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

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.

A novel hepatitis B virus (HBV) subgenotype D (D8) strain, resulting from recombination between genotypes D and E, is circulating in Niger along with HBV/E strains

“…Elsewhere in Africa, several hybrid strains have been described as involving HBV/E and genotypes A, D and G (Bekondi et al, 2007;Garmiri et al, 2009;Kurbanov et al, 2005;Laoi & Crowley, 2008;Meldal et al, 2009;Mulders et al, 2004;Olinger et al, 2006). Molecular analyses often found these same recombinant sites.…”

“…For example, a recombinant between HBV/C and HBV/D is the dominant subgenotype circulating in Tibet (Cui et al, 2002). In Africa, such recombination events have also been described, including recombinants A-D (Owiredu et al, 2001), A-E (Garmiri et al, 2009;Kurbanov et al, 2005), D-E-A and the G insertion (Olinger et al, 2006). Very recently, new HBV/ D-E recombinants were identified in the Central African Republic, Ireland (in a west African patient), Tunisia and Guinea, with all of them sharing the same recombination profile (Bekondi et al, 2007;Garmiri et al, 2009;Laoi & Crowley, 2008;Meldal et al, 2009).…”

Identification of novel recombinants of hepatitis B virus genotypes F and G in human immunodeficiency virus-positive patients from Argentina and Brazil

“…Genotypes/subgenotypes have distinct geographical distributions: HBV/A and HBV/D are found worldwide, HBV/B and HBV/C are found in east/south-east Asia, HBV/E in west/central Africa, and HBV/F and HBV/H in native populations of the Americas (Araujo et al, 2011; Kramvis et al, 2005). HBV/G was described by Stuyver et al (2000) and, despite low prevalence, seems ubiquitous, as it has been reported in Europe (Lacombe et al, 2006;Vieth et al, 2002), the Americas (Alvarado-Esquivel et al, 2006;Alvarado Mora et al, 2011;Bottecchia et al, 2008;Chu et al, 2003;Osiowy et al, 2008), Asia (Shibayama et al, 2005;Toan et al, 2006) and Africa (Olinger et al, 2006;Toan et al, 2006). HBV/G is frequently reported in patients infected with human immunodeficiency virus (HIV) (Dao et al, 2011;Zehender et al, 2003), particularly in men who have sex with men (MSM) (Bottecchia et al, 2008;Osiowy et al, 2008).…”

Hepatitis B virus taxonomy and hepatitis B virus genotypes

“…Using different methods for genotyping, several reports described high rates of double infection with two different HBV genotypes in all parts of the world. Using these methods double infections have been found in 4.4% [56] , 10.9% [57] , 12.5% [58] , 14.1% (Kirschberg et al, unpublished results), 17.3% [59] and 17.5% [60] of HBV infected patients. Even triple infections with HBV of genotype A, B and C have been described in 0.9% of HBV infected intravenous drug users [60] .…”