Identification of hepatitis B virus indigenous to chimpanzees

Abstract

Hepatitis B viruses (HBV) and related viruses, classified in the Hepadnaviridae family, are found in a wide variety of mammals and birds. Although the chimpanzee has been the primary experimental model of HBV infection, this species has not been considered a natural host for the virus. Retrospective analysis of 13 predominantly wild-caught chimpanzees with chronic HBV infection identified a unique chimpanzee HBV strain in 11 animals. Nucleotide and derived amino acid analysis of the complete HBV genome and the gene coding for the hepatitis B surface antigen (S gene) identified sequence patterns that could be used to reliably identify chimpanzee HBV. This analysis indicated that chimpanzee HBV is distinct from known human HBV genotypes and is closely related to HBVs previously isolated from a chimpanzee, gibbons, gorillas, and orangutans.

Figure 1

(A) Phylogenetic comparison of complete HBV genome nucleotide sequences of chimpanzees, humans, and other non-human primates. The respective human genotypes are indicated by the letters A–F on the corresponding branches. GenBank accession numbers for the representative sequences used in the phylogenetic analyses were as follows: Genotype A: V00866, X51970, X70185, S50225, Z35717, M57663; Genotype B: U95551, J02203, X65257, X85254, X97848, X59759, X02496, Y07587, af043593, Z35716, X80925, X97849, X72702, M32138, L27106, X65259, X68292; Genotype C: X75655, X76665, D28880, D00630, D23680, D23681, D23684, M38636, X01587, V00867, X04615, D23682, D23686, X52939, D50517, D50519, D50520, D16665, D50489, D16666, D16667, D12980, M12906; Genotype D: D50521, D50522, D00329, D23679, D23678, D00331, M54923, D00330, X97851, X97850; Genotype E: X75657, X75664; Genotype F: X75658, X75663, X69798.; Gibbon: aj131568, aj131574, aj131569, aj131571, aj131572, aj131573, U46935; Gorilla: aj131567; Orangutan: Y17559, Y17560, Y17561, Y17562, Y17563, Y17564, Y17565; Woolly monkey: af046996; Chimpanzee: D00220. (B) Phylogenetic comparison of the S gene region (nucleotides 157–673). It includes the additional chimpanzees with chronic HBV infection. The respective human genotypes are indicated by the letters A–F. The two chimpanzees apparently infected with human HBV are indicated by numbers in the boxes.

Figure 2

Comparison of regions from Pre S, HBsAg, Core, and X coding regions with translated amino acid sequence differences. The following sequences are shown: (i) individual sequences from chimpanzees CH109, CH926, and D00220; (ii) gorilla HBV (aj131567); (iii) a consensus sequence of gibbon HBV (gib); (iv) a consensus sequence for each genotype (gntya, gntyb, gntyc, gntyd, gntye, and gntyf); and (v) woolly monkey HBV (af046996) (15). Dashes indicate conserved amino acids while changed positions are indicated in lowercase letters. A master sequence based on this comparison is depicted on the bottom line in upper-case letters. Shaded regions are discussed in the text. A comparison of the complete amino acid sequences is published as supplemental data on the PNAS web site, www.pnas.org.

Figure 3

Comparison of the polymerase coding regions with translated amino acid sequence differences and deletion. Sequences shown are described in the legend to Fig. 2. A comparison of the complete amino acid sequences is published as supplemental data on the PNAS web site, www.pnas.org.