Leader sequences downstream of the primer binding site are important for efficient replication of simian immunodeficiency virus

Simian immunodeficiency virus (SIV) infection of macaques is remarkably sim ilar to that of human immunodeficiency virus type 1 (HIV-1) in humans, and the SIV-macaque system is a good model for AIDS research. We have construct ed an SIV proviral DNA clone that is deleted of 97 nucleotides (nt), i.e., construct SDI at positions (+322 to +418) immediately downstream of the pri mer binding site (PBS) of SIVmac239. When this construct was transfected in to COS-7 cells, the resultant viral progeny were severely impaired with reg ard to their ability to replicate in C8166 cells. Further deletion analysis showed that a virus termed SD1, containing a deletion of 23 nt (+322 to +3 44), was able to replicate with wild-type kinetics, while viruses containin g deletions of 21 nt (+398 to +418) (construct SD2) or 53 nt (+345 to +397) (construct SD3) displayed diminished capacity in this regard. Both the SD2 and SD3 viruses were also impaired with regard to ability to package viral RNA, while SD1 viruses were not, The SD and SD3 constructs did not revert to increased replication ability in C8166 cells over 6 months in culture. I n contrast, long-term passage of the SD2 mutated virus resulted in a restor ation of replication capacity, due to the appearance of four separate point mutations. Two of these substitutions were located in leader sequences of viral RNA within the PBS and the dimerization initiation site (DIS), while the other two were located within two distinct Gag proteins, i.e., CA and p 6, The biological relevance of three of these point mutations was confirmed by site directed mutagenesis studies that shelved that SD2 viruses contain ing each of these substitutions had regained a significant degree of viral replication capacity, Thus, leader sequences downstream of the PBS, especia lly the U5-lender stem and the DIS stem-loop, are important for SIV replica tion and for packaging of the viral genome.