Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection.

BACKGROUND: Simian immunodeficiency viruses (SIVs) of chimpanzees and gorillas from Central Africa crossed the species barrier at least four times giving rise to human immunodeficiency virus type 1 (HIV-1) groups M, N, O and P. The paradigm of non-pathogenic lentiviral infections has been challenged by observations of naturally infected chimpanzees with SIVcpz associated with a negative impact on their life span and reproduction, CD4+ T-lymphocyte loss and lymphoid tissue destruction. With the advent and dissemination of new generation sequencing technologies, novel promising markers of immune deficiency have been explored in human and nonhuman primate species, showing changes in the microbiome (dysbiosis) that might be associated with pathogenic conditions. The aim of the present study was to identify and compare enteric viromes of SIVgor-infected and uninfected gorillas using noninvasive sampling and ultradeep sequencing, and to assess the association of virome composition with potential SIVgor pathogenesis in their natural hosts. RESULTS: We analyzed both RNA and DNA virus libraries of 23 fecal samples from 11 SIVgor-infected (two samples from one animal) and 11 uninfected western lowland gorillas from Campo-Ma'an National Park (CP), in southwestern Cameroon. Three bacteriophage families (Siphoviridae, Myoviridae and Podoviridae) represented 67.5 and 68% of the total annotated reads in SIVgor-infected and uninfected individuals, respectively. Conversely, mammalian viral families, such as Herpesviridae and Reoviridae, previously associated with gut- and several mammalian diseases were significantly more abundant (p < 0.003) in the SIVgor-infected group. In the present study, we analyzed, for the first time, the enteric virome of gorillas and their association with SIVgor status. This also provided the first evidence of association of specific mammalian viral families and SIVgor in a putative dysbiosis context. CONCLUSIONS: Our results suggested that viromes might be potentially used as markers of lentiviral disease progression in wild gorilla populations. The diverse mammalian viral families, herein described in SIVgor-infected gorillas, may play a pivotal role in a disease progression still unclear in these animals but already well characterized in pathogenic lentiviral infections in other organisms. Larger sample sets should be further explored to reduce intrinsic sampling variation.

Interactions between SIVNef, SIVGagPol and Alix correlate with viral replication and progression to AIDS in rhesus macaques.

Infection with Simian Immunodeficiency Virus (SIV) leads to high viral loads and progression to Simian AIDS (SAIDS) in rhesus macaques. The viral accessory protein Nef is required for this phenotype in monkeys as well as in HIV-infected humans. Previously, we determined that HIVNef binds HIVGagPol and Alix for optimal viral replication in cells. In this study, we demonstrated that these interactions could correlate with high viral loads leading to SAIDS in the infected host. By infecting rhesus macaques with a mutant SIV(mac239), where sequences in the nef gene that are required for these interactions were mutated, we observed robust viral replication and disease in two out of four monkeys, where they reverted to the wild type genotype and phenotype. These two rhesus macaques also died of SAIDS. Two other monkeys did not progress to disease and continued to harbor mutant nef sequences. We conclude that interactions between Nef, GagPol and Alix contribute to optimal viral replication and progression to disease in the infected host.

Mutations at the C-terminus of the simian immunodeficiency virus envelope glycoprotein affect gp120-gp41 stability on virions.

The transmembrane (TM) subunit of the envelope (Env) glycoprotein of the simian immunodeficiency virus (SIV) contains an unusually long cytoplasmic domain of 164 amino acids. Previously, we identified domains in the SIV TM cytoplasmic tail that are necessary for Env incorporation into virions and viral infectivity. In this study, we investigated the relevance to Env function of the highly conserved sequence comprising the immediate C-terminal 19 residues of TM. To this end, small in-frame deletions as well as a premature stop codon mutation were introduced into the coding region for the SIV TM C-terminus. All the mutant Env glycoproteins were expressed, processed and transported to the cell surface in an essentially wild-type manner. Moreover, the ability of the mutant Env proteins to mediate cell-to-cell fusion was similar to or slightly lower than that of the wild-type Env. However, viruses expressing the mutant Env glycoproteins were found to be poorly infectious in single-cycle infectivity assays. Further characterization of the TM mutant viruses revealed that while exhibiting wild-type levels of the TM protein, they contained significantly lower levels of the Env surface (SU) subunit, which is consistent with increased SU shedding from virions after Env incorporation. This phenotype was independent of Gag processing, since genetic inactivation of the viral protease did not increase SU retention by the resulting immature particles. Our findings indicate that deletions at the C-terminus of the SIV Env promote the instability of the SU-TM association on the virion surface and point to an important role for the TM cytoplasmic domain in modulating Env structure.

Virus replication and disease progression inversely correlate with SIV tat evolution in morphine-dependent and SIV/SHIV-infected Indian rhesus macaques.

We analyzed the association between evolution of the 5' exon of tat and disease progression in an SIV/SHIV macaque model of opiate dependence and AIDS. Cloned tat sequences were obtained by RT-PCR amplification of 3 plasma viruses (recovered at different times) from 6 morphine-dependent and 2 control Indian rhesus macaques inoculated with SHIV(KU-1B) SHIV(89.6P) and SIV/17E-Fr. Approximately ten clones were sequenced for each animal per time point for use in phylogenetic analyses. We found a strong, significant inverse correlation between disease progression and tat diversity in plasma by 20 weeks post-infection. The morphine-dependent macaques developed 2 distinct disease patterns - rapid progressor (Group A) and slow progressor (Group B) - whereas control animals developed into slow progressor only (Group C). The three animals in Group A exhibited approximately 40% (P = 0.01) and approximately 50% (P = 0.028) less diversity than Group B and C animals, respectively, over the 20 weeks. Furthermore, the Group A macaques showed a prominent reemergence of the wild-type SV17E tat sequence used in the inoculum that coincided with disease progression. This suggests that the virus from the original infection represented the most pathogenic form among all animals in these cohorts throughout the first 20 weeks of infection. We were unable to support or rule out a role for immune pressure on tat evolution based on the spectrum of sequence changes in the data set. Thus, in the short duration of this study, the Tat-specific immune pressure cannot explain the different disease outcomes of the six morphine animals nor of the two controls. Our results also suggest that in vivo morphine dependence can contribute to the pathogenesis of SIV/SHIV infection and that it may do so in conjunction with the evolution of viral proteins, such as Tat.

Functional relationship between the matrix proteins of feline and simian immunodeficiency viruses.

To investigate the functional relationship between the matrix (MA) proteins of feline and simian immunodeficiency viruses (FIV and SIV, respectively), we generated chimeric proviruses in which the MA-coding region of an SIV infectious molecular clone was partially or fully replaced by its FIV counterpart. Chimeric SIV proviruses containing the amino-terminal 36 residues or the central and carboxy-terminal regions of the FIV MA assembled into virions as efficiently as wild-type SIV. However, the resulting virions were noninfectious in single-cycle infectivity assays. Furthermore, a chimeric SIV provirus containing the entire FIV MA was found to be severely impaired in virion production due to inefficient membrane binding of the chimeric Gag polyprotein. Interestingly, the assembly defective phenotype of this chimeric Gag precursor could be reversed either by introducing the G31K/G33K double amino acid substitution in the FIV-derived MA domain or by coexpression with wild-type SIV Gag. Of note, a chimeric FIV provirus expressing the SIV MA not only assembled into particles as efficiently as wild-type FIV, but also replicated in feline T cells with wild-type kinetics. Our results thus provide novel information about the functional homology between the MA proteins of distantly related lentiviruses.

Positive and negative modulation of virus infectivity and envelope glycoprotein incorporation into virions by amino acid substitutions at the N terminus of the simian immunodeficiency virus matrix protein.

The matrix (MA) protein of the simian immunodeficiency viruses (SIVs) is encoded by the amino-terminal region of the Gag precursor and is the component of the viral capsid that lines the inner surface of the virus envelope. Previously, we identified domains in the SIV MA that are involved in the transport of Gag to the plasma membrane and in particle assembly. In this study, we characterized the role in the SIV life cycle of highly conserved residues within the SIV MA region spanning the two N-terminal alpha-helices H1 and H2. Our analyses identified two classes of MA mutants: (i) viruses encoding amino acid substitutions within alpha-helices H1 or H2 that were defective in envelope (Env) glycoprotein incorporation and exhibited impaired infectivity and (ii) viruses harboring mutations in the beta-turn connecting helices H1 and H2 that were more infectious than the wild-type virus and displayed an enhanced ability to incorporate the Env glycoprotein. Remarkably, among the latter group of MA mutants, the R22L/G24L double amino acid substitution increased virus infectivity eightfold relative to the wild-type virus in single-cycle infectivity assays, an effect that correlated with a similar increase in Env incorporation. Furthermore, the R22L/G24L MA mutation partially or fully complemented single-point MA mutations that severely impair or block Env incorporation and virus infectivity. Our finding that the incorporation of the Env glycoprotein into virions can be upregulated by specific mutations within the SIV MA amino terminus strongly supports the notion that the SIV MA domain mediates Gag-Env association during particle formation.

Domains in the simian immunodeficiency virus gp41 cytoplasmic tail required for envelope incorporation into particles.

The mechanism by which lentivirus envelope (Env) glycoproteins are packaged into budding virions is poorly understood. Simian immunodeficiency virus (SIV) contains an Env protein with an unusually long cytoplasmic tail. To investigate the role of this domain in the incorporation of the SIV Env into virions, we generated a series of SIV Env mutants carrying small in-frame deletions within the cytoplasmic domain. The effects of these mutations on Env synthesis, processing, and association with Gag particles were analyzed by means of the vaccinia virus expression system. All of the mutant Env glycoproteins were synthesized and processed in a manner similar to that of the wild-type Env. However, deletions affecting domains C-terminal to residue 832 in the SIV Env protein significantly impaired Env incorporation into particles. Cell surface biotinylation assays showed that this phenotype could not be attributed to inefficient cell surface expression of the Env mutants. Furthermore, when the Env deletion mutants were tested for their ability to mediate virus entry in single-cycle infectivity assays, those mutations that impaired Env incorporation also caused a severe defect in virus infectivity. Our results suggest that domains in the C-terminal third of the SIV Env protein are required for Env incorporation into particles and Env-mediated virus entry.

Small variations in the length of the cytoplasmic domain of the simian immunodeficiency virus transmembrane protein drastically affect envelope incorporation and virus entry.

Simian immunodeficiency viruses (SIVs) have an envelope (Env) glycoprotein with an unusually long cytoplasmic domain of 164 amino acids. In this article, we have characterized a series of SIV Env truncation mutants in which the cytoplasmic domain was progressively shortened from its carboxyl terminus by 20 amino acids. Expression by means of the vaccinia virus system showed that all of the SIV Env mutants were expressed and processed into the surface and transmembrane (TM) subunits. When the ability of the Env mutants to associate with SIV Gag particles was examined, we found that deletion of 20 to 80 residues from the carboxyl terminus of the SIV TM cytoplasmic tail abrogated the incorporation of the Env glycoprotein into particles. By contrast, further truncation of the SIV TM protein by 100 to 140 amino acids restored the ability of the Env protein to associate with Gag particles. Interestingly, mutants bearing a 44- or 24-amino acid cytoplasmic domain were incorporated at levels significantly higher than those of the wild-type Env. Single-cycle infectivity assays showed that Env mutants bearing cytoplasmic tails of 144 to 64 amino acids were highly inefficient at mediating virus entry. By contrast, truncation of the cytoplasmic domain to 44 or 24 amino acids drastically enhanced virus infectivity with respect to that conferred by the full-length Env protein. Our results demonstrate that small variations in the length of the SIV Env cytoplasmic domain dramatically influence Env-mediated viral functions.

Vaccination of macaques against pathogenic simian immunodeficiency virus with Venezuelan equine encephalitis virus replicon particles.

Vaccine vectors derived from Venezuelan equine encephalitis virus (VEE) that expressed simian immunodeficiency virus (SIV) immunogens were tested in rhesus macaques as part of the effort to design a safe and effective vaccine for human immunodeficiency virus. Immunization with VEE replicon particles induced both humoral and cellular immune responses. Four of four vaccinated animals were protected against disease for at least 16 months following intravenous challenge with a pathogenic SIV swarm, while two of four controls required euthanasia at 10 and 11 weeks. Vaccination reduced the mean peak viral load 100-fold. The plasma viral load was reduced to below the limit of detection (1,500 genome copies/ml) in one vaccinated animal between 6 and 16 weeks postchallenge and in another from week 6 through the last sampling time (40 weeks postchallenge). The extent of reduction in challenge virus replication was directly correlated with the strength of the immune response induced by the vectors, which suggests that vaccination was effective.

Selective in vitro protection of SIVagm-induced cytolysis by ajoene, [(E)-(Z)-4,5,9-trithiadodeca-1,6,11-triene-9 oxide].

We studied the effect of synthetic ajoene on simian immunodeficiency virus (SIVagm)-mediated cell fusion and subsequent virus-induced cytolysis. Our data indicate that this compound is a strong antifusion agent with a 50% syncytium inhibitory concentration (SIC50%) value of about 2.9 microM. We suggest that ajoene interacts with the cell-specific integrin molecules and sterically hinders the association between fusion (or other co-receptors) and the CD4-gp120 complex at the cell surface of SIV-infected cells. Although ajoene was maximally effective in suppressing syncytium formation during the early period (ie, up to 6 h) of the fusion process, when the compound was recurrently added to the co-cultures, the inhibitory effect was regained and further cell death was markedly delayed. This indicates that ajoene was also effective after the initial cell-to-cell contact stage. These data suggest that ajoene may be a promising approach for the treatment of SIV/human immunodeficiency virus (HIV) infections.