Biology subjects

Barouch, D. H.

Publications and source records attributed to Barouch, D. H..

At least 19 recordsLinked to original sources

bioRxiv2026

Early innate immune signatures correlate with Ad26.COV2.S vaccine durability and protective efficacy

The innate immune system is rapidly activated following antigen exposure and plays a critical role in shaping the ensuing adaptive immune responses. In this study, we performed bulk RNA sequencing and proteomic profiling in a cohort of 25 rhesus macaques following Ad26.COV2.S immunization to characterize early innate correlates of vaccine immunogenicity and protection. Our results show that innate immune activation occurred as early as day 1 post-vaccination and demonstrated an systemic enrichment of antiviral interferon pathways, interleukin signaling, and innate immune cell signatures. These early transcriptomic signatures correlated positively with humoral and cellular immune responses at 6 weeks following vaccination and correlated inversely with viral loads following SARS-CoV-2 challenge. Similar correlates of immunogenicity were observed in a cohort of 25 adult healthy participants vaccinated with Ad26.COV2.S. Taken together, these findings highlight the importance of early activation of the innate immune system for Ad26.COV2.S vaccine immunogenicity and protective efficacy. Graphical SummaryGraphical summary of the model proposed by our findings. Day 1 innate immune signatures are protective of long-term protection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/731069v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@308acaorg.highwire.dtl.DTLVardef@e7e969org.highwire.dtl.DTLVardef@18d1a18org.highwire.dtl.DTLVardef@ac4fb0_HPS_FORMAT_FIGEXP M_FIG C_FIG IMPORTANCEEarly vaccine induction of innate immunity may be critical for vaccine immunogenicity and protective efficacy. In this study, we evaluated innate immune responses following Ad26.COV2.S vaccination in both rhesus macaques and humans. Early induction of innate immune signatures on day 1 following vaccination correlated with subsequent development of adaptive immune responses. These data suggest that the immune programming that occurs immediately after vaccination dictates immunogenicity weeks or months later.

microbiology↗

bioRxiv2026

Distinct phases of immune system programming during ART-suppressed immunodeficiency virus infection

People living with HIV (PLWH) on suppressive antiretroviral therapy (ART) can face non-AIDS complications, partially driven by chronic immune activation. To define immune perturbations during ART-suppressed viral infection, we performed longitudinal single-cell transcriptomic and plasma proteomic analysis of rhesus macaques infected with SIVmac239M and ART-treated for 70 weeks. We identified broad, bi-phasic immune changes. Acute infection involves an interferon-driven signature, correlated with viral replication, that largely resolves with viral control. Cell-associated virus correlated with interferon-stimulated genes in most tissues; however, this was blunted in gut-associated lymph nodes, a feature that may contribute to reservoir persistence. Separate alterations manifest 54-66 weeks-post-infection, after 40 weeks of viral suppression, including broad TGF-{beta} and NF-kB signaling and discrete bursts of inflammatory monocytes, largely restricted to bone marrow. These data highlight the biphasic remodeling of long-term ART-suppressed HIV, identifying specific tissues and cell populations with dysregulation, with implications for the treatment of PLWH.

immunology↗

bioRxiv2026

Displayed and Encoded Antigens on Adenovirus Vectors Optimize Humoral and Cellular Immune Responses in Rhesus Macaques

Adenovirus vector-based vaccines were deployed widely during the COVID-19 pandemic. In this study, we explored the potential of displaying an antigen on the surface of the adenovirus capsid as well as encoding an antigen as a transgene in the adenovirus vector to optimize both humoral and cellular immune responses. We show that displaying SARS-CoV-2 Spike receptor biding domain (RBD) on the Ad5 capsid while simultaneously encoding Spike as a transgene induced robust antibody and T cell responses in rhesus macaques. These data demonstrate that adenoviruses can be utilized simultaneously as both nanoparticle scaffolds and viral vectors.

immunology↗

bioRxiv2025

Origin and Correlates of Viral Rebound in SIV-Infected Rhesus Macaques Following ART Discontinuation

The vast majority of persons living with HIV-1 who discontinue antiretroviral therapy (ART) demonstrate viral rebound, but the tissue-level events that lead to rebound viremia are poorly understood. Here we report the origin, dynamics, and correlates of viral rebound in 16 rhesus macaques (RMs) infected with molecularly barcoded SIVmac239M, treated with ART for 70 weeks, and necropsied on day 12 after ART discontinuation. Barcode analysis of plasma following ART discontinuation identified 1 to 38 rebounding barcode-defined viral lineages per animal, with 1 to 4 rebounding lineages contributing to first measurable rebound viremia. Analysis of barcode viral RNA (vRNA) expression in necropsy tissues revealed presumptive anatomic origin sites for 56 of 175 total rebounding viral lineages, with significant enrichment in the gastrointestinal (GI) tract and GI-associated lymph nodes. Daily transcriptomic and proteomic profiling in peripheral blood following ART discontinuation showed upregulation of pathways related to T cell signaling, cytokine responses, and cellular metabolism prior to detectable rebound viremia. These data suggest that viral rebound following ART discontinuation is initiated by local tissue replication of a limited number of clonal lineages, followed by systemic expansion of the initial rebounding lineages and serial initiation of replication of multiple additional clonal lineages. These findings provide mechanistic insights into the processes that result in viral rebound following ART discontinuation and will contribute to next generation HIV-1 cure strategies.

microbiology↗

bioRxiv2025

Longitudinal transcriptomic analysis of SIV-infected rhesus macaques reveals peripheral immune dynamics throughout untreated SIV infection and long-term antiretroviral therapy

Developing a working knowledge of immune dynamics during prolonged infection and treatment has become critical for both advancing HIV cure strategies and understanding non-AIDS comorbidities, given rises in the age and average time spent on antiretroviral therapy (ART) among people living with HIV. However, at present, we do not fully appreciate the ways in which prolonged suppressive therapy influences immune function. Toward addressing this key knowledge gap comprehensively, we applied single-cell RNA-sequencing (scRNA-seq) to longitudinally profile peripheral blood mononuclear cells from SIV-infected non-human primates longitudinally. Our data reveal significant immune shifts during acute and chronic infection, as well as over five years of subsequent ART. We observe a decline in CD4+ T cells and an increase in aberrant B cells and CD16+ monocytes during untreated chronic infection, as well as widespread dampened transcriptional activity. Further, we uncover transcriptional signatures suggestive of unresolved immune dysregulation during long-term suppressive therapy - most prominently among myeloid cell populations. By examining concurrent measurements of intact proviral DNA, we link peripheral responses to reservoir size via IPDA. We furthermore identify ribosomal-associated pathways as key differentiators of infection stage, treatment status, and time on ART. Finally, we tested whether previously published transcriptional correlates of differential outcomes (e.g. viral rebound, vaccine efficacy) changed over time on ART. Overall, our findings capture dynamic immune remodeling from acute infection through long-term ART, highlighting complexities in achieving complete immune recovery that may influence future therapeutic strategies.

immunology↗

bioRxiv2024

Early spatiotemporal evolution of the immune response elicited by adenovirus serotype 26 vector vaccination in mice

As the first responder to immunological challenges, the innate immune system shapes and regulates the ensuing adaptive immune response. Many clinical studies evaluating the role of innate immunity in initiating vaccine-elicited adaptive immune responses have largely been confined to blood due to inherent difficulty in acquiring tissue samples. However, the absence of vaccine-site and draining lymph node information limits understanding of early events induced by vaccination that could potentially shape vaccine-elicited immunity. We therefore utilized a mouse model to investigate the spatiotemporal evolution of the immune response within the first 24 hours following intramuscular adenovirus serotype 26 (Ad26) vector vaccination in tissues. We show that the Ad26 vaccine-elicited innate immune response commences by one hour and rapidly evolves in tissues and blood within the first 24 hours as reflected by the detection of cytokines, chemokines, cellular responses, and transcriptomic pathways. Furthermore, serum levels of IL-6, MIG, MIP-1, and MIP-1{beta} at 6 hours post-vaccination correlated with the frequency of vaccine-elicited memory CD8+ T cell responses evaluated at 60 days post-vaccination in blood and tissues. Taken together, our data suggests that the immune response to Ad26 vector vaccination commences quickly in tissues by one hour and that events by as early as 6 hours post-vaccination can shape vaccine-elicited CD8+ T cell responses at later memory time points. IMPORTANCEPrior studies have largely concentrated on innate immune activation in peripheral blood following vaccination. In this study, we report the detailed spatial and temporal innate immune activation in tissues following Ad26 vaccination in mice. We observed rapid innate activation rapidly not only in peripheral blood but also in draining lymph nodes and at the site of inoculation. Our findings provide a more detailed picture of host response to vaccination than previously reported.

immunology↗

bioRxiv2024

Protective threshold of a potent neutralizing Zika virus monoclonal antibody in rhesus macaques

Zika virus (ZIKV) is a mosquito-borne flavivirus that caused a global pandemic in 2016-2017 with continued ongoing transmission at low levels in several countries. In the absence of an approved ZIKV vaccine, neutralizing monoclonal antibodies (mAbs) provide an option for the prevention and treatment of ZIKV infection. Previous studies identified a potent neutralizing human mAb ZIKV-117 that reduced fetal infection and death in mice following ZIKV challenge. In this study, we report exquisite potency of ZIKV-117 in a titration study in rhesus macaques to protect against ZIKV challenge. We show complete protection at a dose of 0.016 mg/kg ZIKV-117, which resulted in median serum concentrations of 0.13 {micro}g/mL. The high potency of this mAb supports its potential clinical development as a novel biotherapeutic intervention for ZIKV. ImportanceIn this study, we report the potency of the ZIKV-specific neutralizing antibody ZIKV-117 against ZIKV challenge in a titration study rhesus macaques. This high potency supports the further development of this mAb for ZIKV.

microbiology↗

bioRxiv2024

Global variation in prior exposure shapes antibody neutralization profiles of SARS-CoV-2 variants up to BA.2.86

The highly mutated SARS-CoV-2 variant, BA.2.86, and its descendants are now the most frequently sequenced variants of SARS-CoV-2. We analyze antibody neutralization data from eight laboratories from the UK, USA, Denmark, and China, including two datasets assessing the effect of XBB.1.5 vaccines, to determine the effect of infection and vaccination history on neutralization of variants up to and including BA.2.86, and produce antibody landscapes to describe these neutralization profiles. We find evidence for lower levels of immune imprinting on pre-Omicron variants in sera collected from Denmark and China, which may be explained by lower levels of circulation of the ancestral variant in these countries, and the use of an inactivated virus vaccine in China.

immunology↗

bioRxiv2024

Compartment-Specific Antibody Correlates of Protection to SARS-CoV-2 Omicron in Macaques

Antibodies represent a primary mediator of protection against respiratory viruses such as SARS-CoV-2. Serum neutralizing antibodies (NAbs) are often considered a primary correlate of protection. However, detailed antibody profiles including characterization of antibody functions in different anatomic compartments are not well understood. Here we show that antibody correlates of protection against SARS-CoV-2 challenge are different in systemic versus mucosal compartments in rhesus macaques. In serum, neutralizing antibodies were the strongest correlate of protection and were linked to Spike-specific binding antibodies and other extra-neutralizing antibody functions that create a larger protective network. In contrast, in bronchiolar lavage (BAL), antibody-dependent cellular phagocytosis (ADCP) proved the strongest correlate of protection rather than NAbs. Within BAL, ADCP was linked to mucosal Spike-specific IgG, IgA/secretory IgA, and Fc{gamma}-receptor binding antibodies. Our results support a model in which antibodies with different functions mediate protection at different anatomic sites. The correlation of ADCP and other Fc functional antibody responses with protection in BAL suggests that these antibody responses may be critical for protection against SARS-CoV-2 Omicron challenge in mucosa.

immunology↗

bioRxiv2023

Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells

HIV can persist in a latent form as integrated DNA (provirus) in resting CD4+ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4+ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4+ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts. Significance statementHIV can persist in a latent reservoir unaffected by antiretroviral drugs. The genetic variation of this latent virus population is a major obstacle for eradication efforts, but also a clue to when HIV variants are deposited in the reservoirs. Unfortunately, previous studies assessing when the virus was deposited in latent reservoirs have come to contradictory conclusions. Here, we propose SIV proviral DNA exists in both short- and long-lived CD4+ T cells, and that these two cell subsets harbor different genetically diverged virus populations. Our model explains the contradictory findings and shows that when CD4+ T cells decay under effective drug treatment, which prevents virus replication, the resulting virus divergence decreases and recapitulates observed data. This knowledge should help in improving future eradication efforts.

microbiology↗

bioRxiv2023

Contrasting Effects of SARS-CoV-2 Vaccination vs. Infection on Antibody and TCR Repertoires

Antibodies and helper T cells play important roles in SARS-CoV-2 infection and vaccination. We sequenced B- and T-cell receptor repertoires (BCR/TCR) from the blood of 251 infectees, vaccinees, and controls to investigate whether features of these repertoires could predict subjects SARS-CoV-2 neutralizing antibody titer (NAbs), as measured by enzyme-linked immunosorbent assay (ELISA). We sequenced recombined immunoglobulin heavy-chain (IGH), TCR{beta} (TRB), and TCR{delta} (TRD) genes in parallel from all subjects, including select B- and T-cell subsets in most cases, with a focus on their hypervariable CDR3 regions, and correlated this AIRRseq data with demographics and clinical findings from subjects electronic health records. We found that age affected NAb levels in vaccinees but not infectees. Intriguingly, we found that vaccination and infection have an effect on non-productively recombined IGHs, suggesting an effect that precedes clonal selection. We found that repertoires binding capacity to known SARS-CoV-2-specific CD4+ TRBs performs as well as the best hand-tuned approximate or "fuzzy" matching at predicting a protective level of NAbs, while also being more robust to repertoire sample size and not requiring hand-tuning. The overall conclusion from this large, unbiased, clinically well annotated dataset is that B- and T-cell adaptive responses to SARS-CoV-2 infection and vaccination are surprising, subtle, and diffuse. We discuss methodological and statistical challenges faced in attempting to define and quantify such strong-but-diffuse repertoire signatures and present tools and strategies for addressing these challenges.

immunology↗

bioRxiv2023

Neutralization Escape by SARS-CoV-2 Omicron Subvariant BA.2.86

The continued evolution of SARS-CoV-2 may lead to evasion of vaccine immunity and natural immunity. A highly mutated Omicron variant BA.2.86 has recently been identified with over 30 amino acid changes in Spike compared with BA.2 and XBB.1.5. As of September 4, 2023, BA.2.86 has been identified in 37 sequences from 10 countries, which is likely an underestimate due to limited surveillance. The ability of BA.2.86 to evade NAbs compared with other currently circulating Omicron variants remains unknown. Our data show that NAb responses to BA.2.86 were lower than to BA.2 but were comparable or slightly higher than to the current circulating recombinant variants XBB.1.5, XBB.1.16, EG.5, EG.5.1, and FL.1.5.1.

microbiology↗

bioRxiv2023

Attenuated Mycobacterium tuberculosis Vaccine Protection in a Low Dose Murine Challenge Model

Bacillus Calmette-Guerin (BCG) remains the only clinically approved tuberculosis (TB) vaccine despite limited efficacy. Preclinical studies of next generation TB vaccines have typically used a murine aerosol challenge model that employs a high supraphysiologic challenge dose. Here we show that the protective efficacy of a live attenuated Mycobacterium tuberculosis (Mtb) vaccine candidate {Delta}LprG markedly exceeds that of BCG in a low dose murine aerosol challenge model. BCG vaccination reduced bacterial loads but failed to prevent establishment or dissemination of infection in this model. In contrast, {Delta}LprG prevented detectable infection in 61% of mice and resulted in striking anatomic containment of 100% breakthrough infections to a single lung. Protection was partially abrogated in a repeated low dose challenge model, which revealed serum IL-17A, IL-6, CXCL2, CCL2, IFN-{gamma}, and CXCL1 as correlates of protection. These data demonstrate that {Delta}LprG provides strikingly increased protection compared to BCG, including reduced detectable infection and anatomic containment, in a low dose murine challenge model.

microbiology↗

bioRxiv2023

Waning Immunity Against XBB.1.5 Following Bivalent mRNA Boosters

The SARS-CoV-2 Omicron variant has continued to evolve. XBB is a recombinant between two BA.2 sublineages, XBB.1 includes the G252V mutation, and XBB.1.5 includes the G252V and F486P mutations. XBB.1.5 has rapidly increased in frequency and has become the dominant virus in New England. The bivalent mRNA vaccine boosters have been shown to increase neutralizing antibody (NAb) titers to multiple variants, but the durability of these responses remains to be determined. We assessed humoral and cellular immune responses in 30 participants who received the bivalent mRNA boosters and performed assays at baseline prior to boosting, at week 3 after boosting, and at month 3 after boosting. Our data demonstrate that XBB.1.5 substantially escapes NAb responses but not T cell responses after bivalent mRNA boosting. NAb titers to XBB.1 and XBB.1.5 were similar, suggesting that the F486P mutation confers greater transmissibility but not increased immune escape. By month 3, NAb titers to XBB.1 and XBB.1.5 declined essentially to baseline levels prior to boosting, while NAb titers to other variants declined less strikingly.

immunology↗

bioRxiv2022

Substantial Neutralization Escape by the SARS-CoV-2 Omicron Variant BQ.1.1

Omicron BA.5 has been the globally dominant SARS-CoV-2 variant and has demonstrated substantial neutralization escape compared with prior variants. Additional Omicron variants have recently emerged, including BA.4.6, BF.7, BA.2.75.2, and BQ.1.1, all of which have the Spike R346T mutation. In particular, BQ.1.1 has rapidly increased in frequency, and BA.5 has recently declined to less than half of viruses in the United States. Our data demonstrate that BA.2.75.2 and BQ.1.1 escape NAbs induced by infection and vaccination more effectively than BA.5. BQ.1.1 NAb titers were lower than BA.5 NAb titers by a factor of 7 in two cohorts of individuals who received the monovalent or bivalent mRNA vaccine boosters. These findings provide the immunologic context for the rapid increase in BQ.1.1 prevalence in regions where BA.5 is dominant and have implications for both vaccine immunity and natural immunity.

immunology↗

bioRxiv2022

Rapid Loss of CD4 T Cells by Pyroptosis During Acute SIV Infection in Rhesus Macaques

The mechanisms underlying depletion of CD4 T cells during acute HIV-1 infection are not well understood. Here we show that caspase-1-induced pyroptosis, a highly inflammatory programmed cell death pathway, is the dominant mechanism responsible for the rapid depletion of CD4 T cells in gut-associated lymphatic tissue (GALT), spleen, and lymph nodes during acute simian immunodeficiency virus (SIV) infection in rhesus macaques. Upregulation of interferon-gamma inducible factor 16 (IFI16), a host DNA sensor that triggers pyroptosis, was also observed in tissue-resident CD4 T cells and correlated with viral loads and CD4 T cell loss. In contrast, caspase-3-mediated apoptosis and viral cytotoxicity only accounted for a small fraction of CD4 T cell death. Other programmed cell death mechanisms, including mitochondria-induced caspase-independent cell death, necroptosis, and autophagy, did not significantly contribute to CD4 T cell depletion. These data support a model in which caspase-1-mediated pyroptosis is the principal mechanism that results in CD4 T cell loss in the GALT and lymphoid organs and release of proinflammatory cytokines. These findings contribute to our understanding of the pathogenesis of acute SIV infection and have important implications for the development of therapeutic strategies. ImportanceDifferent mechanisms for CD4 T cell depletion during acute HIV-1 infection have been proposed. In this study, we should in SIV infected rhesus macaques that depletion of CD4 T cells is primarily due to pyroptosis. Other pathophysiologic mechanisms may also contribute in a minor way to CD4 T cell depletion.

microbiology↗

bioRxiv2022

Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques

BackgroundThe rapid spread of the SARS-CoV-2 Omicron (B.1.1.529) variant, including in highly vaccinated populations, has raised important questions about the efficacy of current vaccines. Immune correlates of vaccine protection against Omicron are not known. Methods30 cynomolgus macaques were immunized with homologous and heterologous prime-boost regimens with the mRNA-based BNT162b2 vaccine and the adenovirus vector-based Ad26.COV2.S vaccine. Following vaccination, animals were challenged with the SARS-CoV-2 Omicron variant by the intranasal and intratracheal routes. ResultsOmicron neutralizing antibodies were observed following the boost immunization and were higher in animals that received BNT162b2, whereas Omicron CD8+ T cell responses were higher in animals that received Ad26.COV2.S. Following Omicron challenge, sham controls showed more prolonged virus in nasal swabs than in bronchoalveolar lavage. Vaccinated macaques demonstrated rapid control of virus in bronchoalveolar lavage, and most vaccinated animals also controlled virus in nasal swabs, showing that current vaccines provide substantial protection against Omicron in this model. However, vaccinated animals that had moderate levels of Omicron neutralizing antibodies but negligible Omicron CD8+ T cell responses failed to control virus in the upper respiratory tract. Virologic control correlated with both antibody and T cell responses. ConclusionsBNT162b2 and Ad26.COV2.S provided robust protection against high-dose challenge with the SARS-CoV-2 Omicron variant in macaques. Protection against this highly mutated SARS-CoV-2 variant correlated with both humoral and cellular immune responses.

microbiology↗

bioRxiv2022

Reduced Pathogenicity of the SARS-CoV-2 Omicron Variant in Hamsters

The SARS-CoV-2 Omicron (B.1.1.529) variant has proven highly transmissible and has outcompeted the Delta variant in many regions of the world1. Early reports have also suggested that Omicron may result in less severe clinical disease in humans. Here we show that Omicron is less pathogenic than prior SARS-CoV-2 variants in Syrian golden hamsters. Infection of hamsters with the SARS-CoV-2 WA1/2020, Alpha, Beta, or Delta strains led to 4-10% weight loss by day 4 and 10-17% weight loss by day 6, as expected2,3. In contrast, infection of hamsters with two different Omicron challenge stocks did not result in any detectable weight loss, even at high challenge doses. Omicron infection still led to substantial viral replication in both the upper and lower respiratory tracts and pulmonary pathology, but with a trend towards higher viral loads in nasal turbinates and lower viral loads in lung parenchyma compared with WA1/2020 infection. These data suggest that the SARS-CoV-2 Omicron variant may result in more robust upper respiratory tract infection but less severe lower respiratory tract clinical disease compared with prior SARS-CoV-2 variants.

microbiology↗