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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

¹ Institute of Immunology, National Public Health Laboratory, 20A rue Auguste-Lumière, L-1950 Luxembourg, Luxembourg
² Unité Mixte de Recherche 7565 UHP-CNRS, Laboratoire de Bactériologie-Virologie, Faculté de Médecine, Vanduvre-lès-Nancy, France
³ Laboratoire de Microbiologie Microbienne, Centre de Biotechnologie – Nkolbisson, Yaoundé, Cameroon
⁴ Department of Medical Microbiology and Parasitology and Department of Medicine, College of Medicine of the University of Lagos, Nigeria
⁵ Laboratoire de Biologie Médicale, Hôpital du Point G, Bamako, Mali

Correspondence
Claude P. Muller
Claude.Muller{at}LNS.ETAT.LU

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.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are AM110794 [GenBank] –AM110915 [GenBank] and AM180623 [GenBank] –AM180628 [GenBank] .

A supplementary table showing primers and PCR conditions used for HBV complete-genome amplification and sequencing is available in JGV Online.