Sequence relationships of type D retroviruses which cause simian acquired immunodeficiency syndrome

Abstract Simian acquired immunodeficiency syndrome (SAIDS) in macaque monkeys is caused by type D retroviruses; three independent virus isolates are identified as SRV-1 (SAIDS retrovirus-serotype 1), SRV-2, and MPMV (Mason-Pfizer monkey virus). Virions from these three isolates have serologically related core antigens, but distinct surface proteins. Also, SRV-2 is unique since it apparently induces retroperitoneal fibromatosis in addition to SAIDS. The complete DNA sequence of molecularly cloned SRV-2 is presented and compared to the sequences of SRV-1 and MPMV and to the sewuences of other retroviruses and retroviral-related elements in the genomes of eucaryotic cells. SRV-1 and MPMV show fewer than 6% differences in predicted amino acid sequences encoding gag, prt, pol , and the C-terminal env domain; SRV-2 displays about 15–18% differences in these regions when aligned with SRV-1 or MPMV. Greater variation of predicted amino acid sequences is noted in the externally located N-terminal env domains; SRV-1 and MPMV have 83% homology whereas SRV-2 has 58% homology with either SRV-1 or MPMV. Nucleotide sequences of the LTRs of SRV-1 and MPMV are 88% homologous; SRV-2 shows 70% homology with the LTRs of SRV-1 and MPMV. Comparisons of the predicted pol region amino acid sequences of these simian type D retroviruses with the pol gene of a type B retrovirus, mouse mammary tumor virus (MMTV), reveal about 50% homology. A human endogenous element related to the pol region of MMTV shows about 25% homology of amino acids with the pol sequences of SRV-1 or SRV-2. The prt genes of the simian type D retroviruses are similar in size and predicted amino acid sequence with the prt genes of MMTV and the hamster intracisternal type A particle genome. The C-terminal env domains of the avian type C retrovirus reticuloendotheliosis virus (REV) and the type C baboon endogenous virus (BaEV) have 60 and 85% predicted amino acid homology, respectively, with the C-terminal env domains of SRV-1, SRV-2, and MPMV. Within the gag and pol genes of the simian type D retroviruses there are striking homologies with the rat IgE-binding protein gene. Sequence relatedness of these type D retroviruses with type A, type B, and type C retrovirus genomes and with cellular sequences supports the notion that recombinational events contribute to the genesis and variation of retroviruses. These DNA sequence analyses also provide a basis for considering and comparing mechanisms of immunedysfunction mediated by the simian type D retroviruses and other retroviruses..