Hepatitis B virus subgenotype A1: evolutionary relationships between Brazilian, African and Asian isolates

Abstract

Brazil is a country of low hepatitis B virus (HBV) endemicity in which the genotype A of HBV (HBV/A) is the most prevalent. The complete nucleotide sequences of 26 HBV/A isolates, originating from eight Brazilian states, were determined. All were adw2. Twenty-three belonged to subgenotype A1 and three to A2. By phylogenetic analysis, it was shown that all the 23 HBV/A1 isolates clustered together with isolates from Bangladesh, India, Japan, Nepal, the Philippines and United Arab Emirates, but not with those of Congo, Kenya, Malawi, Rwanda, South Africa, Tanzania, Uganda and Zimbabwe. Four amino acid residues in the polymerase (His138 in the terminal protein domain, Pro18 and His90 in the spacer, and Ser109 in the reverse transcriptase), and one (Phe17) in the precore region, predominated in Latin American and Asian HBV/A1 isolates, but were rarely encountered in African isolates, with the exception of those from Somalia. Specific variations of two adjacent amino acids in the C-terminal domain of the HBx protein, namely Ala146 and Pro147, were found in all the Brazilian, but rarely in the other HBV/A1 isolates. By Bayesian analysis, the existence of an 'Asian-American' clade within subgenotype A1 was supported by a posterior probability value of 0.996. The close relatedness of the Brazilian, Asian and Somalian isolates suggests that the HBV/A1 strains predominant in Brazil did not originate from the five million slaves who were imported from Central and Western Africa from 1551 to 1840, but rather from the 300-400,000 captives forcibly removed from southeast Africa at the middle of the 19th century.

Figure 1. Geographical distribution of HBV/A1 and A2 isolates in Brazil, including the 26 isolates characterized in this work.

Numbers indicate the ratios A1/A2. Numbers in parentheses refer to semi-isolated Afro-Brazilian communities which were established by the slave escapees during the 17^th and 18^th centuries. Data compiled from –, , , .

Figure 2. Phylogenetic analysis based on HBV complete nucleotide sequences.

The phylogenetic tree, performed by using the maximum likelihood method, incorporates 134 HBV/A1 isolates, including the 23 Brazilian isolates sequenced in this study. Subgenotype A1 strains separated into two clades, ‘African’ (blue) and ‘Asian-American’ (green). In addition, sequences of A2, quasi-subgenotype A3 and A4 samples were included as an outgroup (red), which allowed three Brazilian samples to be classified as subgenotype A2. The list of the GenBank accession numbers of the isolates with their subgenotypes and countries of origin is shown in Table S1.

Figure 3. Bayesian maximum clade credibility tree of HBV/A full length nucleotide sequences.

A1 and A2–A4 represent HBV subgenotypes within genotype A. The numbers on the internal nodes represent posterior probabilities. All nodes marked with a dot showed posterior probability >0.95. The branch lengths are proportional to length of time. The names of the continents on the branches indicate the most plausible routes of dissemination. *Sub-Saharan Africa refers to Congo, Kenya, Malawi, Rwanda, Tanzania, Uganda and Zimbabwe.