1887

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Volume 87, Issue 5

Phylogenetic analysis of the precore/core gene of hepatitis B virus genotypes E and A in West Africa: new subtypes, mixed infections and recombinations Free

Abstract

One hundred and twenty-two new hepatitis B virus (HBV) preC/C sequences and three complete genomes from three major countries in West Africa were analysed. The majority of sequences were of genotype E and the only other genotype found was genotype A. Although for genotype E sequences, the genetic diversity of the preC/C gene was about two to three times higher than that of the preS/S gene, it was still considerably lower than that for genotype A sequences. The HBV/E preC/C gene was related most closely to subgenotype D1 and D2 sequences. Evidence of recombination was found in two strains that were of genotype A in the preS/S gene and of genotype E in the preC/C gene. The genotype A strains from Cameroon, Mali and Nigeria could be divided phylogenetically into three subtypes, A3 and two new subtypes, tentatively designated A4 and A5. Each subtype presented a genetic diversity of 2·19–3·85 % and intersubtype distances of 4·47–5·97 %. Interestingly, one sample from Nigeria showed evidence of a triple recombination of genotypes E/D and A, separated by a genotype G-specific insert of 36 bp. Of 110 patients, 19 (17·3 %) showed a coinfection of genotypes A and E, mostly in human immunodeficiency virus-positive children from Cameroon. Thus, in Cameroon, where both genotypes coexist, 37 % of all individuals tested had mixed infections. The low genetic variability in the preC/C gene of genotype E supports our previous speculation about a relatively short evolutionary history of this genotype, in contrast to the subtype-rich African genotype A strains.

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2006-05-01
2024-04-18
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References

  1. Ahmed S. D., Cuevas L. E., Brabin B. J., Kazembe P., Broadhead R., Verhoeff F. H., Hart C. A. 1998; Seroprevalence of hepatitis B and C and HIV in Malawian pregnant women. J Infect 37:248–251 [CrossRef]
     [Google Scholar]
  2. Allain J.-P., Candotti D., Soldan K. & 8 other authors 2003; The risk of hepatitis B virus infection by transfusion in Kumasi, Ghana. Blood 101:2419–2425 [CrossRef]
     [Google Scholar]
  3. Arauz-Ruiz P., Norder H., Visona K. A., Magnius L. O. 1997; Molecular epidemiology of hepatitis B virus in Central America reflected in the genetic variability of the small S gene. J Infect Dis 176:851–858 [CrossRef]
     [Google Scholar]
  4. Baptista M., Kramvis A., Kew M. C. 1999; High prevalence of 1762T 1764A mutations in the basic core promoter of hepatitis B virus isolated from black Africans with hepatocellular carcinoma compared with asymptomatic carriers. Hepatology 29:946–953 [CrossRef]
     [Google Scholar]
  5. Beasley R. P., Hwang L.-Y., Lin C.-C., Chien C.-S. 1981a; Hepatocellular carcinoma and hepatitis B virus: a prospective study of 22 707 men in Taiwan. Lancet ii:1129–1133
     [Google Scholar]
  6. Beasley R. P., Hwang L.-Y., Lin C.-C., Stevens C. E., Wang K.-Y., Sun T.-S., Hsieh F.-J., Szmuness W. 1981b; Hepatitis B immune globulin (HBIG) efficacy in the interruption of perinatal transmission of hepatitis B virus carrier state: initial report of a randomised double-blind placebo-controlled trial. Lancet ii:388–393
     [Google Scholar]
  7. Bowyer S. M., Sim J. G. M. 2000; Relationships within and between genotypes of hepatitis B virus at points across the genome: footprints of recombination in certain isolates. J Gen Virol 81:379–392
     [Google Scholar]
  8. Bowyer S. M., van Staden L., Kew M. C., Sim J. G. M. 1997; A unique segment of the hepatitis B virus group A genotype identified in isolates from South Africa. J Gen Virol 78:1719–1729
     [Google Scholar]
  9. Chu C. M., Karayiannis P., Fowler M. J., Monjardino J., Liaw Y. F., Thomas H. C. 1985; Natural history of chronic hepatitis B virus infection in Taiwan: studies of hepatitis B virus DNA in serum. Hepatology 5:431–434 [CrossRef]
     [Google Scholar]
  10. Edmunds W. J., Medley G. F., Nokes D. J., O'Callaghan C. J., Whittle H. C., Hall A. J. 1996; Epidemiological patterns of hepatitis B virus (HBV) in highly endemic areas. Epidemiol Infect 117:313–325 [CrossRef]
     [Google Scholar]
  11. Girones R., Miller R. H. 1989; Mutation rate of the hepadnavirus genome. Virology 170:595–597 [CrossRef]
     [Google Scholar]
  12. Gray A. H., Fang J. W., Davis G. L., Mizokami M., Wu P. C., Williams R., Schuster S. M., Lau J. Y. 1997; Variations of hepatitis B virus core gene sequence in Western patients with chronic hepatitis B virus infection. J Viral Hepat 4:371–378 [CrossRef]
     [Google Scholar]
  13. Hannoun C., Horal P., Lindh M. 2000; Long-term mutation rates in the hepatitis B virus genome. J Gen Virol 81:75–83
     [Google Scholar]
  14. Hannoun C., Krogsgaard K., Horal P., Lindh M. 2002; Genotype mixtures of hepatitis B virus in patients treated with interferon. J Infect Dis 186:752–759 [CrossRef]
     [Google Scholar]
  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 [CrossRef]
     [Google Scholar]
  16. Hasegawa I., Tanaka Y., Kramvis A. & 7 other authors 2004; Novel hepatitis B virus genotype A subtyping assay that distinguishes subtype Aa from Ae and its application in epidemiological studies. J Virol 78:7575–7581 [CrossRef]
     [Google Scholar]
  17. Kane M. 1995; Global programme for control of hepatitis B infection. Vaccine 13 (Suppl. 1):S47–S49 [CrossRef]
     [Google Scholar]
  18. Kao J.-H., Chen P.-J., Lai M.-Y., Chen D.-S. 2002; Clinical and virological aspects of blood donors infected with hepatitis B virus genotypes B and C. J Clin Microbiol 40:22–25 [CrossRef]
     [Google Scholar]
  19. Kato H., Orito E., Gish R. G., Sugauchi F., Suzuki S., Ueda R., Miyakawa Y., Mizokami M. 2002; Characteristics of hepatitis B virus isolates of genotype G and their phylogenetic differences from the other six genotypes (A through F. J Virol 76:6131–6137 [CrossRef]
     [Google Scholar]
  20. Kidd-Ljunggren K., Öberg M., Kidd A. H. 1995; The hepatitis B virus X gene: analysis of functional domain variation and gene phylogeny using multiple sequences. J Gen Virol 76:2119–2130 [CrossRef]
     [Google Scholar]
  21. 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 [CrossRef]
     [Google Scholar]
  22. Kumar S., Tamura K., Nei M. 2004; mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163 [CrossRef]
     [Google Scholar]
  23. Kurbanov F., Tanaka Y., Fujiwara K. & 11 other authors 2005; A new subtype (subgenotype) Ac (A3) of hepatitis B virus and recombination between genotypes A and E in Cameroon. J Gen Virol 86:2047–2056 [CrossRef]
     [Google Scholar]
  24. 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 [CrossRef]
     [Google Scholar]
  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
     [Google Scholar]
  26. Mangia A., Chung Y. H., Hoofnagle J. H., Birkenmeyer L., Mushahwar I., Di Bisceglie A. M. 1996; Pathogenesis of chronic liver disease in patients with chronic hepatitis B virus infection without serum HBeAg. Dig Dis Sci 41:2447–2452 [CrossRef]
     [Google Scholar]
  27. Minami M., Poussin K., Kew M., Okanoue T., Brechot C., Paterlini P. 1996; Precore/core mutations of hepatitis B virus in hepatocellular carcinomas developed on noncirrhotic livers. Gastroenterology 111:691–700 [CrossRef]
     [Google Scholar]
  28. Mulders M. N., Venard V., Njayou M. & 12 other authors 2004; Low genetic diversity despite hyperendemicity of hepatitis B virus genotype E throughout West Africa. J Infect Dis 190:400–408 [CrossRef]
     [Google Scholar]
  29. Norder H., Couroucé A.-M., Magnius L. O. 1994; Complete genomes, phylogenetic relatedness, and structural proteins of six strains of the hepatitis B virus, four of which represent two new genotypes. Virology 198:489–503 [CrossRef]
     [Google Scholar]
  30. 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 [CrossRef]
     [Google Scholar]
  31. Okamoto H., Imai M., Tsuda F., Tanaka T., Miyakawa Y., Mayumi M. 1987; Point mutation in the S gene of hepatitis B virus for a d/y or w/r subtypic change in two blood donors carrying a surface antigen of compound subtype adyr or adwr. J Virol 61:3030–3034
     [Google Scholar]
  32. Olubuyide I. O., Ola S. O., Aliyu B., Dosumu O. O., Arotiba J. T., Olaleye O. A., Odaibo G. N., Odemuyiwa S. O., Olawuyi F. 1997; Prevalence and epidemiological characteristics of hepatitis B and C infections among doctors and dentists in Nigeria. East Afr Med J 74:357–361
     [Google Scholar]
  33. Orito E., Mizokami M., Ina Y., Moriyama E. N., Kameshima N., Yamamoto M., Gojobori T. 1989; Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. Proc Natl Acad Sci U S A 86:7059–7062 [CrossRef]
     [Google Scholar]
  34. Owiredu W. K. B. A., Kramvis A., Kew M. C. 2001; Molecular analysis of hepatitis B virus genomes isolated from black African patients with fulminant hepatitis B. J Med Virol 65:485–492 [CrossRef]
     [Google Scholar]
  35. Robertson B. H., Margolis H. S. 2002; Primate hepatitis B viruses – genetic diversity, geography and evolution. Rev Med Virol 12:133–141 [CrossRef]
     [Google Scholar]
  36. 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
     [Google Scholar]
  37. Suzuki S., Sugauchi F., Orito E. & 9 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 [CrossRef]
     [Google Scholar]
  38. Thomas H. C., Montano L., Goodall A., de Koning R., Oladapo J., Wiedman K. H. 1982; Immunological mechanisms in chronic hepatitis B virus infection. Hepatology 2:S116–S119
     [Google Scholar]
  39. van Steenbergen J. E., Niesters H. G. M., Op de Coul E. L. M., van Doornum G. J. J., Osterhaus A. D. M. E., Leentvaar-Kuijpers A., Coutinho R. A., van den Hoek J. A. R. 2002; Molecular epidemiology of hepatitis B virus in Amsterdam 1992-1997. J Med Virol 66:159–165 [CrossRef]
     [Google Scholar]
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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 (2006); https://doi.org/10.1099/vir.0.81614-0
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