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1.  Immunogenicity of Seven New Recombinant Yellow Fever Viruses 17D Expressing Fragments of SIVmac239 Gag, Nef, and Vif in Indian Rhesus Macaques 
PLoS ONE  2013;8(1):e54434.
An effective vaccine remains the best solution to stop the spread of human immunodeficiency virus (HIV). Cellular immune responses have been repeatedly associated with control of viral replication and thus may be an important element of the immune response that must be evoked by an efficacious vaccine. Recombinant viral vectors can induce potent T-cell responses. Although several viral vectors have been developed to deliver HIV genes, only a few have been advanced for clinical trials. The live-attenuated yellow fever vaccine virus 17D (YF17D) has many properties that make it an attractive vector for AIDS vaccine regimens. YF17D is well tolerated in humans and vaccination induces robust T-cell responses that persist for years. Additionally, methods to manipulate the YF17D genome have been established, enabling the generation of recombinant (r)YF17D vectors carrying genes from unrelated pathogens. Here, we report the generation of seven new rYF17D viruses expressing fragments of simian immunodeficiency virus (SIV)mac239 Gag, Nef, and Vif. Studies in Indian rhesus macaques demonstrated that these live-attenuated vectors replicated in vivo, but only elicited low levels of SIV-specific cellular responses. Boosting with recombinant Adenovirus type-5 (rAd5) vectors resulted in robust expansion of SIV-specific CD8+ T-cell responses, particularly those targeting Vif. Priming with rYF17D also increased the frequency of CD4+ cellular responses in rYF17D/rAd5-immunized macaques compared to animals that received rAd5 only. The effect of the rYF17D prime on the breadth of SIV-specific T-cell responses was limited and we also found evidence that some rYF17D vectors were more effective than others at priming SIV-specific T-cell responses. Together, our data suggest that YF17D – a clinically relevant vaccine vector – can be used to prime AIDS virus-specific T-cell responses in heterologous prime boost regimens. However, it will be important to optimize rYF17D-based vaccine regimens to ensure maximum delivery of all immunogens in a multivalent vaccine.
doi:10.1371/journal.pone.0054434
PMCID: PMC3545953  PMID: 23336000
2.  Characteristics of Generalized Anxiety Disorder in Patients With Dementia 
Background
Overlap of cognitive and anxiety symptoms (i.e., difficulty concentrating, fatigue, restlessness) contributes to inconsistent, complicated assessment of generalized anxiety disorder (GAD)in persons with dementia.
Methods
Anxious dementia patients completed a psychiatric interview, the Penn State Worry Questionnaire-Abbreviated, and the Rating for Anxiety in Dementia scale. Analyses to describe the 43 patients with and without GAD included the Wilcoxon Mann-Whitney two-sample test, Fisher’s exact test. Predictors of GAD diagnosis were identified using logistic regression.
Results
Those with GAD were more likely to be male, have less severe dementia and endorsed more worry, and anxiety compared to patients without GAD. Gender, muscle tension and fatigue differentiated those with GAD from those without GAD.
Conclusions
Although this study is limited by a small sample, it describes clinical characteristics of GAD in dementia, highlighting the importance of muscle tension and fatigue in recognizing GAD in persons with dementia.
doi:10.1177/1533317511426867
PMCID: PMC3252749  PMID: 22062223
Generalized anxiety disorder; dementia; anxiety symptoms; dementia symptoms; differential diagnosis for generalized anxiety disorder/dementia
3.  DNA/Ad5 vaccination with SIV epitopes induced epitope-specific CD4+ T cells, but few subdominant epitope-specific CD8+ T cells 
Vaccine  2011;29(43):7483-7490.
The goals of a T cell-based vaccine for HIV are to reduce viral peak and setpoint and prevent transmission. While it has been relatively straightforward to induce CD8+ T cell responses against immunodominant T cell epitopes, it has been more difficult to broaden the vaccine-induced CD8+ T cell response against subdominant T cell epitopes. Additionally, vaccine regimens to induce CD4+ T cell responses have been studied only in limited settings. In this study, we sought to elicit CD8+ T cells against subdominant epitopes and CD4+ T cells using various novel and well-established vaccine strategies. We vaccinated three Mamu-A*01+ animals with five Mamu-A*01-restricted subdominant SIV-specific CD8+ T cell epitopes. All three vaccinated animals made high frequency responses against the Mamu-A*01-restricted Env TL9 epitope with one animal making a low frequency CD8+ T cell response against the Pol LV10 epitope. We also induced SIV-specific CD4+ T cells against several MHC class II DRBw*606-restricted epitopes. Electroporated DNA with pIL-12 followed by a rAd5 boost was the most immunogenic vaccine strategy. We induced responses against all three Mamu-DRB*w606-restricted CD4 epitopes in the vaccine after the DNA prime. Ad5 vaccination further boosted these responses. Although we successfully elicited several robust epitope-specific CD4+ T cell responses, vaccination with subdominant MHC class epitopes elicited few detectable CD8+ T cell responses. Broadening the CD8+ T cell response against subdominant MHC class I epitopes was, therefore, more difficult than we initially anticipated.
doi:10.1016/j.vaccine.2011.07.048
PMCID: PMC3186839  PMID: 21839132
4.  Treatment Response for Late-Life Generalized Anxiety Disorder: Moving Beyond Symptom-Based Measures 
Response to treatment for late-life generalized anxiety disorder has been defined by a variety of methods, all based on statistically significant reductions in symptom severity. However, it is unknown whether these improvements in symptom severity are associated with meaningful differences in everyday functioning. The current study used four methods to define response to treatment for 115 primary care patients, age 60 and older, with a principal or co-principal diagnosis of generalized anxiety disorder. The methods examined included percent improvement, reliable change index and minimal clinically significant differences. Agreement among classification methods and their associations with general and mental health related quality of life were assessed. Results indicated moderate agreement among symptom-based classification methods and significant associations with measures of quality of life.
doi:10.1097/NMD.0b013e31822feda6
PMCID: PMC3187557  PMID: 21964278
GAD; older adults; treatment response; quality of life
5.  The Majority of Freshly Sorted Simian Immunodeficiency Virus (SIV)-Specific CD8+ T Cells Cannot Suppress Viral Replication in SIV-Infected Macrophages 
Journal of Virology  2012;86(8):4682-4687.
Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) primarily infect activated CD4+ T cells but can infect macrophages. Surprisingly, ex vivo tetramer-sorted SIV-specific CD8+ T cells that eliminated and suppressed viral replication in SIV-infected CD4+ T cells failed to do so in SIV-infected macrophages. It is possible, therefore, that while AIDS virus-infected macrophages constitute only a small percentage of all virus-infected cells, they may be relatively resistant to CD8+ T cell-mediated lysis and continue to produce virus over long periods of time.
doi:10.1128/JVI.06324-11
PMCID: PMC3318662  PMID: 22318140
6.  Chinese origin rhesus macaque major histocompatibility complex class I molecules promiscuously present epitopes from SIV associated with molecules of Indian origin; implications for immunodominance and viral escape 
Immunogenetics  2011;63(9):587-597.
The presentation of identical peptides by different major histocompatibility complex class I (MHC-I) molecules, termed promiscuity, is a controversial feature of T cell-mediated immunity to pathogens. The astounding diversity of MHC-I molecules in human populations, presumably to enable binding of equally diverse peptides, implies promiscuity would be a rare phenomenon. However, if it occurs, it would have important implications for immunity. We screened 77 animals for responses to peptides known to bind MHC-I molecules that were not expressed by these animals. Some cases of supposed promiscuity were determined to be the result of either non-identical optimal peptides or were simply not mapped to the correct MHC-I molecule in previous studies. Cases of promiscuity, however, were associated with alterations of immunodominance hierarchies, either in terms of the repertoire of peptides presented by the different MHC-I molecules or in the magnitude of the responses directed against the epitopes themselves. Specifically, we found that the Mamu-B*017:01-restricted peptides Vif HW8 and cRW9 were also presented by Mamu-A2*05:26 and targeted by an animal expressing that allele. We also found that the normally subdominant Mamu-A1*001:01 presented peptide Gag QI9 was also presented by Mamu-B*056:01. Both A2*05:26 and B*056:01 are molecules typically or exclusively expressed by animals of Chinese origin. These data clearly demonstrate that MHC-I epitope promiscuity, though rare, might have important implications for immunodominance and for the transmission of escape mutations, depending on the relative frequencies of the given alleles in a population.
doi:10.1007/s00251-011-0538-4
PMCID: PMC3156284  PMID: 21626440
Simian immunodeficiency virus; Epitope promiscuity; Major histocompatibility complex; CD8+ T lymphocyte; Macaca mulatta
7.  CD8+ T Cell Escape Mutations in Simian Immunodeficiency Virus SIVmac239 Cause Fitness Defects In Vivo, and Many Revert after Transmission▿† 
Journal of Virology  2011;85(23):12804-12810.
Virus-specific CD8+ T lymphocytes select for escape mutations in human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). To assess the effects of these mutations on viral fitness, we introduced escape mutations into 30 epitopes (bound by five major histocompatibility complex class I [MHC-I] molecules) in three different viruses. Two of these MHC-I alleles are associated with elite control. Two of the three viruses demonstrated reduced fitness in vivo, and 27% of the introduced mutations reverted. These findings suggest that T cell epitope diversity may not be such a daunting problem for the development of an HIV vaccine.
doi:10.1128/JVI.05841-11
PMCID: PMC3209381  PMID: 21957309
8.  Pyrosequencing Reveals Restricted Patterns of CD8+ T Cell Escape-Associated Compensatory Mutations in Simian Immunodeficiency Virus ▿ ‡  
Journal of Virology  2011;85(24):13088-13096.
CD8+ T cells play a major role in the containment of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication. CD8+ T cell-driven variations in conserved regions under functional constraints result in diminished viral replicative capacity. While compensatory mutations outside an epitope can restore replicative capacity, the kinetics with which they arise remains unknown. Additionally, certain patterns of linked mutations associated with CD8+ T cell epitope escape in these highly conserved regions may lead to variable levels of viral fitness. Here, we used pyrosequencing to investigate the kinetics and patterns of mutations surrounding the Mamu-A1*00101-bound Gag181-189CM9 CD8+ T cell epitope. We obtained more than 400 reads for each sequencing time point, allowing us to confidently detect the emergence of viral variants bearing escape mutations with frequencies as low as 1% of the circulating virus. With this level of detail, we demonstrate that compensatory mutations generally arise concomitantly with Gag181-189CM9 escape mutations. We observed distinct patterns of linked flanking mutations, most of which were found downstream of Gag181-189CM9. Our data indicate that, whereas Gag181-189CM9 escape is much more complex that previously appreciated, it occurs in a coordinated fashion, with very specific patterns of flanking mutations required for immune evasion. This is the first detailed report of the ontogeny of compensatory mutations that allow CD8+ T cell epitope escape in infected individuals.
doi:10.1128/JVI.05650-11
PMCID: PMC3233179  PMID: 21994463
9.  Heat shock protein 27 (HSP27): biomarker of disease and therapeutic target 
Heat shock protein 27 (HSP27) is a multidimensional protein which acts as a protein chaperone and an antioxidant and plays a role in the inhibition of apoptosis and actin cytoskeletal remodeling. In each of these capacities, HSP27 has been implicated in different disease states playing both protective and counter-protective roles. The current review presents HSP27 in multiple disease contexts: renal injury and fibrosis, cancer, neuro-degenerative and cardiovascular disease, highlighting its role as a potential biomarker and therapeutic target.
doi:10.1186/1755-1536-5-7
PMCID: PMC3464729  PMID: 22564335
10.  Cognitive Behavior Therapy for Generalized Anxiety Disorder Among Older Adults in Primary Care: A Randomized Clinical Trial 
Jama  2009;301(14):1460-1467.
Context
Cognitive behavior therapy (CBT) is effective for late-life generalized anxiety disorder (GAD), but, only pilot studies have been conducted in primary care, where older adults most often seek treatment. .
Objective
To examine effects of CBT relative to enhanced usual care (EUC) in older adults with GAD in primary care.
Design, Setting, and Participants
A randomized clinical trial with 134 older adults (mean age, 66.9 years) recruited from March 2004 to August 2006 in two primary care settings. Treatment was provided for 3 months; assessments were conducted at baseline, post-treatment (3 months), and over a 12-month follow-up (6, 9, 12, and 15 months).
Intervention
CBT (n = 70) was conducted in the primary care clinics. Treatment included education and awareness, relaxation training, cognitive therapy, exposure, problem-solving skills training, and behavioral sleep management. Patients assigned to EUC (n = 64) received biweekly calls to ensure patient safety and provide minimal support.
Main Outcome Measures
Primary outcomes included worry severity (Penn State Worry Questionnaire) and GAD severity (GAD Severity Scale).. Secondary outcomes included anxiety (Hamilton Anxiety Rating Scale, Beck Anxiety Inventory), coexistent depressive symptoms (Beck Depression Inventory II), and physical/mental health quality of life (SF-12).
Results
CBT significantly improved worry severity [45.6; 95% CI 44.4 to 47.8; vs. 54.4; 95% CI 51.4 to 57.3; p < .0001), depressive symptoms (10.2; 95% CI 8.5 to 11.9; vs. 12.8; 95% CI 10.5 to 15.1; p = .02), and general mental health (49.6; 95% CI 47.4 to 51.8; vs. 45.3; 95% CI 42.6 to 47.9; p=.008) compared with EUC. . According to intent-to-treat analyses, response rates defined according to worry severity were higher following CBT than EUC at 3 months (40.0% [28/70] vs. 21.9% [14/64], p = .02).
Conclusion
Compared to EUC, CBT resulted in greater improvement in worry severity, depressive symptoms, and general mental health for older patients with GAD in primary care.
doi:10.1001/jama.2009.458
PMCID: PMC3328789  PMID: 19351943
11.  Early Response to Psychotherapy and Long-term Change in Worry Symptoms in Older Adults with Generalized Anxiety Disorder 
Objectives
To determine the association of early and long-term reductions in worry symptoms after cognitive behavioral therapy for generalized anxiety disorder (GAD) in older adults.
Design
Substudy of larger randomized controlled trial
Setting
Family medicine clinic and large multi-specialty health organization in Houston, TX, between March 2004 and August 2006
Participants
Patients (N=76) 60 years or older with a principal or coprincipal diagnosis of GAD, excluding those with significant cognitive impairment, bipolar disorder, psychosis or active substance abuse.
Intervention
Cognitive behavioral therapy, up to 10 sessions over 12 weeks, or enhanced usual care (regular, brief telephone calls and referrals to primary care provider as needed)
Measurements
Penn State Worry Questionnaire (PSWQ) administered by telephone at baseline, 1 month (mid-treatment), 3 months (post-treatment), and at 3-month intervals through 15 months (1-year follow-up). We used binary logistic regression analysis to determine the association between early (1-month) response and treatment responder status (reduction of more than 8.5 points on the PSWQ) at 3 and 15 months. We also used hierarchical linear modeling to determine the relationship of early response to the trajectory of score change after post-treatment.
Results
Reduction in PSWQ scores after the first month predicted treatment response at post-treatment and follow-up, controlling for treatment arm and baseline PSWQ score. The magnitude of early reduction also predicted the slope of score change from post-treatment through the 15-month assessment.
Conclusions
Early symptom reduction is associated with long-term outcomes after psychotherapy in older adults with GAD.
doi:10.1097/JGP.0b013e3181f18061
PMCID: PMC3058752  PMID: 21427643
psychotherapy; generalized anxiety disorder; older adults
12.  The involvement of multiple caregivers in cognitive-behavior therapy for anxiety in persons with dementia 
Aging & mental health  2011;15(3):291-298.
Objectives
Peaceful Mind, a cognitive-behavioral therapy for treating anxiety in persons with dementia, is a promising new treatment currently under investigation. This article reports results of our examination of a modification of the treatment protocol in two cases that included multiple caregivers in treating two persons with dementia.
Method
Two case presentations of the benefits and challenges of including multiple caregivers in treatment are discussed. Treatment outcome data for these cases were collected as part of a larger investigation of Peaceful Mind.
Results
The involvement of multiple collaterals resulted in several benefits, including increased family communication, as well as increased opportunities for the practice of new skills. These cases have also presented unique challenges requiring alterations in therapy structure and attention to issues of family conflict.
Conclusions
Including multiple collaterals in cognitive-behavioral therapy for treating anxiety in persons with dementia is feasible and may be beneficial in maximizing treatment gains and increasing the family’s investment in therapy.
doi:10.1080/13607860903493374
PMCID: PMC3086554  PMID: 21491216
cognitive-behavioral therapy; anxiety; dementia
13.  The TRIM5α Genotype of Rhesus Macaques Affects Acquisition of Simian Immunodeficiency Virus SIVsmE660 Infection after Repeated Limiting-Dose Intrarectal Challenge ▿ 
Journal of Virology  2011;85(18):9637-9640.
It has recently been shown that polymorphism at the rhesus macaque TRIM5 locus can affect simian immunodeficiency virus (SIV) replication. Here we show that TRIM5 alleles can also affect acquisition of SIVsmE660. Animals coexpressing the TRIM5TFP and TRIM5CypA alleles took significantly longer to become infected with SIVsmE660, but not SIVmac239, after repeated limiting-dose intrarectal challenge than did animals expressing other TRIM5 allele combinations. Our results indicate that the TRIM5 alleles can be a barrier to productive infection and that this should be taken into account when designing acquisition studies using SIVsmE660 or related viruses.
doi:10.1128/JVI.05074-11
PMCID: PMC3165772  PMID: 21734037
14.  A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules 
Immunogenetics  2012;64(6):421-434.
The SIV-infected rhesus macaque (Macaca mulatta) is the most established model of AIDS disease systems, providing insight into pathogenesis and a model system for testing novel vaccines. The understanding of cellular immune responses based on the identification and study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide-binding motif, provides valuable information to decipher outcomes of infection and vaccine efficacy. Detailed characterization of Mamu-B*039:01, a common allele expressed in Chinese rhesus macaques, revealed a unique MHC:peptide-binding preference consisting of glycine at the second position. Peptides containing a glycine at the second position were shown to be antigenic from animals positive for Mamu-B*039:01. A similar motif was previously described for the Dd mouse MHC allele, but for none of the human HLA molecules for which a motif is known. Further investigation showed that one additional macaque allele, present in Indian rhesus macaques, Mamu-B*052:01, shares this same motif. These “G2” alleles were associated with the presence of specific residues in their B pocket. This pocket structure was found in 6% of macaque sequences but none of 950 human HLA class I alleles. Evolutionary studies using the “G2” alleles points to common ancestry for the macaque sequences, while convergent evolution is suggested when murine and macaque sequences are considered. This is the first detailed characterization of the pocket residues yielding this specific motif in nonhuman primates and mice, revealing a new supertype motif not present in humans.
Electronic supplementary material
The online version of this article (doi:10.1007/s00251-011-0598-5) contains supplementary material, which is available to authorized users.
doi:10.1007/s00251-011-0598-5
PMCID: PMC3349854  PMID: 22322672
HLA supertype; MHC; Peptide-binding motif; Rhesus macaque
15.  Reduction of CD4+ T Cells In Vivo Does Not Affect Virus Load in Macaque Elite Controllers ▿  
Journal of Virology  2011;85(14):7454-7459.
A small percentage of human immunodeficiency virus (HIV)- and simian immunodeficiency virus (SIV)-infected individuals spontaneously control virus replication. The majority of these elite controllers mount high-frequency virus-specific CD4+ T cell responses. To evaluate the role these responses might play in viral control, we depleted two elite controller macaques of CD4+ cells. SIV-specific CD4+ T cell responses did not return to baseline levels until 8 weeks postdepletion. Viral loads remained stable throughout the experiment, suggesting that SIV-specific CD4+ T cell responses may not play a direct role in controlling chronic viral replication in these elite controllers.
doi:10.1128/JVI.00738-11
PMCID: PMC3126606  PMID: 21593153
16.  The Roles of Social Support and Self-efficacy in Physical Health's Impact on Depressive and Anxiety Symptoms in Older Adults 
Physical illness may precipitate psychological distress among older adults. This study examines whether social support and self-efficacy moderate the associations between physical health and depression and anxiety. Predictions were tested in 222 individuals age 60 or older presenting for help with worry. Physical health was assessed through self-report (subjective) and physical diagnoses (objective). Objective physical health did not have a significant association with depression or anxiety. Worse subjective physical health was associated with increased somatic anxiety, but not with depression or worry. The relationship between subjective physical health and depressive symptoms was moderated by self-efficacy and social support. As predicted, when self-efficacy was low, physical health had its strongest negative association with depressive symptoms such that as physical health improved, depressive symptoms also improved. However, the moderation effect was not as expected for social support; at high levels of social support, worse physical health was associated with increased depressive affect.
doi:10.1007/s10880-010-9211-6
PMCID: PMC3053526  PMID: 21110074
elderly; depression; anxiety; social support; self-efficacy; physical health
17.  CD8+ gamma-delta TCR+ and CD4+ T cells produce IFN-γat 5–7 days after yellow fever vaccination in Indian rhesus macaques, before the induction of classical antigen-specific T cell responses 
Vaccine  2010;28(51):8183-8188.
The yellow fever 17D (YF-17D) vaccine is one of the most efficacious vaccines developed to date. Interestingly, vaccination with YF-17D induces IFN-γ production early after vaccination (d 5–7) before the development of classical antigen-specific CD8+ and CD4+ T cell responses. Here we investigated the cellular source of this early IFN-γ production. At days 5 and 7 post vaccination activated CD8+ gamma-delta TCR T cells produced IFN-γ and TNF-α. Activated CD4+ T cells produced IFN-γ and TNF-α at day 7 post vaccination. This early IFN-γ production was also induced after vaccination with recombinant YF-17D (rYF-17D), but was not observed after recombinant Adenovirus type 5 (rAd5) vaccination. Early IFN-γ production, therefore, might be an important aspect of yellow fever vaccination.
doi:10.1016/j.vaccine.2010.09.090
PMCID: PMC3179417  PMID: 20939995
Yellow Fever vaccine; IFN-γ; Rhesus model
18.  Simian Immunodeficiency Virus-specific CD4+ T Cells from Successful Vaccinees Target the SIV Gag Capsid 
Immunogenetics  2010;62(10):701-707.
We recently demonstrated that vaccinated rhesus macaques controlled viral replication of a heterologous SIV challenge. Here, we analyzed anamnestic SIV-specific CD4+ T-cell responses expanding immediately after challenge and show that successful vaccinees consistently targeted a short region of the Gag-p27 Capsid (amino acids 249-291). We have also defined the Major Histocompatibility Complex Class II (MHC-II) restricting alleles for several of these responses and show that DQ-restricted CD4+ T-cells depend on unique combinations of both the DQA and DQB alleles. Analysis of SIV-specific CD4+ T-cell responses elicited by a successful vaccine may have important implications in the understanding of vaccine design.
doi:10.1007/s00251-010-0473-9
PMCID: PMC3018234  PMID: 20812010
HIV; SIV; CD4+ T-cells; Mamu-MHC; Major Histocompatibility Complex; Rhesus macaques
19.  Peaceful Mind: An Open Trial of Cognitive-Behavioral Therapy for Anxiety in Persons With Dementia 
International psychogeriatrics / IPA  2010;22(6):1012-1021.
Background
Anxiety has a high prevalence among individuals with dementia, and it has a significant negative impact on their functioning; yet intervention studies are lacking. We developed Peaceful Mind, a cognitive-behavioral intervention for persons with dementia. In this article, we describe the intervention and results of an open trial evaluating the feasibility and utility of the intervention and assessment procedures.
Methods
Peaceful Mind is implemented over a period of 3 months in the participant's home with involvement of a caregiver or “collateral.” Dyads are followed for an additional 3 months via telephone. An assortment of simplified skills is offered, including self-awareness, breathing, behavioral activation, calming thoughts, and sleep skills.
Results
Nine participants were enrolled, eight completed the 3-month assessment, and seven completed the 6-month assessment. Overall, participants and collaterals were satisfied with the intervention and reported that they benefited in terms of anxiety, depression, and collateral distress.
Conclusions
A randomized controlled trial would help determine whether this promising new treatment has a statistically significant impact on anxiety in this population.
doi:10.1017/S1041610210000694
PMCID: PMC3071800  PMID: 20550745
CBT; caregiver; intervention; home
20.  The live-attenuated yellow fever vaccine 17D induces broad and potent T cell responses against several viral proteins in Indian rhesus macaques – implications for recombinant vaccine design 
Immunogenetics  2010;62(9):593-600.
The yellow fever vaccine 17D (YF17D) is one of the most effective vaccines. Its wide use and favorable safety profile make it a prime candidate for recombinant vaccines. It is believed that neutralizing antibodies account for a large measure of the protection afforded to YF17D-vaccinated individuals, however cytotoxic T lymphocyte (CTL) responses have been described in the setting of YF17D vaccination. YF17D is an ssRNA flavivirus that is translated as a full-length polyprotein, several domains of which pass into the lumen of the endoplasmic reticulum (ER). The processing and presentation machinery for MHC class I-restricted CTL responses favor cytoplasmic peptides that are transported into the ER by the transporter associated with antigen presentation (TAP) proteins. In order to inform recombinant vaccine design, we sought to determine if YF17D-induced CTL responses preferentially targeted viral domains that remain within the cytoplasm. We performed whole YF17D proteome mapping of CTL responses in 6 Indian rhesus macaques vaccinated with YF17D using overlapping YF17D peptides. We found that the ER luminal E protein was the most immunogenic viral protein followed closely by the cytoplasmic NS3 and NS5 proteins. These results suggest that antigen processing and presentation in this model system is not preferentially affected by the subcellular location of the viral proteins that are the source of CTL epitopes. The data also suggest potential immunogenic regions of YF17D that could serve as the focus of recombinant T cell vaccine development.
doi:10.1007/s00251-010-0461-0
PMCID: PMC3136048  PMID: 20607226
Yellow Fever 17D; Vaccine; Cytotoxic T Lymphocyte; Indian Rhesus Macaque
21.  GagCM9-Specific CD8+ T Cells Expressing Limited Public TCR Clonotypes Do Not Suppress SIV Replication In Vivo 
PLoS ONE  2011;6(8):e23515.
Several lines of evidence suggest that HIV/SIV-specific CD8+ T cells play a critical role in the control of viral replication. Recently we observed high levels of viremia in Indian rhesus macaques vaccinated with a segment of SIVmac239 Gag (Gag45–269) that were subsequently infected with SIVsmE660. These seven Mamu-A*01+ animals developed CD8+ T cell responses against an immunodominant epitope in Gag, GagCM9, yet failed to control virus replication. We carried out a series of immunological and virological assays to understand why these Gag-specific CD8+ T cells could not control virus replication in vivo. GagCM9-specific CD8+ T cells from all of the animals were multifunctional and were found in the colonic mucosa. Additionally, GagCM9-specific CD8+ T cells accessed B cell follicles, the primary residence of SIV-infected cells in lymph nodes, with effector to target ratios between 20–250 GagCM9-specific CD8+ T cells per SIV-producing cell. Interestingly, vaccinated animals had few public TCR clonotypes within the GagCM9-specific CD8+ T cell population pre- and post-infection. The number of public TCR clonotypes expressed by GagCM9-specific CD8+ T cells post-infection significantly inversely correlated with chronic phase viral load. It is possible that these seven animals failed to control viral replication because of the narrow TCR repertoire expressed by the GagCM9-specific CD8+ T cell population elicited by vaccination and infection.
doi:10.1371/journal.pone.0023515
PMCID: PMC3162554  PMID: 21887264
23.  Macaque Long-Term Nonprogressors Resist Superinfection with Multiple CD8+ T Cell Escape Variants of Simian Immunodeficiency Virus▿  
Journal of Virology  2010;85(1):530-541.
Human immunodeficiency virus (HIV)-positive individuals can be superinfected with different virus strains. Individuals who control an initial HIV infection are therefore still at risk for subsequent infection with divergent viruses, but the barriers to such superinfection remain unclear. Here we tested long-term nonprogressors' (LTNPs') susceptibility to superinfection using Indian rhesus macaques that express the major histocompatibility complex class I (MHC-I) allele Mamu-B*17, which is associated with control of the pathogenic AIDS virus SIVmac239. The Mamu-B*17-restricted CD8+ T cell repertoire is focused almost entirely on 5 epitopes. We engineered a series of SIVmac239 variants bearing mutations in 3, 4, or all 5 of these epitopes and used them to serially challenge 2 Mamu-B*17-positive LTNPs. None of the escape variants caused breakthrough replication in LTNPs, although they readily infected Mamu-B*17-negative naive macaques. In vitro competing coculture assays and examination of viral evolution in hosts lacking Mamu-B*17 suggested that the mutant viruses had negligible defects in replicative fitness. Both LTNPs maintained robust immune responses, including simian immunodeficiency virus (SIV)-specific CD8+ and CD4+ T cells and neutralizing antibodies. Our results suggest that escape mutations in epitopes bound by “protective” MHC-I molecules may not be sufficient to establish superinfection in LTNPs.
doi:10.1128/JVI.01025-10
PMCID: PMC3014170  PMID: 20962091
24.  CD8+ T Cell Recognition of Cryptic Epitopes Is a Ubiquitous Feature of AIDS Virus Infection▿ †  
Journal of Virology  2010;84(21):11569-11574.
Vaccines designed to elicit AIDS virus-specific CD8+ T cells should engender broad responses. Emerging data indicate that alternate reading frames (ARFs) of both human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) encode CD8+ T cell epitopes, termed cryptic epitopes. Here, we show that SIV-specific CD8+ T cells from SIV-infected rhesus macaques target 14 epitopes in eight ARFs during SIV infection. Animals recognized up to five epitopes, totaling nearly one-quarter of the anti-SIV responses. The epitopes were targeted by high-frequency responses as early as 2 weeks postinfection and in the chronic phase. Hence, previously overlooked ARF-encoded epitopes could be important components of AIDS vaccines.
doi:10.1128/JVI.01419-10
PMCID: PMC2953171  PMID: 20739530
25.  Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing▿  
Journal of Virology  2010;84(22):12087-12092.
Rapid evolution and high intrahost sequence diversity are hallmarks of human and simian immunodeficiency virus (HIV/SIV) infection. Minor viral variants have important implications for drug resistance, receptor tropism, and immune evasion. Here, we used ultradeep pyrosequencing to sequence complete HIV/SIV genomes, detecting variants present at a frequency as low as 1%. This approach provides a more complete characterization of the viral population than is possible with conventional methods, revealing low-level drug resistance and detecting previously hidden changes in the viral population. While this work applies pyrosequencing to immunodeficiency viruses, this approach could be applied to virtually any viral pathogen.
doi:10.1128/JVI.01378-10
PMCID: PMC2977871  PMID: 20844037

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