wide variety of genotypes and geographic origins of hepatitis B virus in Belgian children. J Pediatr Gastroenterol Nutr 32, 274-277.
24. Maddison, D. R. & Maddison, W. P. (2003). MacClade 4: Analysis of Phylogeny and Character Evolution, 4th edn. Sunderland, MA: Sinauer Associates.
25. Magnius, L. O. & Norder, H. (1995). Subtypes, genotypes and molecular epidemiology of the hepatitis B virus as reflected by sequence variability of the S-gene. Intervirology 38, 24-34.
26. Martin, D. P. (2009). Recombination detection and analysis using RDP3. Methods Mol Biol 537, 185-205.
27. Mathet, V. L., Cuestas, M. L., Ruiz, V., Minassian, M. L., Rivero, C., Trinks, J., Daleoso, G., León, L. M., Sala, A. & other authors (2006). Detection of hepatitis B virus (HBV) genotype E carried - even in the presence of high titers of anti-HBs antibodies - by an Argentinean patient of African descent who had received vaccination against HBV. J Clin Microbiol 44, 3435-3439.
28. Motta-Castro, A. R., Martins, R.M., Yoshida, C. F., Teles, S. A., Paniago, A. M., Lima, K. M. & Gomes, S. A. (2005). Hepatitis B virus infection in isolated Afro-Brazilian communities. J Med Virol 77, 188-193.
29. Motta-Castro, A. R., Martins, R. M., Araujo, N. M., Niel, C., Facholi, G. B., Lago, B. V., Mello, F. C. & Gomes, S. A. (2008). Molecular epidemiology of hepatitis B virus in an isolated Afro-Brazilian community. Arch Virol 153, 2197-2205.
30. Mulders, M. N., Venard, V., Njayou, M., Edorh, A. P., Bola Oyefolu, A. O., Kehinde, M. O., Muyembe Tamfum, J. J., Nebie, Y. K., Maiga, I. & other authors (2004). Low genetic diversity despite hyperendemicity of hepatitis B virus genotype E throughout West Africa. J Infect Dis 190, 400-408.
31. Norder, H., Hammas, B., Lofdahl, S., Courouce, A. M. & Magnius, L. O. (1992). Comparison of the amino acid sequences of nine different serotypes of hepatitis B surface antigen and genomic classification of the corresponding hepatitis B virus strains. J Gen Virol 73, 1201-1208.
32. Odemuyiwa, S. O., Mulders, M. N., Oyedele, O. I., Ola, S. O., Odaibo, G. N., Olaleye, D. O. & Muller, C. P. (2001). Phylogenetic analysis of new hepatitis B virus isolates from Nigeria supports endemicity of genotype E in West Africa. J Med Virol 65, 463-469.
33. Okamoto, H., Imai, M., Kametani, M., Nakamura, T. & Mayumi, M. (1987). Genomic heterogeneity of hepatitis B virus in a 54-year-old woman who contracted the infection through materno-fetal transmission. Jpn J Exp Med 57, 231-236.
34. Olinger, C. M., Venard, V., Njayou, M., Oyefolu, A. O., Maiga, I., Kemp, A. J., Omilabu, S. A., le Faou, A. & Muller, C. P. (2006). Phylogenetic analysis of the precore/core gene of hepatitis B virus genotypes E and A in West Africa: new subtypes, mixed infections and recombinations. J Gen Virol 87, 1163-1173.
35. Osiowy, C., Giles, E., Tanaka, Y., Mizokami, M. & Minuk, G. Y. (2006). Molecular evolution of hepatitis B virus over 25 years. J Virol 80, 10307-10314.
36. Palumbo, E., Scotto, G., Faleo, G., Cibelli, D. C., Saracino, A. & Angarano, G. (2007). Prevalence of HBV-genotypes in immigrants affected by HBV-related chronic active hepatitis. Arq Gastroenterol 44, 54-57.
37. Posada, D. & Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
38. Pult, I., Abbott, N., Zhang, Y. Y. & Summers, J. (2001). Frequency of spontaneous mutations in an avian hepadnavirus infection. J Virol 75, 9623-9632.
39. Quintero, A., Martínez, D., Alarcón De Noya, B., Costagliola, A., Urbina, L., González, N., Liprandi, F., Castro De Guerra, D. & Pujol, F. H. (2002). Molecular epidemiology of hepatitis B virus in Afro-Venezuelan populations. Arch Virol 147, 1829-1836.
40. Rodas, C., Gelvez, N. & Keyeux, G. (2003). Mitochondrial DNA studies show asymmetrical Amerindian admixture in Afro-Colombian and Mestizo populations. Hum Biol 75, 13-30.
41. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74, 5463-5467.
42. Simmonds, P. & Midgley, S. (2005). Recombination in the genesis and evolution of hepatitis B virus genotypes. J Virol 79, 15467-15476.
43. Sitnik, R., Pinho, J. R., Bertolini, D. A., Bernardini, A. P., Da Silva, L. C. & Carrilho, F. J. (2004). Hepatitis B virus genotypes and precore and core mutants in Brazilian patients. J Clin Microbiol 42, 2455-2460.
44. Sitnik, R., Sette, H., Jr, Santana, R. A., Menezes, L. C., Graca, C. H., Dastoli, G. T., Silbert, S. & Pinho, J. R. (2007). Hepatitis B virus genotype E detected in Brazil in an African patient who is a frequent traveler. Braz J Med Biol Res 40, 1689-1692.
45. Stuyver, L., De Gendt, S., Van Geyt, C., Zoulim, F., Fried, M., Schinazi, R. F. & Rossau, R. (2000). A new genotype of hepatitis B virus: complete genome and phylogenetic relatedness. J Gen Virol 81, 67-74.
46. Suzuki, S., Sugauchi, F., Orito, E., Kato, H., Usuda, S., Siransy, L., Arita, I., Sakamoto, Y., Yoshihara, N. & other authors (2003). Distribution of hepatitis B virus (HBV) genotypes among HBV carriers in the Cote d'Ivoire: complete genome sequence and phylogenetic relatedness of HBV genotype E. J Med Virol 69, 459-465.
47. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
48. Toro, C., Jiménez, V., Rodríguez, C., Del Romero, J., Rodés, B., Holguín, A., Alvarez, P., García-Campello, M., Gómez-Hernando, C. & other authors (2006). Molecular and epidemiological characteristics of blood-borne virus infections among recent immigrants in Spain. J Med Virol 78, 1599-1608.
49. van Steenbergen, J. E., Niesters, H. G., Op de Coul, E. L., van Doornum, G. J., Osterhaus, A. D., Leentvaar-Kuijpers, A., Coutinho, R. A. & van den Hoek, J. A. (2002). Molecular epidemiology of hepatitis B virus in Amsterdam 1992-1997. J Med Virol 66, 159-165.
50. Vray, M., Debonne, J. M., Sire, J. M., Tran, N., Chevalier, B., Plantier, J. C., Fall, F., Vernet, G., Simon, F. & Mb, P. S. (2006). Molecular epidemiology of hepatitis B virus in Dakar, Senegal. J Med Virol 78, 329-334.
51. Zaaijer, H. L., Bouter, S. & Boot, H. J. (2008). Substitution rate of the hepatitis B virus surface gene. J Viral Hepat 15, 239-245.
52. Zhou, Y. & Holmes, E. C. (2007). Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J Mol Evol 65, 197-205.
53. Zwickl, D. J. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis, The University of Texas at Austin.