Exchange of genetic sequences of long terminal repeat and the env gene by a promiscuous primate type D retrovirus Cindy N. Chiu 1 , Rita Mitra, Ing-Ming Chiu * Department of Internal Medicine and Comprehensive Cancer Center, The Ohio State University, Davis Medical Research Center, 480 West 9th Avenue, Columbus, OH 43210, USA Received 7 April 2003; received in revised form 27 June 2003; accepted 4 July 2003 Abstract Squirrel monkey retrovirus (SMRV) is a New World primate type D retrovirus. It was shown that SMRV-related sequences could be detected in another New World species, the skunk. It was further suggested that SMRV and an Old World primate type C retrovirus, baboon endogenous virus (BaEV), may have exchanged their env gene sequences. In this study, we sought to understand which sequences were exchanged between the genomic DNAs of SMRV and skunk. We also sought to determine the sequences exchanged between SMRV and BaEV. Here, we demonstrate that the long terminal repeat of SMRV is present in the skunk genome. We also show, by nucleotide sequence analysis, that the env gene that encodes the p15E glycoprotein of BaEV was most likely transduced from the corresponding gene of a primate type D retrovirus. Our results demonstrate that SMRV is a promiscuous virus with its pol gene homologous to the pol genes of type A, type B and avian type C viruses and a portion of its env gene homologous to the env genes of primate type C retroviruses. However, the primer binding sequence is unique to type D retroviruses. These kinds of recombination are likely to occur more than once in the evolution of retroviruses. The promiscuous nature of retroviruses and the recent incidence of unintended retroviral integration into a gene therapy patient underscore the importance of understanding how retroviral sequences are recombined among themselves and how they are integrated into the mammalian genome. # 2003 Elsevier B.V. All rights reserved. Keywords: Retrovirus; Long terminal repeat; Env sequence; Homologous recombination; Evolution Squirrel monkey retrovirus (SMRV) is a New World primate type D retrovirus. This virus can be propagated in a variety of tissue culture cell lines, including canine osteosarcoma cells, owl monkey cells (Chiu et al., 1983), marmoset cells (Sun et al., 1995) and human lympho- blastoid cells (Oda et al., 1988; Middleton et al., 1992). The virus is an endogenous virus with 10  /15 copies of DNA sequences present in the squirrel monkey genome (Chiu et al., 1983). Furthermore, the SMRV-related sequences have been identified in other primates includ- ing human (Chiu et al., 1984). The human SMRV- related sequences were further cloned and sequenced and were shown to be related, not only to SMRV, but also to type B and avian type C retroviruses (Callahan et al., 1985) and type A retroviruses (Chiu et al., 1985). Molecular cloning and nucleotide sequence analysis of SMRV showed that its pol gene is 45  /50% similar to those of type A, type B and avian type C retroviruses (Chiu et al., 1984, 1985). The primer binding sequence of SMRV is distinct from these other retroviruses (Chiu and Skuntz, 1986). Subsequently, other type D retro- viruses were shown to share the same primer binding sequence with SMRV (Power et al., 1986; Sonigo et al., 1986; Thayer et al., 1987). Interestingly, Southern blotting hybridization as well as heteroduplexing analy- sis showed that SMRV shares env gene sequence homology with baboon endogenous virus (BaEV), a primate type C virus (Chiu et al., 1983, 1984). In addition, SMRV-related sequences were also present in a New World species, the skunk (Benveniste et al., 1978). * Corresponding author. Tel.:  /1-614-293-4803; fax:  /1-614-293- 5550. E-mail address: chiu.1@osu.edu (I.-M. Chiu). 1 Present address: Center for Neural Science, New York University, 4 Washington Place, Room 809, New York, NY 10003, USA. Virus Research 96 (2003) 107  /111 www.elsevier.com/locate/virusres 0168-1702/03/$ - see front matter # 2003 Elsevier B.V. All rights reserved. doi:10.1016/S0168-1702(03)00178-3