Macaques Infected with Cloned Simian Immunodeficiency Virus Show RecurringnefGene Alterations

Abstract

We compared nef gene sequences isolated by polymerase chain reaction from peripheral blood lymphocyte DNA of macaques that had been inoculated with either biologically (E11S) or molecularly (clone 8) cloned SIV/Mne. Two samples from each animal obtained either early (weeks 2-8) or late (weeks 21-137) after infection were analyzed. Three substitutions in the predicted Nef amino acid sequence were seen in all animals at the late time point, and two other substitutions were seen in all except one. Two of the common exchanges are located approximately 40 residues apart in the Nef core sequence but are juxtaposed on the tertiary structure as judged by computer modeling using the structure of the HIV Nef core protein as a guide. Most recurrent in vivo changes replaced a residue found in the cloned Nef sequence with one present in a consensus derived by aligning the Nef sequences of the SIV/Sm clade. Recombinant virus containing a macaque-adapted (MA nef) nef on the clone 8 backbone was 3-fold more infectious on SMAGI cells than the original virus. A lymphocyte line infected with SIV-clone 8-MAnef contained a large proportion of cells carrying provirus with defective nef genes. These findings suggest that the nef gene of the cloned SIV/Mne had undergone attenuating mutations during propagation in tissue culture that were "corrected" in vivo.

Highly Pathogenic Simian Immunodeficiency Virus mne Variants That Emerge during the Course of Infection Evolve Enhanced Infectivity and the Ability To Downregulate CD4 but Not Class I Major Histocompatibility Complex Antigens

“…SIVmne027 was cloned from lymph node tissue of a macaque with declining CD4 ϩ cell counts and early signs of AIDS. This animal was inoculated with the SIVmne isolate from which SIVmneCL8 was cloned (8,31). The in vivo pathogenicities of SIVmne170 and SIVmne027 have been recently described (38).…”

“…Chimeric viruses containing regions of the highly pathogenic proviral clones, SIVmne170 and SIVmne027, in the background of the minimally pathogenic clone, SIVmneCL8, were constructed using conserved restriction sites (31,(38)(39)(40). The restriction site positions are numbered according to the sequence of SIVmneCL8 (GenBank accession no.…”

“…Although most studies with the SIV-macaque model have focused on defining the molecular determinants of virulence by using highly pathogenic strains and clones of SIV, the model has also provided a system in which to study genetic and phenotypic changes in a primate lentivirus as they relate to the development of AIDS (reviewed in reference 72). Importantly, like variants of HIV-1 that emerge during infection of humans, variant viruses that evolve in macaques infected with macrophage-tropic, minimally cytopathic, non-syncytium-inducing virus derived from Macaca nemestrina (SIVmneCL8) are rapidly replicating, are highly cytopathic, and may be syncytium inducing in culture (31,40,56,60,61). They also have increased ability to escape from host neutralizing antibody responses (11,61).…”

“…Downregulation of MHC class I may assist virus replication in vivo by protecting infected cells from CD8 ϩ cytotoxic T-lymphocyte (CTL)-mediated killing (15). Interestingly, nef variants are selected with disease progression, suggesting that particular activities may be associated with replication and persistence (31,41). However, despite these intriguing observations, the importance and relevance of each of these activities for efficient viral replication in vivo remain unclear.…”

“…To further delineate the properties and determinants of viruses that may be critical for SIV replication in vivo and progression to AIDS, we compared a minimally pathogenic, parental SIVmne clone (SIVmneCL8) with two highly pathogenic variant viruses (SIVmne170 and SIVmne027) cloned from late stages of infection (31,(38)(39)(40). We found that nef alleles from the variants enhanced viral infectivity, and they effectively downregulated surface expression of CD4 but not MHC class I.…”