An experimental animal model in which the course of immunodeficiency virus infection parallels the pathogenesis of the human disease is critical for the study of human AIDS. Simian immunodeficiency virus (SIV) induces an immunodeficiency syndrome in infected macaques that is remarkably similar in pathogenesis to human AIDS. An important use of this animal model system is the detailed study of pathogenesis and viral determinants of disease since many studies of this type are not feasible in humans. The purpose of this project is to investigate host and viral factors involved in variable disease progression in SIV-infected macaques and the lack of disease in African primates infected with their own strains of SIV.

 To investigate the role of host factors in SIV-infection of macaques, we used a well-defined molecularly cloned virus (SIVsmE543-3). Previous studies in our lab have demonstrated that PBMC of individual macaques show vastly different susceptibility to SIVsmE543-3 infection in vitro and susceptibility is predictive of subsequent plasma viremia following inoculation. Recent studies have now identified that this difference is attributable to allelic polymorphisms in the SPRY domain of TRIM5 alpha gene. In contrast, SIVmac appears to be uniquely adapted for resistance to multiple alleles of rhesus macaque TRIM5. We evaluated the effect of expression of the restrictive alleles on subsequent viremia in a cohort of 43 rhesus SIVsmE543-3-infected rhesus macaques. The restrictive genotypes were associated with significantly lower viremia than observed in macaques with the permissive genotype, as well as emergence of escape mutations in the SIV capsid protein. The specific amino acid substitutions found in viruses that escaped from TRIM5 restriction are presently being introduced into an E543-3 background in an effort to generate more reproducible viremia. This difference in susceptibility to TRIM5 polymorphism between SIVsm and SIVmac may explain the greater degree of protection achieved in immunized macaques challenged with repeated low dose intrarectal challenges with SIVsmE660 versus SIVmac251. Full length infectious clones of the related challenge stock, SIVsmE660 have also been generated by close to full length RT-PCR from the virus stock. Three of these viruses replicate efficiently in rhesus PBMC in vitro and their susceptibility to TRIM5 is under investigation. Two clones are presently being evaluated for in vivo viral replication and pathogenesis in rhesus macaques following both intravenous and intrarectal inoculation. SIV NEUROPATHOGENESIS. SIV and HIV are both associated with the development of encephalitis. For HIV, the onset of AIDS dementia is generally a late stage finding. In contrast, most models of SIV encephalitis (SIVE) use animals that progress rapidly to disease. We observed a small number of conventional progressors that developed SIVE. The evolution of SIV in the cerebral spinal fluid (CSF) was compared with the virus that evolved in the plasma of two rhesus macaques that developed SIVE. While the virus in the CSF and plasma were similar during primary infection, distinct substitutions were observed sequentially in the two compartments. These findings are consistent with compartmentalization between the brain and blood during development of neuro-AIDS and the evolution of viruses with distinct genotypes and potentially distinct biological phenotypes in the brain. One of these isolates, SIVsmH631Br induced SIVE in one of four macaques;virus isolated from the brain off this animal (SIVsmH783Br) induced SIVE in 3 of the 4 animals that have progressed to endstage disease with two additional animals still under study. Evolution of virus in the brain, CSF, blood and lymphoid tissues will be evaluated using deep sequencing and single genome amplification of selected samples and full length infectious clones representative of this virus will be generated. ASYMPTOMATIC INFECTION OF NATURAL HOST SPECIES. A second goal of this project is to study the mechanisms underlying the lack of pathogenicity of SIV for their natural host species, with emphasis on SIVagm from vervet monkeys. SIVagm is capable of inducing AIDS in PT macaques but African green monkeys (AGM) do not develop overt signs of disease following infection.
We perturbed the development of adaptive immune responses by combined administration of anti-CD8 and CD20 antibodies during primary infection of PTM, and AGM and compared these animals to historical controls infected with the same virus. Depletion resulted in a 1-log increase in primary viremia and a 4-log increase in post-acute viremia in PTM and three of the four PTM were euthanized within 6 weeks of inoculation due to massive CMV reactivation and disease. In contrast, all four lymphocyte-depleted AGM remained healthy. Plasma viremia showed only a brief trend to a higher level viremia during primary infection but the groups were indistinguishable during chronic infection. These data suggest that adaptive immune responses are critical in pathogenic SIV infection in PTM. However, the maintenance of a disease-free course of SIV infection in AGM likely depends on a number of mechanisms including non-adaptive immune mechanisms. In a study of a cohort of SIV-infected and nave vervet AGM, we found that many of the CD4+ T cells from African green monkeys down-regulate CD4 in vivo as they enter the memory pool and that this occurs independent of SIV infection. These CD4-negative memory T cells maintain functions that are normally attributed to CD4 T cells including production of IL-2, production of IL-17, expression of FoxP3 and expression of CD40L;however lack of CD4 expression apparently protects these activated cells from infection by SIVagm in vivo. Thus the absence of SIV-induced disease progression in natural hosts species may be partially explained by preservation of a subset of T cells that maintain CD4 T cell function while being resistant to SIV-infection in vivo.

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Cissé, Ousmane H; Ma, Liang; Wei Huang, Da et al. (2018) Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis. MBio 9:
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