Is the Gut the Major Source of Virus in Early Simian Immunodeficiency Virus Infection?

The acute phases of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infection are characterized by rapid and profound depletion of CD4⁺ T cells from the guts of infected individuals. The large number of CD4⁺ T cells in the gut (a large fraction of which are activated and express the HIV/SIV coreceptor CCR5), the high level of infection of these cells, and the temporal coincidence of this CD4⁺ T-cell depletion with the peak of virus in plasma in acute infection suggest that the intestinal mucosa may be the major source of virus driving the peak viral load. Here, we used data on CD4⁺ T-cell proportions in the lamina propria of the rectums of SIV-infected rhesus macaques (which progress to AIDS) and sooty mangabeys (which do not progress) to show that in both species, the depletion of CD4⁺ T cells from this mucosal site and its maximum loss rate are often observed several days before the peak in viral load, with few CD4⁺ T cells remaining in the rectum by the time of peak viral load. In contrast, the maximum loss rate of CD4⁺ T cells from bronchoalveolar lavage specimens and lymph nodes coincides with the peak in virus. Analysis of the kinetics of depletion suggests that, in both rhesus macaques and sooty mangabeys, CD4⁺ T cells in the intestinal mucosa are a highly susceptible population for infection but not a major source of plasma virus in acute SIV infection.The acute phase of human immunodeficiency virus (HIV) infection is characterized by moderate CD4⁺ T-cell depletion in blood, followed by a transient partial restoration of CD4⁺ T-cell numbers and eventually by a slow long-term CD4⁺ T-cell decline in the chronic phase that lasts for several years. Studies of CD4⁺ T-cell depletion in mucosal sites, often conducted with simian immunodeficiency virus (SIV)-infected macaques, have demonstrated that mucosal CD4⁺ T-cell depletion is more rapid and profound (3, 10, 13, 19, 21). The severe depletion of cells in the gut in early infection is thought to be driven in part by the phenotype of the cells present, which are predominantly CCR5⁺ and in general more activated than their circulating counterparts. As such, these mucosal CD4⁺ T cells are highly susceptible to productive infection with the dominant CCR5-tropic strains of HIV and SIV present in early infection (20). The rapid depletion of CD4⁺ T cells at mucosal sites is accompanied by relatively high numbers of infected cells (10, 13) and is temporally associated with the peak viral load in plasma, suggesting that the infection of mucosal CD4⁺ T cells may be responsible for the majority of virus replication occurring during acute infection (10, 15, 21, 22).The size of the CD4⁺ T-cell pool in the gut is a matter of some controversy, with estimates ranging from ∼5 to 50% of the total body pool of these cells (reviewed in reference 5). Regardless of the precise numbers, the gut (and particularly the mucosal lamina propria) contains a significant proportion of the body CD4⁺ CCR5⁺ memory T cells, which are depleted very early in infection. However, whether CD4⁺ T cells in the gut are merely a target of early infection or whether they are a major driver of early viral growth and peak viral loads in acute infection is unclear. Here we use a combination of experimental data and modeling to demonstrate that the gut is unlikely to be a major source of virus production in acute SIV infection.     

The Biology of Kaposi＇s Sarcoma-Associated Herpesvirus and the Infection of Human Immunodeficiency Virus

Kaposi sarcoma-associated herpesvirus (KSHV),also known as human herpesvirus 8 (HHV-8),is discovered in 1994 from Kaposi's sarcoma (KS) lesion of an acquired immunodeficiency syndrome (AIDS)patient.In addition to its association with KS,KSHV has also been implicated as the causative agent of two other AIDS-associated malignancies:primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD).KSHV is a complex DNA virus that not only has the ability to promote cellular growth and survival for tumor development,but also can provoke deregulated angiogenesis,inflammation,and modulate the patient's immune system in favor of tumor growth.As KSHV is a necessary but not sufficient etiological factor for KS,human immunodeficiency virus (HIV) is a very important cofactor.Here we review the basic information about the biology of KSHV,development of pathogenesis and interaction between KSHV and HIV.     

TRIM5α Modulates Immunodeficiency Virus Control in Rhesus Monkeys

The cytoplasmic TRIM5α proteins of certain mammalian lineages efficiently recognize the incoming capsids of particular retroviruses and potently restrict infection in a species-specific manner. Successful retroviruses have evolved capsids that are less efficiently recognized by the TRIM5α proteins of the natural hosts. To address whether TRIM5α contributes to the outcome of retroviral infection in a susceptible host species, we investigated the impact of TRIM5 polymorphisms in rhesus monkeys on the course of a simian immunodeficiency virus (SIV) infection. Full-length TRIM5α cDNAs were derived from each of 79 outbred monkeys and sequenced. Associations were explored between the expression of particular TRIM5 alleles and both the permissiveness of cells to SIV infection in vitro and clinical sequelae of SIV infection in vivo. Natural variation in the TRIM5α B30.2(SPRY) domain influenced the efficiency of SIVmac capsid binding and the in vitro susceptibility of cells from the monkeys to SIVmac infection. We also show the importance in vivo of the interaction of SIVmac with different allelic forms of TRIM5, demonstrating that particular alleles are associated with as much as 1.3 median log difference in set-point viral loads in SIVmac-infected rhesus monkeys. Moreover, these allelic forms of TRIM5 were associated with the extent of loss of central memory (CM) CD4+ T cells and the rate of progression to AIDS in the infected monkeys. These findings demonstrate a central role for TRIM5α in limiting the replication of an immunodeficiency virus infection in a primate host.     

Hepatitis B Virus Infection in Human Immunodeficiency Virus Infected Southern African Adults: Occult or Overt – That Is the Question

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) share transmission routes and are endemic in sub-Saharan Africa. The objective of the present study was to use the Taormina definition of occult HBV infection, together with stringent amplification conditions, to determine the prevalence and characteristics of HBV infection in antiretroviral treatment (ART)-naïve HIV^+ve adults in a rural cohort in South Africa. The presence of HBV serological markers was determined by enzyme linked immunoassay (ELISA) tests. HBV DNA-positivity was determined by polymerase chain reaction (PCR) of at least two of three different regions of the HBV genome. HBV viral loads were determined by real-time PCR. Liver fibrosis was determined using the aspartate aminotransferase-to-platelet ratio index. Of the 298 participants, 231 (77.5%) showed at least one HBV marker, with 53.7% HBV DNA^−ve (resolved) and 23.8% HBV DNA^+ve (current) [8.7% HBsAg^+ve: 15.1% HBsAg^−ve]. Only the total number of sexual partners distinguished HBV DNA^+ve and HBV DNA^−ve participants, implicating sexual transmission of HBV and/or HIV. It is plausible that sexual transmission of HBV and/or HIV may result in a new HBV infection, superinfection and re-activation as a consequence of immunesuppression. Three HBsAg^−ve HBV DNA^+ve participants had HBV viral loads <200 IU/ml and were therefore true occult HBV infections. The majority of HBsAg^−ve HBV DNA^+ve participants did not differ from HBsAg^+ve HBV DNA^+ve (overt) participants in terms of HBV viral loads, ALT levels or frequency of liver fibrosis. Close to a quarter of HIV^+ve participants were HBV DNA^+ve, of which the majority were HBsAg^−ve and were only detected using nucleic acid testing. Detection of HBsAg^−ve HBV DNA^+ve subjects is advisable considering they were clinically indistinguishable from HBsAg^+ve HBV DNA^+ve individuals and should not be overlooked, especially if lamivudine is included in the ART.     

Simian-Human Immunodeficiency Infection – Is the Course Set in the Acute Phase?

Identifying early predictors of infection outcome is important for the clinical management of HIV infection, and both viral load and CD4+ T cell level have been found to be useful predictors of subsequent disease progression. Very high viral load or extensively depleted CD4+ T cells in the acute phase often result in failure of immune control, and a fast progression to AIDS. It is usually assumed that extensive loss of CD4+ T cells in the acute phase of HIV infection prevents the establishment of robust T cell help required for virus control in the chronic phase. We tested this hypothesis using viral load and CD4+ T cell number of SHIV-infected rhesus macaques. In acute infection, the lowest level of CD4+ T cells was a good predictor of later survival; animals having less than 3.3% of baseline CD4+ T cells progressed to severe disease, while animals with more than 3.3% of baseline CD4+ T cells experienced CD4+ T cell recovery. However, it is unclear if the disease progression was caused by early depletion, or was simply a result of a higher susceptibility of an animal to infection. We derived a simple relationship between the expected number of CD4+ T cells in the acute and chronic phases for a constant level of host susceptibility or resistance. We found that in most cases, the depletion of CD4+ T cells in chronic infection was consistent with the prediction from the acute CD4+ T cell loss. However, the animals with less than 3.3% of baseline CD4 T cells in the acute phase were approximately 20% more depleted late in the infection than expected based on constant level of virus control. This suggests that severe acute CD4 depletion indeed impairs the immune response.     

Will Multiple Coreceptors Need To Be Targeted by Inhibitors of Human Immunodeficiency Virus Type 1 Entry?

Despite being able to use the Bonzo coreceptor as efficiently as CCR5 in transfected cells, pediatric human immunodeficiency virus type 1 isolate P6 was unable to replicate in peripheral blood mononuclear cells (PBMC) lacking the CCR5 receptor. Furthermore, its replication in wild-type PBMC was completely inhibited by inhibitors of CCR5-mediated entry. Similarly, maternal isolate M6 could use CCR5, CXCR4, Bonzo, and other coreceptors in transfected cells but was completely sensitive to inhibitors of CCR5- and CXCR4-mediated entry when grown in PBMC. The ability of these viruses to use coreceptors in addition to CCR5 and CXCR4 in vitro was, therefore, irrelevant to their drug sensitivity in primary cells. We argue that CCR5 and CXCR4 should remain the primary targets for antiviral drug development, pending strong evidence to the contrary.     

Integrin α4β7 Is Downregulated on the Surfaces of Simian Immunodeficiency Virus SIVmac239-Infected Cells

Simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) infection results in an early and enduring depletion of intestinal CD4⁺ T cells. SIV and HIV bind integrin α4β7, thereby facilitating infection of lymphocytes that home to the gut-associated lymphoid tissue (GALT). Using an ex vivo flow cytometry assay, we found that SIVmac239-infected cells expressed significantly lower levels of integrin α4β7 than did uninfected cells. This finding suggested a potential viral effect on integrin α4β7 expression. Using an in vitro model, we confirmed that integrin α4β7 was downregulated on the surfaces of SIVmac239-infected cells. Further, modulation of integrin α4β7 was dependent on de novo synthesis of viral proteins, but neither cell death, the release of a soluble factor, nor a change in activation state was involved. Downregulation of integrin α4β7 may have an unappreciated role in the CD4 depletion of the mucosal-associated lymphoid compartments, susceptibility to superinfection, and/or immune evasion.Infection of macaques with simian immunodeficiency virus (SIV) and humans with human immunodeficiency virus (HIV), regardless of the route of transmission, results in early establishment of infection in the gut-associated lymphoid tissue (GALT) (3, 23, 25). Consequently, the CD4⁺ T cells of the GALT are depleted, and intestinal integrity is compromised (4, 21, 37). The mechanism of GALT depletion, as well as the mechanism of viral localization to the GALT, remains poorly understood.GALT localization is mediated, at least in part, by integrins, a large family of “sticky” cell surface proteins (24, 35, 36). Integrins facilitate conversation between the environment and a cell, thereby influencing cellular adhesion, trafficking, proliferation, and signaling. Consequently, numerous viruses, despite having a small number of proteins, have developed mechanisms to exploit integrins and hence cellular processes, in order to facilitate viral replication and immune evasion (17, 24, 34, 36). Examples of such viruses include human cytomegalovirus (39), rotavirus (14), and SIV/HIV (40). One well-studied integrin, α4β7, mediates migration of lymphocytes to the GALT (31, 33). In 2008, Arthos et al. demonstrated that HIV-1 glycoprotein, gp120, binds integrin α4β7, facilitating infection of CD4⁺ T cells and increasing viral replication efficiency (1).Recent in vivo studies have revealed that CD4⁺ T cells expressing high amounts of integrin α4β7 (integrin α4β7 high) are preferentially infected during acute SIV infection (15, 38). In addition, integrin α4β7 high CD4⁺ T cells contain greater than one provirus per cell during peak viral infection, suggesting that the cells are unusually susceptible to superinfection. Unexpectedly, superinfection is not observed in integrin α4β7 high CD4⁺ T cells after peak viral infection (15). Integrin α4β7 high-expressing CD4⁺ T cells are also depleted from the circulation parallel to the loss of intestinal CD4⁺ cells, suggesting a fundamental role for integrin α4β7 in SIV pathogenesis (38). The mechanism underlying the depletion of integrin α4β7 high-expressing cells and whether SIV-infected cells are directly or indirectly involved remain unknown. Thus, understanding the single-cell dynamics of integrin α4β7 during SIV infection may improve our understanding of SIV and HIV pathogenesis and clarify the role of integrin α4β7 signaling in mucosal trafficking.To examine the single-cell dynamics of integrin α4β7 expression during SIV infection, we used a novel, ex vivo, flow cytometry assay (M. Reynolds, unpublished data). We observed that infected, Gag p27⁺ cells expressed significantly (P = 0.0085) lower levels of integrin α4β7 than uninfected, CD4⁺ T cells from the same animal, at the same time point. Thus, we hypothesized that SIV decreases integrin α4β7 expression on the surfaces of virus-infected cells. In vitro, integrin α4β7 expression was downregulated on SIVmac239-infected cells as rapidly as 24 h postinfection. Unexpectedly, integrin α4β7 levels were also perturbed on uninfected cells with an increase in number of cells with intermediate integrin α4β7 expression. The modulation of integrin α4β7 was dependent on de novo synthesis of a viral protein(s), but neither cell death, release of a soluble factor, nor a change in activation state were involved. Combined, this finding suggests an as-yet-unidentified viral effect on integrin α4β7 that may influence depletion of the mucosal associated lymphoid compartments, susceptibility to superinfection, and/or immune evasion during SIV infection.     

Mutations in the α-helix Directly C-terminal to the Major Homology Region of Human Immunodeficiency Virus Type 1 Capsid Protein Disrupt Gag Multimerization and Markedly Impair Virus Particle Production

The X-ray crystallographic structure of HIV-1 capsid protein suggests that the dimer interface of the dimerization domain is mainly formed from a putative α-helix structure of 14 amino acids (Gag residues 311–324) and lies directly C-terminal to the capsid major homology region. We found that a deletion mutation in the α-helix drastically reduces virus particle production. Alanine-scanning mutagenetic analysis indicated that substitution mutations at residues Q311, V313, K314, W316, and M317 all impair virus particle production markedly. Membrane flotation assays suggested that some mutations in the dimer interface have slight effects on the efficient binding of Gag to membranes. Indirect immunofluorescence studies revealed that mutants defective in virus production exhibit a subcellular distribution pattern similar to that of wild-type. However, velocity sedimentation analysis showed that mutations significantly impairing virus particle production were also detrimental to Gag multimerization, suggesting that the impaired virus production may be due to a defect in Gag multimerization. These results support the proposal that residues in the capsid dimer interface play a crucial role in promoting Gag multimerization, possibly by facilitating stable Gag–Gag interactions.     

Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B—Response

Abstract The year of origin estimated by Lukashov and Goudsmit for HIV-1 subtype B is 1976 (95% CI, 1974–1977); this is significantly different from our prior estimate, 1967 (95% CI, 1960–1971). We review published evidence, which suggests that their estimate is too late.     

“Resistance” to PSC-RANTES Revisited: Two Mutations in Human Immunodeficiency Virus Type 1 HIV-1SF162 or Simian-Human Immunodeficiency Virus SHIVSF162-p3 Do Not Confer Resistance

Resistance of human immunodeficiency virus type 1 (HIV-1) to small-molecule CCR5 inhibitors is well demonstrated, but resistance to macromolecular CCR5 inhibitors (e.g., PSC-RANTES) that act by both CCR5 internalization and receptor blockade had not been reported until recently (3). The report of a single simian-human immunodeficiency virus SHIV_SF162-p3 variant with one V3 and one gp41 sequence change in gp160 that conferred both altered replicative fitness and resistance to PSC-RANTES was therefore surprising. We introduced the same two mutations into both the parental HIV-1_SF162 and the macaque-adapted SHIV_SF162-p3 and found minor differences in entry fitness but no changes in sensitivity to inhibition by either PSC-RANTES or the small-molecule allosteric inhibitor TAK-779. We attribute the earlier finding to confounding fitness effects with inhibitor sensitivity.A recent study by Dudley et al. (3) claimed to be “the first to describe the immediate selection and infection of a drug-resistant SHIV [simian-human immunodeficiency virus] variant in the face of a protective vaginal microbicide, PSC-RANTES.” The article further concluded, “This rhesus CCR5-specific/PSC-RANTES resistance selection is particularly alarming given the relative homogeneity of the SHIV_SF162-p3 stock compared to the potential exposure to a heterogeneous HIV-1 [human immunodeficiency virus type 1] population in human transmission.” The study described a SHIV_SF162-p3 variant with two amino acid substitutions, K315R in the V3 loop region (present as a minor component of the p3 challenge stock) and N640D in HR2 of gp41, that conferred greater replicative fitness and greater relative resistance to both the CCR5 inhibitor PSC-RANTES (to which the single macaque harboring this variant had been exposed prior to infection) and the small-molecule allosteric CCR5 inhibitor TAK-779 (1).While the development of HIV-1 strains resistant to small-molecule CCR5 inhibitors has been observed (11, 14), this result was surprising for several reasons. First, the inhibitory mechanism of PSC-RANTES is different from those of the small-molecule allosteric inhibitors; the ability of the macromolecule to induce profound and prolonged intracellular coreceptor sequestration, together with its ability to sterically block coreceptor use, should provide additional barriers to the development of resistant viruses that retain use of CCR5 (10). Second, this interpretation is supported by the failure to generate PSC-RANTES-resistant strains in multiple long-term in vitro selection studies (R.N. and D.E.M., unpublished results). Finally, the development of escape mutants in an in vivo setting would be expected to require sustained inhibitory concentrations of the drug at sites of replication. The Dudley et al. study was based on a single-dose experiment under conditions in which even at the highest dose used, no detectable systemic exposure occurred (6).The determination of resistance can be confounded by the fitness of a virus isolate (7), and the claim of resistance to PSC-RANTES was surprising given that infection with the parental HIV-1_SF162 isolate with the consensus GPGR₃₁₅ sequence is highly susceptible to PSC-RANTES inhibition (D.E.M., unpublished data) (Fig. ​(Fig.11 and Table ​Table1).1). These concerns prompted us to determine the impact of the K315R and N640D sequence variants on the entry fitness and sensitivity of both HIV-1_SF162 and SHIV_SF162-p3 to PSC-RANTES or TAK-779 in a single-round infection assay using either human or rhesus CCR5-expressing U87.CD4 target cells. We felt that it was important to extend the experiments of Dudley et al. (3) to HIV-1 since it is inhibition of HIV-1 infection of humans that is the intended application of a microbicide containing PSC-RANTES or related recombinant molecules (4, 12). We used site-directed mutagenesis to create three variants of the wild-type SF162 env sequence (R315, N640): K315, N640; R315, D640 (equivalent to the “resistant” SHIV_SF162-p3 variant from macaque 584), and K315, D640. These four env genes were used to complement a luciferase reporter HIV-1 construct in a standard single-round infection assay that has the advantage of a dynamic range of up to 8 logs (9, 15). We found that D640 conferred a small but significant entry advantage over N640 in the single-cycle assay (Table ​(Table1),1), in agreement with the results reported by Dudley et al. (3). However, none of the SF162 mutations conferred any significant resistance to either PSC-RANTES or TAK-779 (Fig. ​(Fig.11 and Table ​Table1),1), whether or not we corrected for the modest difference in entry efficiency. We repeated these experiments using the SHIV_SF162-p3 env clone that has the same sequence as that used in the experiments of Dudley et al. (3, 5) to determine if the finding of resistance was related to the other sequence differences between the macaque-adapted SHIV and SF162. Neither R315, D640, nor the combination of the two “resistance” mutations conferred resistance to either PSC-RANTES or TAK-779 on target cells expressing either human or rhesus CCR5 (Table ​(Table11 and Fig. 1C and D). The D640 substitution again conveyed a small entry advantage over N640 (data not shown). We thus conclude that the two mutations in SHIV_SF162-p3 that were claimed to confer resistance to PSC-RANTES using either human or rhesus CCR5 for entry were selected by replicative fitness in macaque 584 and not by drug resistance. We find no evidence that the two mutations have any impact on the PSC-RANTES sensitivity of either HIV-1_SF162 or SHIV_SF162-p3 (Fig. ​(Fig.1),1), and we were unable to confirm the 5.5-fold increase in resistance to PSC-RANTES on target cells expressing human CCR5 or the 7-fold increase on target cells expressing rhesus CCR5 reported by Dudley et al. (3). We therefore attribute the conclusions of Dudley et al. (3) to confounding fitness effects with inhibitor sensitivity. Multiple rounds of replication in the assays employed by Dudley et al. (3) likely amplified the relatively minor differences in entry fitness that we (and they) observed and made the precise assessment of 50% inhibitory concentration (IC₅₀) values more difficult, particularly given that 10-fold dilutions of inhibitors were used in their experiments.Open in a separate windowFIG. 1.Inhibition of HIV-1_SF162 env mutants by PSC-RANTES. (A) Single-round infection assay performed with U87.CD4.human CCR5 target cells using the four SF162 sequence variants with half-log dilutions of PSC-RANTES added 30 min prior to infection. Data are relative light units (RLU) and are summarized in a different format in the first row of data in Table ​Table1.1. (B) Means ± standard errors (SE) of the 50% inhibitory concentration of PSC-RANTES on each SF162 variant from three replicate experiments plotted as the reciprocal of the log IC₅₀ (pIC₅₀) in moles. Higher pIC₅₀ values indicate greater sensitivity to inhibition, but the differences depicted are not statistically significant. (C) Means ± SE of the 50% inhibitory concentrations of PSC-RANTES from three replicate experiments using the four sequence variants of SHIV_SF162-p3 with target cells expressing human CCR5. Note the different order of the columns for the SHIV_SF162-p3 variants; the “wild-type” SHIV has a different V3 sequence than the “wild-type” HIV-1_SF162, as well as 31 amino acid substitutions in other regions of envelope (5). (D) Means ± SE of the 50% inhibitory concentration of PSC-RANTES from three replicate experiments using the four sequence variants of SHIV_SF162-p3 with rhesus CCR5-expressing U87.CD4 target cells. WT, wild type; M, moles.

TABLE 1.

HIV-1 SF162 or SHIV_SF162-p3 V3 and/or HR2 mutations do not confer resistance to CCR5 inhibitors for entry via either human or rhesus CCR5

Use of recombinant interferon-α in Human Immunodeficiency Virus (HIV)-infected individuals

Rationale and objective Interferon alpha (IFN-) has anti-retroviral activity and is a possible HIV infection-limiting factor. The aim of this work is to prevent or delay disease progression in asymptomatic Human Immunodeficiency Virus (HIV) carriers.Design and interventions Recombinant IFN alpha-2b (3×10⁶ IU 3 times weekly) was compared. to no treatment (control) in a randomized trial. Endpoints were: (i) appearance of any CDC group IV symptoms and (ii) disease progression (which excluded shifts to group IVC2 or reversible IVA, or IVB). The trial lasted from October 1987 to February 1992.Setting The trial was performed at the Santiago de las Vegas sanatorium, a specialized institution for the care of HIV-infected and AIDS patients.Population Subjects were anti-HIV-1 seropositive, Western blot-confirmed, asymptomatic (CDC group II), or with generalized lymphadenopathies (CDC group III). The groups had 79 (control) and 71 (IFN) patients.Main results Long-term IFN- treatments significantly reduced the proportion of patients who shifted to any group IV (control: 46/79; IFN: 14/71;p<0.001) or developed AIDS (control: 27/79; IFN: 12/71;p<0.05). IFN also delayed progression to AIDS (95% confidence interval for 0.5 probability of progression) from 67–83 to 116–180 months after infection. The IFN group had significantly less opportunistic infections and non-infectious complications. CD4 cell count and hemoglobin decreased in the control but not in the IFN group. Fewer IFN-treated patients developed positive serum HIV antigen detection.Conclusion IFN alpha treatment during the early stages of infection seems to be beneficial to the patients.Abbreviations CI confidence interval - AIDS Acquired Immunodeficiency syndrome - HIV Human Immunodeficiency Virus - IFN Interferon - CDC Center for Disease Control (USA) - SD standard deviation     

What Does Virus Evolution Tell Us about Virus Origins?

Despite recent advances in our understanding of diverse aspects of virus evolution, particularly on the epidemiological scale, revealing the ultimate origins of viruses has proven to be a more intractable problem. Herein, I review some current ideas on the evolutionary origins of viruses and assess how well these theories accord with what we know about the evolution of contemporary viruses. I note the growing evidence for the theory that viruses arose before the last universal cellular ancestor (LUCA). This ancient origin theory is supported by the presence of capsid architectures that are conserved among diverse RNA and DNA viruses and by the strongly inverse relationship between genome size and mutation rate across all replication systems, such that pre-LUCA genomes were probably both small and highly error prone and hence RNA virus-like. I also highlight the advances that are needed to come to a better understanding of virus origins, most notably the ability to accurately infer deep evolutionary history from the phylogenetic analysis of conserved protein structures.     

Infection with “Escaped” Virus Variants Impairs Control of Simian Immunodeficiency Virus SIVmac239 Replication in Mamu-B*08-Positive Macaques

An understanding of the mechanism(s) by which some individuals spontaneously control human immunodeficiency virus (HIV)/simian immunodeficiency virus replication may aid vaccine design. Approximately 50% of Indian rhesus macaques that express the major histocompatibility complex (MHC) class I allele Mamu-B*08 become elite controllers after infection with simian immunodeficiency virus SIVmac239. Mamu-B*08 has a binding motif that is very similar to that of HLA-B27, a human MHC class I allele associated with the elite control of HIV, suggesting that SIVmac239-infected Mamu-B*08-positive (Mamu-B*08⁺) animals may be a good model for the elite control of HIV. The association with MHC class I alleles implicates CD8⁺ T cells and/or natural killer cells in the control of viral replication. We therefore introduced point mutations into eight Mamu-B*08-restricted CD8⁺ T-cell epitopes to investigate the contribution of epitope-specific CD8⁺ T-cell responses to the development of the control of viral replication. Ten Mamu-B*08⁺ macaques were infected with this mutant virus, 8X-SIVmac239. We compared immune responses and viral loads of these animals to those of wild-type SIVmac239-infected Mamu-B*08⁺ macaques. The five most immunodominant Mamu-B*08-restricted CD8⁺ T-cell responses were barely detectable in 8X-SIVmac239-infected animals. By 48 weeks postinfection, 2 of 10 8X-SIVmac239-infected Mamu-B*08⁺ animals controlled viral replication to <20,000 viral RNA (vRNA) copy equivalents (eq)/ml plasma, while 10 of 15 wild-type-infected Mamu-B*08⁺ animals had viral loads of <20,000 vRNA copy eq/ml (P = 0.04). Our results suggest that these epitope-specific CD8⁺ T-cell responses may play a role in establishing the control of viral replication in Mamu-B*08⁺ macaques.A few individuals spontaneously control the replication of human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) to very low levels. The precise mechanisms underlying this control are of great interest, as a clear understanding of what constitutes a successful immune response may aid in developing an AIDS vaccine. Particularly pressing questions for vaccine design include which proteins to use as immunogens, the extent to which increasing the breadth and magnitude of responses is advantageous, how immunodomination affects T-cell responses, and if biasing the immune response toward particular effector profiles is beneficial. Characterization of immune responses made by elite controllers (ECs) may reveal patterns that can then be applied to vaccine formulation and evaluation.HIV ECs are generally not infected with grossly unfit viruses (6, 42). Instead, elite control of immunodeficiency virus replication is correlated with the presence of particular major histocompatibility complex class I (MHC-I) alleles (11, 12, 18, 32, 41, 55). The association of MHC-I alleles with the control of viremia implicates CD8⁺ T cells as being mediators of this immune containment. Several lines of evidence support this hypothesis. These lines of evidence include the correlation between the appearance of CD8⁺ T-cell responses and the resolution of peak viremia during acute infection (7, 29), the finding that alleles associated with viral control restrict dominant acute-phase CD8⁺ T-cell responses (3), and the finding that responses directed against epitopes restricted by these alleles frequently select for viral escape variants (4, 27, 38). Perhaps most compelling is the observation that for a few HIV-infected individuals, the selection of escape variants by an immunodominant HLA-B27-restricted T-cell response temporally preceded substantial increases in viremia (17, 21, 53). While viruses exhibiting escape variants in epitopes restricted by protective alleles are often detectably less fit in vitro (10, 38, 43, 51), recent data have found normal, high levels of replication in vivo upon the transmission of some of these variants (15).The association of control with MHC-I alleles does not, of course, implicate solely CD8⁺ T cells. MHC-I molecules are also ligands for killer immunoglobulin receptors (KIRs), which are predominantly expressed on natural killer (NK) cells. Genetic studies of HIV-infected humans suggest a model in which individuals with particular KIR/HLA combinations are predisposed to control HIV replication more readily than those with other KIR/HLA combinations (36, 37). These data were supported by functional studies of this KIR/HLA pairing in vitro, which demonstrated an inhibition of HIV replication by such NK cells (2). The relative contributions of NK and CD8⁺ T-cell responses to control have yet to be elucidated and may be closely intertwined.Previously, the experimental depletion of circulating CD8⁺ cells from SIVmac239-infected ECs resulted in a sharp spike in viremia, which resolved as CD8⁺ cells repopulated the periphery (19). During the reestablishment of control of SIV replication, CD8⁺ T cells targeting multiple epitopes restricted by alleles associated with elite control expanded in frequency, providing strong circumstantial evidence for their role in maintaining elite control (19, 31). However, CD8 depletion antibodies used in macaques also remove NK cells, which, at least in vitro, also inhibit SIV replication (19). It was therefore difficult to make definitive conclusions regarding the separate contributions of these subsets to maintaining the control of SIV replication in vivo.Here we investigate elite control in the rhesus macaque model for AIDS. We focused on the macaque MHC-I allele most tightly associated with the control of SIVmac239, Mamu-B*08. Approximately 50% of Mamu-B*08-positive (Mamu-B*08⁺) animals infected with SIVmac239 become ECs (32). Peptides presented by Mamu-B*08 share a binding motif with peptides presented by HLA-B27. Although these two MHC-I genes are dissimilar in domains that are important for peptide binding, each molecule can bind peptides that are presented by the other molecule (33). This striking similarity suggests that the elite control of SIVmac239 in Mamu-B*08⁺ animals is a good model for the elite control of HIV.Seven SIVmac239 epitopes restricted by Mamu-B*08 accrue variation in Mamu-B*08⁺ rhesus macaques (30, 31). For an eighth Mamu-B*08-restricted epitope, which is also restricted by Mamu-B*03 (Mamu-B*03 differs from Mamu-B*08 by 2 amino acids in the α1 and α2 domains [9, 32]), escape has been documented only for SIV-infected Mamu-B*03⁺ macaques (16). Variation in these CD8⁺ T-cell epitopes accumulates with different kinetics, starting during acute infection for those targeted by high-magnitude responses.In this study, we addressed the question of whether the elite control of SIVmac239 in Mamu-B*08⁺ animals is mediated by the known high-frequency CD8⁺ T-cell responses targeting Mamu-B*08-restricted epitopes. To this end, we introduced point mutations into eight epitopes, with the goal of reducing or abrogating immune responses directed against these epitopes during acute infection. We hypothesized that Mamu-B*08⁺ macaques would be unable to control SIV replication without these Mamu-B*08-restricted T-cell responses.