Molecular Characterization of Duck Hepatitis B Virus Isolates from South African Ducks NOMATHIBANE P. MANGISA, 1,  HEIDI E. SMUTS, 2,  ANNA KRAMVIS, 1 C. WENDY LINLEY, 3 MICHELLE SKELTON, 1 TIMOTHY J. TUCKER, 4 PAULINE DE LA M. HALL, 5 DEL KAHN, 3 ALLISON R. JILBERT 6 & MICHAEL C. KEW, 1, * 1 MRC/CANSA/University Molecular Hepatology Research Unit and Department of Medicine, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa 2 Division of Medical Virology/NHLS, University of Cape Town, Cape Town, South Africa 3 Department of Surgery, University of Cape Town, Cape Town, South Africa 4 Medical Research Council, Tygervalley, South Africa 5 Division of Anatomical Pathology, University of Cape Town, Cape Town, South Africa 6 Institute of Medical and Veterinary Science and University of Adelaide, Adelaide, Australia Received August 1, 2003; Accepted October 6, 2003 Abstract. The objective of the study was to characterize the genome of duck hepatitis B virus (DHBV) isolates from South African Pekin ducks. Duck serum and liver samples were collected from two com- mercial duck farms from geographically distinct regions of South Africa. In total, 498 duck serum samples were tested for the presence of DHBV DNA using either sub-genomic or full-length polymerase chain reaction (PCR) assays. The overall prevalence of DHBV infection in South African ducks was 47%. In addition, 30% of 59 liver tissues tested were DHBV DNA-positive. Six randomly selected serum or liver samples were used to clone and sequence the genomes of the South African DHBV strains. All six isolates had DHBV genomes of 3,021 nucleotides with three characteristic overlapping reading frames encoding the polymerase, surface and core gene products. No X-like gene with a traditional start codon was found. Following phylogenetic analysis, the South African DHBV isolates clustered with DHBV isolates from other ‘‘Western’’ countries, including United States of America, Canada, Germany and India. On trans- lation of the open reading frames, the South African isolates were found to share signature amino acids in the polymerase and surface genes with the ‘‘Western’’ country isolates as opposed to those of Chinese DHBV isolates. Key words: Chinese and Western isolates, cloning, phylogenetic analysis, sequencing Introduction The duck hepatitis B virus (DHBV) belongs to the family Hepadnaviridae [1,2]. This family is di- vided into two genera: Orthohepadnavirus and Avihepadnavirus [1,2]. Members of Orthohepadna- virus infect humans, woodchucks, ground squir- rels, arctic squirrels, woolly monkeys, orangu- tangs, chimpanzees and gibbons. Members of Avihepadnavirus are found in birds including the duck [3,4], grey heron [5], Ross goose (Gen- Bank # M95589), snow goose [6] and the white stork [7]. The genomic organization of the mammalian and avian hepadnaviruses is similar [4,8]. All have a small, relaxed circular and partially double- stranded DNA genome of approximately 3,000 nucleotides (nt), which is maintained by 5¢ *Author for all correspondence: E-mail address: kewmc@medicine.wits.ac.za   These authors contributed equally to the study. Virus Genes 28:2, 179–186, 2004 Ó 2004 Kluwer Academic Publishers. Manufactured in The Netherlands.