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T cell exhaustion is associated with failure to clear chronic infections and malignant cells. Defining the molecular mechanisms of T cell exhaustion and reinvigoration is essential to improving immunotherapeutic modalities. Here we confirmed pervasive phenotypic, functional and transcriptional differences between memory and exhausted antigen-specific CD8+ T cells in human hepatitis C virus (HCV) infection before and after treatment. After viral cure, phenotypic changes in clonally stable exhausted T cell populations suggested differentiation toward a memory-like profile. However, functionally, the cells showed little improvement, and critical transcriptional regulators remained in the exhaustion state. Notably, T cells from chronic HCV infection that were exposed to antigen for less time because of viral escape mutations were functionally and transcriptionally more similar to memory T cells from spontaneously resolved HCV infection. Thus, the duration of T cell stimulation impacts exhaustion recovery, with antigen removal after long-term exhaustion being insufficient for the development of functional T cell memory. Lauer and colleagues examine CD8+ T cells following cure of human hepatitis C virus (HCV) infection. CD8+ T cells exposed to chronic HCV-specific activation show durable functional, phenotypic and transcriptional exhaustion that is maintained even after antigen stimulus is removed.

Ending the hepatitis C virus (HCV) epidemic requires stopping transmission among networks of persons who inject drugs. Identifying transmission networks by using genomic epidemiology may inform community responses that can quickly interrupt transmission. We retrospectively identified HCV RNA-positive specimens corresponding to 459 persons in settings that use the state laboratory, including correctional facilities and syringe services programs, in Wisconsin, USA, during 2016-2017. We conducted next-generation sequencing of HCV and analyzed it for phylogenetic linkage by using the Centers for Disease Control and Prevention Global Hepatitis Outbreak Surveillance Technology platform. Analysis showed that 126 persons were linked across 42 clusters. Phylogenetic clustering was higher in rural communities and associated with female sex and younger age among rural residents. These data highlight that HCV transmission could be reduced by expanding molecular-based surveillance strategies to rural communities affected by the opioid crisis.

Effective function of CD8

Effective function of CD8+ T cells and enhanced innate activation of dendritic cells (DC) in response to HIV-1 is linked to protective antiviral immunity in controllers. Manipulation of DC targeting the master regulator TANK-binding Kinase 1 (TBK1) might be useful to acquire controller-like properties. Here, we evaluated the impact of TBK1-primed DC inducing protective CD8+ T cell responses in lymphoid tissue and peripheral blood and their association with reduced HIV-1 disease progression in vivo in the humanized bone marrow, liver and thymus (hBLT) mouse model. A higher proportion of hBLT-mice vaccinated with TBK1-primed DC exhibited less severe CD4+ T cell depletion following HIV-1 infection compared to control groups. This was associated with infiltration of CD8+ T cells in the white pulp from the spleen, reduced spread of infected p24+ cells to secondary lymphoid organs and with preserved abilities of CD8+ T cells from the spleen and blood of vaccinated animals to induce specific polyfunctional responses upon antigen stimulation. Therefore, TBK1-primed DC might be an useful tool for subsequent vaccine studies.Author summaryEmulating protective immunological characteristics from individuals capable of spontaneously controlling HIV-1 infection might be useful for the development of a protective vaccine. Enhanced function of dendritic cells (DC) in these HIV-1 controllers depends on the activation of TANK-binding Kinase 1 (TBK1) and might associate with protective T cells. Our study evaluated the ability of DCs trained through TBK1 activation inducing protective adaptive immune responses against HIV-1 and reducing disease progression in vivo, using a humanized mouse model. Our data indicate that mice vaccinated with tailored DC exhibit delayed disease progression, increased induction of protective CD8+ T lymphocyte subsets in the lymphoid tissue and blood upon antigen recognition. Therefore, trained-DC might be an useful tool for future HIV-1 vaccine designs.

Structure-based immunogen design Vaccine design for highly mutable pathogens is hindered by a paucity of conserved immunogenic epitopes. Gaiha et al. employed a structure-based technique using network theory to assign scores to protein structure in order to infer mutational constraints (see the Perspective by McMichael and Carrington). The authors validated the method on proteins with published functional outcomes and then assessed mutational constraints within the HIV proteome. Highly networked residues strongly associated with immune control of HIV infection and may lead to protective immunogens for pathogens for which there is currently no efficient vaccine. Science , this issue p. 480 ; see also p. 438

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.

Humanized bone marrow-liver-thymus (HuBLT) mice have facilitated the study of human immune function and human-restricted pathogens, including human immunodeficiency virus type 1 (HIV-1). These mice not only support robust HIV-1 infection, but also uniquely harbor long-term in vivo development of HLA-restricted human T cells and recapitulate many aspects of acute and chronic HIV-1 pathogenesis. However, HuBLT mice challenged with HIV-1 exhibit variable T-cell responses across individual mice, hindering the ability to confidently detect HIV-1–specific responses or vaccine-associated effects. To understand the source of this variability, we comprehensively analyzed T-cell development, diversity, and priming in HuBLT mice. We found that while T-cell diversity, thymic development, and differentiation appeared intact in HuBLT mice, there was a defect in T-cell function, polarization, and priming that correlated with poor reconstitution of innate immune cells, particularly monocytes. While virtually all HuBLT mice were well-reconstituted with T and B cells, there was variable reconstitution of monocytes that positively correlated with T-cell function as well as TH1 polarization. Monocyte reconstitution also positively correlated with CD8+ T-cell responses in vivo during acute HIV-1 infection and the selection of viral variants. Thus, despite proper T-cell reconstitution, a deficiency in innate immune reconstitution in HuBLT mice hinders the development of more robust antigen-specific T-cell responses, which if improved would enhance the model’s ability to better recapitulate human adaptive immunity.

BackgroundThe current opioid epidemic across the United States has fueled a surge in the rate of new HCV infections among young persons who inject drugs (PWIDs). Paramount to interrupting transmission is targeting these high-risk populations and understanding the underlying network structures facilitating transmission within these communities.MethodsDeep sequencing data were obtained for 52 participants from 32 injecting partnerships enrolled in the UFO Partner Study which is a prospective study of self-described injecting dyad partnerships from a large community-based study of HCV infection in young adult PWIDs from San Francisco. Phylogenetically linked transmission events were identified using traditional genetic-distance measures and viral deep sequence phylogenies reconstructed to determine the statistical support of inferences and the direction of transmission within partnerships.ResultsUsing deep sequencing data, we found that 12 of 32 partnerships were genetically similar and clustered. Three additional phylogenetic clusters were found describing novel putative transmission links outside of the injecting relationship. Transmission direction was inferred correctly for five partnerships with the incorrect transmission direction inferred in more than 50% of cases. Notably, we observed that phylogenetic linkage was most often associated with a lower number of network partners and involvement in a sexual relationship.ConclusionsDeep sequencing of HCV among self-described injecting partnerships demonstrates that the majority of transmission events originate from outside of the injecting partnership. Furthermore, these findings caution that phylogenetic methods may be unable to routinely infer the direction of transmission among PWIDs especially when transmission events occur in rapid succession within high-risk networks.SummaryDeep sequencing of HCV from 32 self-described injecting partnerships revealed that only 37% were genetically similar and inferring the direction of transmission using phylogenetic tools is challenging as HCV transmission is complex and multifaceted.

Summary: Changes in antibody glycosylation are linked to inflammation across several diseases. Alterations in bulk antibody galactosylation can predict rheumatic flares, act as a sensor for immune activation, predict gastric cancer relapse, track with biological age, shift with vaccination, change with HIV reservoir size on therapy, and decrease in HIV and HCV infections. However, whether changes in antibody Fc biology also track with reservoir rebound time remains unclear. The identification of a biomarker that could forecast viral rebound time could significantly accelerate the downselection and iterative improvement of promising HIV viral eradication strategies. Using a comprehensive antibody Fc-profiling approach, the level of HIV-specific antibody Fc N-galactosylation is significantly associated with time to rebound after treatment discontinuation across three independent cohorts. Thus virus-specific antibody glycosylation may represent a promising, simply measured marker to track reservoir reactivation.

An effective strategy to cure HIV will likely require a potent and sustained antiviral T cell response. Here we explored the utility of chimeric antigen receptor (CAR) T cells, expressing the CD4 ectodomain to confer specificity for the HIV envelope, to mitigate HIV-induced pathogenesis in bone marrow, liver, thymus (BLT) humanized mice. CAR T cells expressing the 4–1BB/CD3-ζ endodomain were insufficient to prevent viral rebound and CD4(+) T cell loss after the discontinuation of antiretroviral therapy. Through iterative improvements to the CAR T cell product, we developed Dual-CAR T cells that simultaneously expressed both 4–1BB/CD3-ζ and CD28/CD3-ζ endodomains. Dual-CAR T cells exhibited expansion kinetics that exceeded 4–1BB-, CD28- and third-generation costimulated CAR T cells, elicited effector functions equivalent to CD28-costimulated CAR T cells and prevented HIV-induced CD4(+) T cell loss despite persistent viremia. Moreover, when Dual-CAR T cells were protected from HIV infection through expression of the C34-CXCR4 fusion inhibitor, these cells significantly reduced acute-phase viremia, as well as accelerated HIV suppression in the presence of antiretroviral therapy and reduced tissue viral burden. Collectively, these studies demonstrate the enhanced therapeutic potency of a novel Dual-CAR T cell product with the potential to effectively treat HIV infection.

Ending the hepatitis C virus (HCV) epidemic requires stopping transmission among networks of people who inject drugs (PWID). Identification of transmission networks through the application of genomic epidemiology may inform community response models that can quickly interrupt transmission. We retrospectively identified HCV RNA-positive specimens corresponding to 459 individuals tested in public health settings, including correctional facilities and syringe service programs, in Wisconsin from 2016-2017. Next-generation sequencing of HCV was conducted and analyzed for phylogenetic linkage using the CDC’s Global Hepatitis Outbreak Surveillance Technology platform. Transmission network analysis showed that 126 individuals were linked across 42 clusters (range: 2-11 individuals per cluster). Phylogenetic clustering was higher in rural communities and associated with female gender and younger age among rural residents. These data highlight that the increasing rurality of opioid injection use and HCV transmission among young PWID could be better supported by the expansion of molecular-based surveillance strategies to reduce transmission.Article Summary LineIntegrating existing public health surveillance and molecular analyses with Global Hepatitis Outbreak Surveillance Technology allows for the identification and characterization of growing HCV transmission clusters among key populations in Wisconsin.

T cell exhaustion is associated with failure to clear chronic infections and malignant cells. Defining the molecular mechanisms of T cell exhaustion and reinvigoration is essential to improving immunotherapeutic modalities. Here we confirmed pervasive phenotypic, functional, and transcriptional differences between memory and exhausted antigen-specific CD8+ T cells in human hepatitis C virus (HCV) infection before and after treatment. After viral cure, phenotypic changes in clonally stable exhausted T cell populations suggested differentiation towards a memory-like profile. However, functionally, the cells showed little improvement and critical transcriptional regulators remained in the exhaustion state. Notably, T cells from chronic HCV infection that were exposed to antigen for less time because of viral escape mutations were functionally and transcriptionally more similar to memory T cells from spontaneously resolved HCV infection. Thus, T cell stimulation duration impacts exhaustion recovery, with antigen removal after long-term exhaustion being insufficient for development of functional T cell memory.

Summary Spontaneous control of HIV infection has been repeatedly linked to antiviral CD8+ T cells but is not always permanent. To address mechanisms of durable and aborted control of viremia, we evaluated immunologic and virologic parameters longitudinally among 34 HIV-infected subjects with differential outcomes. Despite sustained recognition of autologous virus, HIV-specific proliferative and cytolytic T cell effector functions became selectively and intrinsically impaired prior to aborted control. Longitudinal transcriptomic profiling of functionally impaired HIV-specific CD8+ T cells revealed altered expression of genes related to activation, cytokine-mediated signaling, and cell cycle regulation, including increased expression of the antiproliferative transcription factor KLF2 but not of genes associated with canonical exhaustion. Lymphoid HIV-specific CD8+ T cells also exhibited poor functionality during aborted control relative to durable control. Our results identify selective functional impairment of HIV-specific CD8+ T cells as prognostic of impending aborted HIV control, with implications for clinical monitoring and immunotherapeutic strategies.

Over 30 key leaders in the field participated in a 1-day workshop entitled ‘Recent Advances and Opportunities in the Development and Use of Humanized Immune System Mouse Models’ to discuss the benefits and limitations of using human fetal tissue versus non-fetal tissue sources to generate mice with a humanized immune system. This Comment summarizes the workshop discussions, including highlights of some of the key advances made through the use of humanized mice in improving the understanding of immune system function and developing novel therapeutics for the treatment of infectious, immunological and allergic diseases, as well as current challenges in the production, characterization and utilization of these animal models.

BLT (bone marrow-liver-thymus) humanized mice, which reconstitute a functional human immune system, develop prototypic human virus-specific CD8(+) T cell responses following infection with human immunodeficiency virus type 1 (HIV-1). We explored the utility of the BLT model for HIV-1 vaccine development by immunizing BLT mice against the conserved viral Gag protein, utilizing a rapid prime-boost protocol of poly(lactic-co-glycolic) acid microparticles and a replication-defective herpes simplex virus (HSV) recombinant vector. After HIV-1 challenge, the mice developed broad, proteome-wide gamma interferon-positive (IFN-γ(+)) T cell responses against HIV-1 that reached magnitudes equivalent to what is observed in HIV-1-infected individuals. The functionality of these responses was underscored by the consistent emergence of escape mutations in multiple CD8(+) T cell epitopes during the course of infection. Although prechallenge vaccine-induced responses were largely undetectable, the Gag immunization increased both the magnitude and the kinetics of anamnestic Gag-specific T cell responses following HIV-1 infection, and the magnitude of these postchallenge Gag-specific responses was inversely correlated with acute HIV-1 viremia. Indeed, Gag immunization was associated with a modest but significant 0.5-log reduction in HIV-1 viral load when analyzed across four experimental groups of BLT mice. Notably, the HSV vector induced elevated plasma concentrations of polarizing cytokines and chemotactic factors, including interleukin-12p70 (IL-12p70) and MIP-1α, which were positively correlated with the magnitude of Gag-specific responses. Overall, these results support the ability of BLT mice to recapitulate human pathogen-specific T cell responses and to respond to immunization; however, additional improvements to the model are required to develop a robust system for testing HIV-1 vaccine efficacy. IMPORTANCE Advances in the development of humanized mice have raised the possibility of a small-animal model for preclinical testing of an HIV-1 vaccine. Here, we describe the capacity of BLT humanized mice to mount broadly directed HIV-1-specific human T cell responses that are functionally active, as indicated by the rapid emergence of viral escape mutations. Although immunization of BLT mice with the conserved viral Gag protein did not result in detectable prechallenge responses, it did increase the magnitude and kinetics of postchallenge Gag-specific T cell responses, which was associated with a modest but significant reduction in acute HIV-1 viremia. Additionally, the BLT model revealed immunization-associated increases in the plasma concentrations of immunomodulatory cytokines and chemokines that correlated with more robust T cell responses. These data support the potential utility of the BLT humanized mouse for HIV-1 vaccine development but suggest that additional improvements to the model are warranted.

Author(s): Hahn, Judith A; Tully, Damien C; Evans, Jennifer L; Morris, Meghan D; Briceno, Alya; Bean, David J; Allen, Todd M; Page, Kimberly | Abstract: BackgroundHepatitis C virus (HCV), a major cause of morbidity and mortality, is common and rising among young persons who inject drugs (PWID). Reducing the level of viremia may be an intervention, yet the impact of viremia on HCV transmission is unknown.MethodsWe conducted a prospective study of injecting partnerships (Partner Study) of young adult (age l 30 years) PWID within the UFO Study, which enrolled those at risk for HCV or with seronegative viremic infection and up to 3 HCV RNA-positive regular injecting partners. We examined the level of HCV viremia and stage of infection in the HCV-positive partner in regression analyses of HCV transmission events that were corroborated via HCV phylogenetic linkage analyses.ResultsWe enrolled 69 at-risk/acutely infected PWID. There were 25 new HCV infections (incidence rate, 35.9 per 100 person-years; 95% confidence interval [CI], 24.3-53.2 per 100 person-years); 12/25 (48%) were phylogenetically linked to at least 1 partner. We found no association between the infected partner's quantitative level of HCV viremia and likely transmission in multivariate analyses (adjusted odds ratio [AOR], 0.90; 95% confidence interval [CI], 0.55-1.46); however, seronegative viremic infection in the infected partner was associated with increased transmission (AOR, 28.02; 95% CI, 5.61-139.95).ConclusionsThe HCV viremia level was not associated with increased odds of transmission, yet acute HCV infection (seronegative viremic) was. Explanations include high-risk behavior during acute infection or missed fluctuations in viremia during acute infection. Both point to the need for frequent testing to detect new infection and attempt to prevent onward transmission.

Background: Identification of HIV-1 genomes responsible for establishing clinical infection in newly infected individuals is fundamental to prevention and pathogenesis research. Processing, storage, and transportation of the clinical samples required to perform these virologic assays in resource-limited settings requires challenging venipuncture and cold chain logistics. Here, we validate the use of dried-blood spots (DBS) as a simple and convenient alternative to collecting and storing frozen plasma.Methods: We performed parallel nucleic acid extraction, single genome amplification (SGA), next generation sequencing (NGS), and phylogenetic analyses on plasma and DBS.Results: We demonstrated the capacity to extract viral RNA from DBS and perform SGA to infer the complete nucleotide sequence of the transmitted/founder (TF) HIV-1 envelope gene and full-length genome in two acutely infected individuals. Using both SGA and NGS methodologies, we showed that sequences generated from DBS and plasma display comparable phylogenetic patterns in both acute and chronic infection. SGA was successful on samples with a range of plasma viremia, including samples as low as 1,700 copies/ml and an estimated ~50 viral copies per blood spot. Further, we demonstrated reproducible efficiency in gp160 env sequencing in DBS stored at ambient temperature for up to three weeks or at -20ºC for up to five months.Conclusions: These findings support the use of DBS as a practical and cost-effective alternative to frozen plasma for clinical trials and translational research conducted in resource-limited settings.

The oxides formed on the surface of the alloy 690 in hydrogenated supercritical water at 400 °C for 1000 h were investigated using scanning electron microscopy, transmission electron microscopy, scanning transmission electron microscopy and energy-dispersive X-ray spectroscopy. The oxides on the surface of the alloy 690 exhibited multi-layer structure: an outer layer consisted of granular crystallites (NiO and NiFe2O4) and a compact inner layer (spinel and Cr2O3). Chemical analysis indicated that the outer layer was enriched in nickel but depleted in chromium, whereas the inner layer was enriched in chromium and iron but depleted in nickel. The inner layer was also characterized as layered structure by Fe-rich spinel on top of continuous Cr2O3 layer. Besides, Cr2O3 nodules were readily observed at the oxides/alloy interface.

Hepatitis C virus (HCV) entry inhibitors have been hypothesized to prevent infection of the liver after transplantation. ITX5061 is a scavenger receptor class B type I antagonist that blocks HCV entry and infection in vitro. We assessed the safety and efficacy of ITX5061 to limit HCV infection of the graft. The study included 23 HCV-infected patients undergoing liver transplantation. The first 13 "control" patients did not receive drug. The subsequent 10 patients received 150 mg of ITX5061 immediately before and after transplant and daily for 1 week thereafter. ITX5061 pharmacokinetics and plasma HCV RNA were quantified. Viral genetic diversity was measured by ultradeep pyrosequencing (UDPS). ITX5061 was well tolerated with measurable plasma concentrations during therapy. Although the median HCV RNA reduction was greater in ITX-treated patients at all time points in the first week after transplantation, there was no difference in the overall change in the area over the HCV RNA curve in the 7-day treatment period. However, in genotype (GT) 1-infected patients, treatment was associated with a sustained reduction in HCV RNA levels compared to the control group (area over the HCV RNA curve analysis, P = 0.004). UDPS revealed a complex and evolving pattern of HCV variants infecting the graft during the first week. ITX5061 significantly limited viral evolution where the median divergence between day 0 and day 7 was 3.5% in the control group compared to 0.1% in the treated group. In conclusion, ITX5061 reduces plasma HCV RNA after transplant notably in GT 1-infected patients and slows viral evolution. Following liver transplantation, the likely contribution of extrahepatic reservoirs of HCV necessitates combining entry inhibitors such as ITX5061 with inhibitors of replication in future studies.

Despite the extensive viral quasispecies that develops in an individual during the course of HIV-1 infection, transmission is typically established by a single donor viral variant. Recent studies now provide insight into the phenotypic properties influencing this selection process at transmission, including the contribution of resistance to type I interferons.

Mutationally constrained epitopes of variable pathogens represent promising targets for vaccine design but are not reliably identified by sequence conservation. In this study, we employed structure-based network analysis, which applies network theory to HIV protein structure data to quantitate the topological importance of individual amino acid residues. Mutation of residues at important network positions disproportionately impaired viral replication and occurred with high frequency in epitopes presented by protective human leukocyte antigen (

Certain major histocompatibility complex class I (MHC-I) alleles are associated with spontaneous control of viral replication in human immunodeficiency virus (HIV)-infected people and simian immunodeficiency virus (SIV)-infected rhesus macaques (RMs). These cases of "elite" control of HIV/SIV replication are often immune-mediated, thereby providing a framework for studying anti-lentiviral immunity. In this study, we examined how vaccination impacts SIV replication in RMs expressing the MHC-I allele Mamu-B*17 Approximately 21% of Mamu-B*17+ and 50% of Mamu-B*08+ RMs control chronic-phase viremia after SIVmac239 infection. Because CD8+ T cells targeting Mamu-B*08-restricted SIV epitopes have been implicated in virologic suppression in Mamu-B*08+ RMs, we investigated whether this might also be true for Mamu-B*17+ RMs. Two groups of Mamu-B*17+ RMs were vaccinated with genes encoding Mamu-B*17-restricted epitopes in Vif and Nef. These genes were delivered by themselves (group 1) or together with env (group 2). Group 3 included MHC-I-matched RMs and served as the control group. Surprisingly, the group 1 vaccine regimen had little effect on viral replication compared to group 3, suggesting that unlike Mamu-B*08+ RMs, preexisting SIV-specific CD8+ T cells alone do not facilitate long-term virologic suppression in Mamu-B*17+ RMs. Remarkably, however, 5/8 group 2 vaccinees controlled viremia to

Due to error-prone replication, HIV-1 generates a diverse population of viruses within a chronically infected individual. When HIV-1 is transmitted to a new individual, one or a few viruses establish the new infection, leading to a genetic bottleneck in the virus population. Understanding the timing and nature of this bottleneck may provide insight into HIV-1 vaccine design and other preventative strategies. We examined the HIV-1 population in three women enrolled in a unique prospective cohort in South Africa who were followed closely during the earliest stages of HIV-1 infection. We found very little HIV-1 diversity in the blood and female genital tract during the first 2 weeks after virus was detected in the bloodstream. These results are compatible with a very early HIV-1 population bottleneck, suggesting the need to study the HIV-1 population in the female genital tract before virus is detectable in the bloodstream., Heterosexual transmission of human immunodeficiency virus type 1 (HIV-1) is associated with a significant bottleneck in the viral quasispecies population, yet the timing of that bottleneck is poorly understood. We characterized HIV-1 diversity in the blood and female genital tract (FGT) within 2 weeks after detection of infection in three women enrolled in a unique prospective cohort in South Africa. We assembled full-length HIV-1 genomes from matched cervicovaginal lavage (CVL) samples and plasma. Deep sequencing allowed us to identify intrahost single-nucleotide variants (iSNVs) and to characterize within-sample HIV-1 diversity. Our results demonstrated very little HIV-1 diversity in the FGT and plasma by the time viremia was detectable. Within each subject, the consensus HIV-1 sequences were identical in plasma and CVL fluid. No iSNV was present at >6% frequency. One subject had 77 low-frequency iSNVs across both CVL fluid and plasma, another subject had 14 iSNVs in only CVL fluid from the earliest time point, and the third subject had no iSNVs in CVL fluid or plasma. Overall, the small amount of diversity that we detected was greater in the FGT than in plasma and declined over the first 2 weeks after viremia was detectable, compatible with a very early HIV-1 transmission bottleneck. To our knowledge, our study represents the earliest genomic analysis of HIV-1 in the FGT after transmission. Further, the use of metagenomic sequencing allowed us to characterize other organisms in the FGT, including commensal bacteria and sexually transmitted infections, highlighting the utility of the method to sequence both HIV-1 and its metagenomic environment. IMPORTANCE Due to error-prone replication, HIV-1 generates a diverse population of viruses within a chronically infected individual. When HIV-1 is transmitted to a new individual, one or a few viruses establish the new infection, leading to a genetic bottleneck in the virus population. Understanding the timing and nature of this bottleneck may provide insight into HIV-1 vaccine design and other preventative strategies. We examined the HIV-1 population in three women enrolled in a unique prospective cohort in South Africa who were followed closely during the earliest stages of HIV-1 infection. We found very little HIV-1 diversity in the blood and female genital tract during the first 2 weeks after virus was detected in the bloodstream. These results are compatible with a very early HIV-1 population bottleneck, suggesting the need to study the HIV-1 population in the female genital tract before virus is detectable in the bloodstream.

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. We developed CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs compact probe sets that achieve full coverage of known sequence diversity and that scale well with this diversity. To illustrate applications of CATCH, we focused on capturing viral genomes. We designed, synthesized, and validated multiple probe sets, including one that targets whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriched unique viral content on average 18× and allowed us to assemble genomes that we could not otherwise recover, while accurately preserving within-sample diversity. We used this approach to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of viral infections in samples with unknown content. Together, this work demonstrates a path toward more sensitive, cost-effective metagenomic sequencing.

Background The factors determining differential HIV disease outcome among individuals expressing protective HLA alleles such as HLA-B*27:05 and HLA-B*57:01 remain unknown. We here analyse two HIV-infected subjects expressing both HLA-B*27:05 and HLA-B*57:01. One subject maintained low-to-undetectable viral loads for more than a decade of follow up. The other progressed to AIDS in

Certain major histocompatibility complex class I (MHC-I) alleles (e.g., HLA-B*27 ) are enriched among human immunodeficiency virus type 1 (HIV-1)-infected individuals who suppress viremia without treatment (termed “elite controllers” [ECs]). Likewise, Mamu-B*08 expression also predisposes rhesus macaques to control simian immunodeficiency virus (SIV) replication. Given the similarities between Mamu-B*08 and HLA-B*27, SIV-infected Mamu-B*08 + animals provide a model to investigate HLA-B*27-mediated elite control. We have recently shown that vaccination with three immunodominant Mamu-B*08-restricted epitopes (Vif RL8, Vif RL9, and Nef RL10) increased the incidence of elite control in Mamu-B*08 + macaques after challenge with the pathogenic SIVmac239 clone. Furthermore, a correlate analysis revealed that CD8 + T cells targeting Nef RL10 was correlated with improved outcome. Interestingly, this epitope is conserved between SIV and HIV-1 and exhibits a delayed and atypical escape pattern. These features led us to postulate that a monotypic vaccine-induced Nef RL10-specific CD8 + T-cell response would facilitate the development of elite control in Mamu-B*08 + animals following repeated intrarectal challenges with SIVmac239. To test this, we vaccinated Mamu-B*08 + animals with nef inserts in which Nef RL10 was either left intact (group 1) or disrupted by mutations (group 2). Although monkeys in both groups mounted Nef-specific cellular responses, only those in group 1 developed Nef RL10-specific CD8 + T cells. These vaccine-induced effector memory CD8 + T cells did not prevent infection. Escape variants emerged rapidly in the group 1 vaccinees, and ultimately, the numbers of ECs were similar in groups 1 and 2. High-frequency vaccine-induced CD8 + T cells focused on a single conserved epitope and therefore did not prevent infection or increase the incidence of elite control in Mamu-B*08 + macaques. IMPORTANCE Since elite control of chronic-phase viremia is a classic example of an effective immune response against HIV/SIV, elucidating the basis of this phenomenon may provide useful insights into how to elicit such responses by vaccination. We have previously established that vaccine-induced CD8 + T-cell responses against three immunodominant epitopes can increase the incidence of elite control in SIV-infected Mamu-B*08 + rhesus macaques—a model of HLA-B*27-mediated elite control. Here, we investigated whether a monotypic vaccine-induced CD8 + T-cell response targeting the conserved “late-escaping” Nef RL10 epitope can increase the incidence of elite control in Mamu-B*08 + monkeys. Surprisingly, vaccine-induced Nef RL10-specific CD8 + T cells selected for variants within days after infection and, ultimately, did not facilitate the development of elite control. Elite control is, therefore, likely to involve CD8 + T-cell responses against more than one epitope. Together, these results underscore the complexity and multidimensional nature of virologic control of lentivirus infection.

To enable the life extension of Light Water Reactors (LWRs) beyond 60 years, it is critical to gain adequate knowledge for making conclusive predictions to assure the integrity of duplex stainless steel reactor components, e.g. primary pressure boundary and reactor vessel internal. Microstructural changes in the ferrite of thermally aged, neutron irradiated only, and neutron irradiated after being thermally aged cast austenitic stainless steels (CASS) were investigated using atom probe tomography. The thermal aging was performed at 400 °C for 10,000 h and the irradiation was conducted in the Halden reactor at ~315 °C to 0.08 dpa (5.6 × 1019 n/cm2 E > 1 MeV). Low dose neutron irradiation at a dose rate of 5 × 10-9 dpa/s was found to induce spinod,al decomposition in the ferrite of as-cast microstructure, and further to enhance the spinodal decomposition in the thermally aged cast alloys. Regarding the G-phase precipitates, the neutron irradiation dramatically increases the precipitate size, and alters the composition of the precipitates with increased, Mn, Ni, Si and Mo and reduced Fe and Cr contents. Lastly, The results have shown that low dose neutron irradiation can further accelerate the degradation of ferrite in a duplex stainless steel at the LWRmore » relevant condition.« less

Corrosion testing of UNS N10003 in molten fluoride salt was performed in purified molten 27LiF-BeF2 (66–34 mol%) (FLiBe) salt at 700°C for 1,000 h, in pure nickel and graphite capsules. In the nickel capsule tests, the near-surface region of the alloy exhibited an approximately 200 nm porous structure, an approximately 3.5 μm chromium-depleted region, and MoSi2 precipitates. In the tests performed in graphite capsules, the alloy samples gained weight because of the formation of a variety of Cr3C2, Cr7C3, Mo2C, and Cr23C6 carbide phases on the surface and in the subsurface regions of the alloy. A Cr-depleted region was observed in the near-surface region where Mo thermally diffused toward either the surface or the grain boundary, which induced an approximately 1.4 μm Ni3Fe alloy layer in this region. The carbide-containing layer extended to approximately 7 μm underneath the Ni3Fe layer. The presence of graphite dramatically changes the mechanisms of corrosion attack in UNS N10003 in molten FLiBe salt. In t...

Humanized mice are valuable models for the research and development of vaccine strategies and therapeutic interventions to control or eradicate HIV. The BLT humanized mouse model is particularly promising because the combination of transplantation of human fetal pluripotent hematopoietic stem cells with surgical engraftment of human fetal thymic tissue results in improved T cell reconstitution, maturation, and selection. To date, the BLT humanized mouse model has been used to study many aspects of HIV infection including prevention, mucosal transmission, HIV-specific innate and adaptive immunity, viral latency, and novel antiretroviral and immune-based therapies for suppression and reservoir eradication. Here we describe recent advances and applications of the BLT humanized mouse model of HIV infection and discuss opportunities to further improve this valuable small animal model.

In support of structural material development for the fluoride-salt-cooled high-temperature reactor (FHR), corrosion tests of 316 stainless steel were performed in the potential primary coolant, molten Li2BeF4 (FLiBe) at 700 °C for an exposure duration up to 3000 h. Tests were performed in both 316 stainless steel and graphite capsules. Corrosion in both capsule materials occurred by the dissolution of chromium from the stainless steel into the salt which led to the depletion of chromium predominantly along the grain boundaries of the test samples. The samples tested in graphite capsules showed a factor of two greater depth of corrosion attack as measured in terms of chromium depletion, compared to those tested in 316 stainless steel capsules. The samples tested in graphite capsules showed the formation of Cr7C3 particulate phases throughout the depth of the corrosion layer. Samples tested in both types of capsule materials showed the formation of MoSi2 phase due to increased activity of Mo and Si as a result of Cr depletion, and furthermore corrosion promoted the formation of a α-ferrite phase in the near-surface regions of the 316 stainless steel. Based on the corrosion tests, the corrosion attack depth in FLiBe salt was predicted as 17.1 μm/year and 31.2 μm/year for 316 stainless steel tested in 316 stainless steel and in graphite capsules respectively. It is in an acceptable range compared to the Hastelloy-N corrosion in the Molten Salt Reactor Experiment (MSRE) fuel salt.

Concurrent evolution of grain size and porosity in solids is a technically important problem involving curvature-driven motion of grain boundaries and the pore motion by surface diffusion. A phase field approach comprising a system of Cahn–Hilliard and Allen–Cahn equations has been developed recently to tackle this problem. Through a formal asymptotic analysis, the current work demonstrates that the phase field model recovers the corresponding sharp-interface dynamics of the co-evolution of grain boundaries and pores; this analysis also fixes the model kinetic parameters in terms of real materials properties. As a case study, the model was used to investigate the effect of porosity on the kinetics of grain growth in CeO2 in 3D. It is shown that the model captures the phenomenon of pore breakaway often observed in experiments. Pores on three- and four-grain junctions were found to move along with the migrating boundary, while edge pores (on the boundary between two grains) were found to easily separate from the boundary. The simulations showed that pore breakaway leads to abnormal grain growth. The simulations also showed that grain growth kinetics in CeO2 changes from boundary controlled to pore controlled as the amount of porosity increases. The kinetic growth parameters such as the growth exponent and the rate constant (or equivalently the activation energy) were found to depend strongly on the precise amount and distribution of porosity, which reconciles the different experimental results reported for grain growth in CeO2.

The mechanisms of oxygen stoichiometry variation in UO2at different temperature and oxygen partial pressure are important for understanding the dynamics of microstructure in these crystals. However, very limited experimental studies have been performed to understand the atomic structure of UO2near surface and defect effects of near surface on stoichiometry in which the system can exchange atoms with the external reservoir. In this study, the near (110) surface relaxation and stoichiometry in UO2have been studied with density functional theory (DFT) calculations. On the basis of the point-defect model (PDM), a general expression for the near surface stoichiometric variation is derived by using DFT total-energy calculations and atomistic thermodynamics, in an attempt to pin down the mechanisms of oxygen exchange between the gas environment and defected UO2. By using the derived expression, it is observed that, under poor oxygen conditions, the stoichiometry of near surface is switched from hyperstoichiometric at 300 K with a depth around 3 nm to near-stoichiometric at 1000 K and hypostoichiometric at 2000 K. Furthermore, at very poor oxygen concentrations and high temperatures, our results also suggest that the bulk of the UO2prefers to be hypostoichiometric, although the surface is near-stoichiometric.

Effector memory T cell (TEM) responses display potent antiviral properties and have been linked to stringent control of simian immunodeficiency virus (SIV) replication. Since recurrent antigen stimulation drives the differentiation of CD8+ T cells toward the TEM phenotype, in this study we incorporated a persistent herpesviral vector into a heterologous prime/boost/boost vaccine approach to maximize the induction of TEM responses. This new regimen resulted in CD8+ TEM-biased responses in four rhesus macaques, three of which controlled viral replication to

Development of vaccines against mosquito-borne Flaviviruses is complicated by the occurrence of antibody-dependent enhancement (ADE), which can increase disease severity. Long-term delivery of neutralizing antibodies (nAbs) has the potential to effectively block infection and represents an alternative to vaccination. The risk of ADE may be avoided by using prophylactic nAbs harboring amino acid mutations L234A and L235A (LALA) in the immunoglobulin G (IgG) constant region. Here, we used recombinant adeno-associated viruses (rAAVs) to deliver the anti-dengue virus 3 (DENV3) nAb P3D05. While the administration of rAAV-P3D05-rhesus immunoglobulin G1 (rhIgG1)-LALA to rhesus macaques engendered DENV3-neutralizing activity in serum, it did not prevent infection. The emergence of viremia following DENV3 challenge was delayed by 3–6 days in the rAAV-treated group, and replicating virus contained the envelope mutation K64R. This neutralization-resistant variant was also confirmed by virus outgrowth experiments in vitro. By delivering P3D05 with unmutated Fc sequences, we further demonstrated that DENV3 also evaded wild-type nAb prophylaxis, and serum viral loads appeared to be higher in the presence of low levels of unmutated P3D05-rhIgG1. Our study shows that a vectored approach for long-term delivery of nAbs with the LALA mutations is promising, but prophylaxis using a single nAb is likely insufficient at preventing DENV infection and replication.

HIV broadly neutralizing antibodies (bnAbs) have been shown to occasionally display unusual virus neutralization profiles with nonsigmoidal slopes and plateaus at in vi vo, however, is undetermined. In the current study, we selected two bnAbs, PGT121 and 3BNC117, as they incompletely neutralize the clade C simian-human immunodeficiency virus (SHIV) stock (SHIV-327c) at 85% and 70%, respectively, and performed a protection study in rhesus macaques. The animals were intravenously (i.v.) administered PGT121 or 3BNC117 at 10 and 2 mg/kg of body weight before being rectally challenged with a single high dose of SHIV-327c. PGT121 protected 6 out of 7 monkeys, while 6 out of 7 3BNC117-pretreated animals became infected, although with significantly delayed plasma viremia compared to the control animals. These data suggest that complete neutralization is not imperative for bnAbs to prevent infection but that with increasing levels of incomplete neutralization the sterilizing activity diminishes. IMPORTANCE Multiple antibodies have been identified that potently neutralize a broad range of circulating HIV strains. However, not every virus-antibody combination results in complete neutralization of the input virus, suggesting that a fraction of virus particles are resistant to antibody neutralization despite high antibody concentrations. This observation of “incomplete neutralization” is associated with nonsigmoidal neutralization curves plateauing below 100% neutralization, but the significance of the phenomenon for the ability of neutralizing antibodies to mediate protective effects in vivo is undetermined. In this study, we show that the broadly neutralizing antibody PGT121, which neutralized only up to 85% of the SHIV-327c challenge stock in vitro , protected 6 out of 7 rhesus macaques against infection while the antibody 3BNC117, which neutralized up to 70% of SHIV-327c in vitro , did not prevent, though it significantly delayed, establishment of infection, suggesting that with increasing levels of incomplete neutralization the ability of a bnAb to mediate sterilizing protection diminishes.

HIV-1 is able to evade innate antiviral responses during acute infection to establish a chronic systemic infection which, in the absence of antiretroviral therapy (ART), typically progresses to severe immunodeficiency. Understanding these early innate immune responses against HIV-1 and their mechanisms of failure is relevant to the development of interventions to better prevent HIV-1 transmission. Human beta defensins (HBDs) are antibacterial peptides but have recently also been associated with control of viral replication. HBD1 and 2 are expressed in PBMCs as well as intestinal tissue, but their expression in vivo during HIV-1 infection has not been characterized. We demonstrate that during acute HIV-1 infection, HBD1 but not HBD2 is highly upregulated in circulating monocytes but returns to baseline levels during chronic infection. HBD1 expression in monocytes can be induced by HIV-1 in vitro, although direct infection may not entirely account for the increase in HBD1 during acute infection. We provide evidence that HIV-1 triggers antiviral IFN-α responses, which act as a potent inducer of HBD1. Our results show the first characterization of induction of an HBD during acute and chronic viral infection in humans. HBD1 has been reported to have low activity against HIV-1 compared to other defensins, suggesting that in vivo induced defensins may not significantly contribute to the robust early antiviral response against HIV-1. These data provide important insight into the in vivo kinetics of HBD expression, the mechanism of HBD1 induction by HIV-1, and the role of HBDs in the early innate response to HIV-1 during acute infection.

Distinct molecular pathways govern the differentiation of CD8+ effector T cells into memory or exhausted T cells during acute and chronic viral infection but these are not well-studied in humans. Here, we employed an integrative systems immunology approach to identify transcriptional commonalities and differences between virus-specific CD8+ T cells from patients with persistent and spontaneously resolving hepatitis C virus (HCV) infection during the acute phase. We observed dysregulation of metabolic processes during early persistent infection that were linked to changes in expression of genes related to nucleosomal regulation of transcription, T cell differentiation, and the inflammatory response and correlated with subject age, sex and the presence of HCV-specific CD4+ T cell populations. These early changes in HCV-specific CD8+ T cell transcription preceded the overt establishment of T cell exhaustion, making this signature a prime target in the search for the regulatory origins of T cell dysfunction in chronic viral infection.

Cytotoxic T-Lymphocytes (CTLs) kill pathogen-infected or transformed cells following interaction of their T-cell receptors (TCRs) with foreign (e.g. virus-derived) peptides bound to MHC-I molecules on the target cell. TCR binding triggers CTLs to secrete perforin, which forms pores in the target cell membrane, promoting target death. Here, we show that by conjugating drug-loaded lipid nanoparticles to the surface of CTLs, their lytic machinery can be co-opted to lyse the cell-bound drug carrier, providing triggered release of drug cargo upon target cell recognition. Protein encapsulated in T-cell-bound nanoparticles was released following culture of CTLs with target cells in an antigen dose- and perforin-dependent manner and coincided with target cell lysis. Using this approach, we demonstrate the capacity of HIV-specific CTLs to deliver an immunotherapeutic agent to an anatomical site of viral replication. This strategy provides a novel means to couple drug delivery to the action of therapeutic cells in vivo., Ragon Institute of MGH, MIT and Harvard, National Institutes of Health (U.S.) (IH (AI111860)

Investigating creep crack growth under extreme environmental conditions is a challenging yet essential undertaking for the assessment of structural lifetimes of critical components subjected to extreme working conditions for long periods of time. For example, there is currently a need to evaluate structural materials for Next Generation Nuclear Plants (NGNPs) which will operate very high temperature helium-cooled reactors (VHTRs) for generating electricity and use by-product process heat for applications such as hydrogen production and desalination. The primary helium coolant is expected to operate at temperatures at or above 750 °C. In order to evaluate candidate materials for the intermediate heat exchangers, such as Inconel 617 and Alloy 800H, we have developed a creep crack growth (CCG) test apparatus which was designed to test compact tension specimens at temperatures up to 850 °C in controlled environments, including impure helium environments, following ASTM standard E 1457–13. Details of the design of the CCG apparatus and representative results are presented.

This study assessed cellular and soluble markers of immune activation in HIV-1 seronegative MSM. MSM immune profiles were characterized by an increased expression of CD57 on T cells and endotoxemia. Endotoxin presence was linked to recent high-risk exposure and associated with elevated cytokine levels and decreased CD4+/CD8+ T cell ratios. Taken together, these data show elevated levels of inflammation linked to periods of endotoxemia resulting in a significantly different immune phenotype in a subset of MSM at a high risk of HIV-1 acquisition., National Institutes of Health (U.S.) (Grant P01 AI074415)

The acquisition and maintenance of NK-cell function is mediated by inhibitory killer-cell immunoglobulin-like receptors (KIRs) through their interaction with HLA class I molecules. Recently, HLA-C expression levels were shown to be correlated with protection against multiple outcomes of HIV-1 infection; however, the underlying mechanisms are poorly understood. As HLA-C is the natural ligand for the inhibitory receptors KIR2DL1 and KIR2DL2/3, we sought to determine whether HLA-C group haplotypes affect NK-cell responses during primary HIV-1 infection. The phenotypes and functional capacity of NK cells derived from HIV-1-positive and HIV-1-negative individuals were assessed (N = 42 and N = 40, respectively). HIV-1 infection was associated with an increased frequency of KIR2DL1-3(+) NK cells. Further analysis showed that KIR2DL1(+) NK cells were selectively increased in individuals homozygous for HLA-C2, while HLA-C1-homozygous individuals displayed increased proportions of KIR2DL2/3(+) NK cells. KIR2DL1-3(+) NK cells were furthermore more polyfunctional during primary HIV-1 infection in individuals also encoding for their cognate HLA-C group haplotypes, as measured by degranulation and IFN-γ and TNF-α production. These results identify a novel relationship between HLA-C and KIR2DL(+) NK-cell subsets and demonstrate that HLA-C-mediated licensing modulates NK-cell responses to primary HIV-1 infection.

A novel phase field model has been developed to investigate grain growth in porous polycrystalline UO2. Based on a system of Cahn–Hilliard and Allen–Cahn equations, the model takes into consideration both the curvature driven grain boundary motion and pore migration by surface diffusion. As such, the model accounts for the interaction between pore and grain boundary kinetics, which tends to retard the growth process. The phase field model parameters are found in terms of measurable material properties. Hence, quantitative results that can be compared with experiments were obtained. The model has been used to investigate the effect of porosity on the kinetics of grain growth in UO2. It is found that, as the amount of porosity increases, grain growth in UO2 gradually changes from boundary controlled growth to pore controlled growth. For high porosity levels, the grain growth completely stops after a short evolution time. It is also found that the inhomogeneous distribution of pores leads to abnormal grain growth even without taking into account the anisotropy in grain boundary energy and mobility. The effects of porosity, temperature and initial microstructure on grain growth were thoroughly investigated. The model predictions are in good agreement with published experimental results of grain growth in UO2.

The crystalline-to-amorphous transition in nanocrystalline silicon carbide (ncSiC) has been studied using 1.25 MeV electron irradiation. When compared to literature values for single crystal silicon carbide under electron irradiation, an increase in the dose to amorphization (DTA) was observed, indicative of an increase in radiation resistance. Factors that contribute to this improvement are grain refinement, grain texture, and a high density of stacking faults (SFs) in this sample of ncSiC. To test the effect of SFs on the DTA, density functional theory simulations were conducted. It was found that SFs reduced the energy barriers for both Si interstitial migration and the rate-limiting defect recovery reaction, which may explain the increased DTA.