B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced ...BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.
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•LIBRA-seq: high-throughput mapping of BCR sequence to antigen specificity•Identified HIV- and influenza-specific B cells in two HIV-infected subjects•Predicted antigen reactivity for thousands of single B cells•Identified a previously unknown broadly neutralizing HIV antibody
LIBRA-seq enables high-throughput mapping of B cell receptor sequence to antigen specificity at the single-cell level.
Background Emergomycosis, histoplasmosis, sporotrichosis and blastomycosis are endemic to southern Africa; the first two are AIDS-related mycoses. We described laboratory-diagnosed cases of endemic ...and imported mycoses in South Africa over a decade and discuss available diagnostic tools, reasons for the current under-estimation of cases and future strategies to improve case ascertainment. Materials and methods We analysed electronic pathology laboratory data from all public laboratories and one large private laboratory in South Africa from 2010-2020. Diagnostic specimens processed at the national mycology reference laboratory were also included. We classified cases as proven, probable and possible based on the method of identification. Results We identified 682 cases, of which 307 were proven, 279 were probable and 96 were possible. Of 307 culture-confirmed cases, 168 were identified by phenotypic methods plus sequencing, 128 by phenotypic methods alone and 11 by direct PCR. Of 279 probable cases, 176 had yeasts observed on histology, 100 had a positive Histoplasma antigen test and 3 a positive pan-dimorphic PCR test. All 96 possible cases had compatible clinical syndrome with inflammatory infiltrates on skin tissue histology. A majority of cases had an unspecified endemic mycosis (207/682, 30.4%), followed by sporotrichosis (170/682, 24.9%), emergomycosis (154/682, 22.6%), histoplasmosis (133/682, 19.5%), blastomycosis (14/682, 2.1%) and talaromycosis (4/682, 0.6%). Conclusions This study reports a relatively low number of cases over a decade considering an estimated large population at risk, suggesting that a substantial fraction of cases may remain undiagnosed. There is a need to increase awareness among healthcare workers and to develop rapid point-of-care diagnostic tools and make these widely accessible.
The Antibody Mediated Prevention trials showed that the broadly neutralizing antibody (bnAb) VRC01 prevented acquisition of human immunodeficiency virus-1 (HIV-1) sensitive to VRC01. Using AMP trial ...data, here we show that the predicted serum neutralization 80% inhibitory dilution titer (PT
) biomarker-which quantifies the neutralization potency of antibodies in an individual's serum against an HIV-1 isolate-can be used to predict HIV-1 prevention efficacy. Similar to the results of nonhuman primate studies, an average PT
of 200 (meaning a bnAb concentration 200-fold higher than that required to reduce infection by 80% in vitro) against a population of probable exposing viruses was estimated to be required for 90% prevention efficacy against acquisition of these viruses. Based on this result, we suggest that the goal of sustained PT
<200 against 90% of circulating viruses can be achieved by promising bnAb regimens engineered for long half-lives. We propose the PT
biomarker as a surrogate endpoint for evaluatinon of bnAb regimens, and as a tool for benchmarking candidate bnAb-inducing vaccines.
The VRC01 Antibody Mediated Prevention (AMP) efficacy trials conducted between 2016 and 2020 showed for the first time that passively administered broadly neutralizing antibodies (bnAbs) could ...prevent HIV-1 acquisition against bnAb-sensitive viruses. HIV-1 viruses isolated from AMP participants who acquired infection during the study in the sub-Saharan African (HVTN 703/HPTN 081) and the Americas/European (HVTN 704/HPTN 085) trials represent a panel of currently circulating strains of HIV-1 and offer a unique opportunity to investigate the sensitivity of the virus to broadly neutralizing antibodies (bnAbs) being considered for clinical development. Pseudoviruses were constructed using envelope sequences from 218 individuals. The majority of viruses identified were clade B and C; with clades A, D, F and G and recombinants AC and BF detected at lower frequencies. We tested eight bnAbs in clinical development (VRC01, VRC07-523LS, 3BNC117, CAP256.25, PGDM1400, PGT121, 10-1074 and 10E8v4) for neutralization against all AMP placebo viruses (n = 76). Compared to older clade C viruses (1998-2010), the HVTN703/HPTN081 clade C viruses showed increased resistance to VRC07-523LS and CAP256.25. At a concentration of 1μg/ml (IC80), predictive modeling identified the triple combination of V3/V2-glycan/CD4bs-targeting bnAbs (10-1074/PGDM1400/VRC07-523LS) as the best against clade C viruses and a combination of MPER/V3/CD4bs-targeting bnAbs (10E8v4/10-1074/VRC07-523LS) as the best against clade B viruses, due to low coverage of V2-glycan directed bnAbs against clade B viruses. Overall, the AMP placebo viruses represent a valuable resource for defining the sensitivity of contemporaneous circulating viral strains to bnAbs and highlight the need to update reference panels regularly. Our data also suggests that combining bnAbs in passive immunization trials would improve coverage of global viruses.
HIV-1 infection continues to be a global health challenge and a vaccine is urgently needed. Broadly neutralizing antibodies (bNAbs) are considered essential as they inhibit multiple HIV-1 strains, ...but they are difficult to elicit by conventional immunization. In contrast, non-neutralizing antibodies that correlated with reduced risk of infection in the RV144 HIV vaccine trial are relatively easy to induce, but responses are not durable. To overcome these obstacles, adeno-associated virus (AAV) vectors were used to provide long-term expression of antibodies targeting the V2 region of the HIV-1 envelope protein, including the potent CAP256-VRC26.25 bNAb, as well as non-neutralizing CAP228 antibodies that resemble those elicited by vaccination. AAVs mediated effective antibody expression in cell culture and immunocompetent mice. Mean concentrations of human immunoglobulin G (IgG) in mouse sera increased rapidly following a single AAV injection, reaching 8–60 μg/mL for CAP256 antibodies and 44–220 μg/mL for CAP228 antibodies over 24 weeks, but antibody concentrations varied for individual mice. Secreted antibodies collected from serum retained the expected binding and neutralizing activity. The vectors generated here are, therefore, suitable for the delivery of V2-targeting HIV antibodies, and they could be used in a vectored immunoprophylaxis (VIP) approach to sustain the level of antibody expression required to prevent HIV infection.
BackgroundEmergomycosis, histoplasmosis, sporotrichosis and blastomycosis are endemic to southern Africa; the first two are AIDS-related mycoses. We described laboratory-diagnosed cases of endemic ...and imported mycoses in South Africa over a decade and discuss available diagnostic tools, reasons for the current under-estimation of cases and future strategies to improve case ascertainment.Materials and methodsWe analysed electronic pathology laboratory data from all public laboratories and one large private laboratory in South Africa from 2010-2020. Diagnostic specimens processed at the national mycology reference laboratory were also included. We classified cases as proven, probable and possible based on the method of identification.ResultsWe identified 682 cases, of which 307 were proven, 279 were probable and 96 were possible. Of 307 culture-confirmed cases, 168 were identified by phenotypic methods plus sequencing, 128 by phenotypic methods alone and 11 by direct PCR. Of 279 probable cases, 176 had yeasts observed on histology, 100 had a positive Histoplasma antigen test and 3 a positive pan-dimorphic PCR test. All 96 possible cases had compatible clinical syndrome with inflammatory infiltrates on skin tissue histology. A majority of cases had an unspecified endemic mycosis (207/682, 30.4%), followed by sporotrichosis (170/682, 24.9%), emergomycosis (154/682, 22.6%), histoplasmosis (133/682, 19.5%), blastomycosis (14/682, 2.1%) and talaromycosis (4/682, 0.6%).ConclusionsThis study reports a relatively low number of cases over a decade considering an estimated large population at risk, suggesting that a substantial fraction of cases may remain undiagnosed. There is a need to increase awareness among healthcare workers and to develop rapid point-of-care diagnostic tools and make these widely accessible.
Despite prolific efforts to characterize the antibody response to human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) mono-infections, the response to chronic co-infection with ...these two ever-evolving viruses is poorly understood. Here, we investigate the antibody repertoire of a chronically HIV-1/HCV co-infected individual using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq). We identify five HIV-1/HCV cross-reactive antibodies demonstrating binding and functional cross-reactivity between HIV-1 and HCV envelope glycoproteins. All five antibodies show exceptional HCV neutralization breadth and effector functions against both HIV-1 and HCV. One antibody, mAb688, also cross-reacts with influenza and coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We examine the development of these antibodies using next-generation sequencing analysis and lineage tracing and find that somatic hypermutation established and enhanced this reactivity. These antibodies provide a potential future direction for therapeutic and vaccine development against current and emerging infectious diseases. More broadly, chronic co-infection represents a complex immunological challenge that can provide insights into the fundamental rules that underly antibody-antigen specificity.
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•LIBRA-seq is applied to characterize antibody responses to HIV-1/HCV co-infection•A diverse set of functional HIV-1/HCV cross-reactive antibodies are identified•A glycan-directed antibody exhibits exceptionally broad anti-viral recognition•Antibody somatic hypermutation is a major determinant for HIV-1/HCV cross-reactivity
Pilewski et al. uses LIBRA-seq to identify multiple, functional HIV-1/HCV cross-reactive antibodies with diverse epitope specificities. This study identifies a glycan-reactive, broadly anti-viral antibody recognizing the NTD of SARS-CoV-2, in addition to antigens from multiple other viruses. The authors further show that somatic hypermutation both establishes and enhances HIV-1/HCV cross-reactivity.
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