Combinatorial immune refocusing within the influenza hemagglutinin RBD improves cross-neutralizing antibody responses

The receptor-binding domain (RBD) of influenza virus hemagglutinin (HA) elicits potently neutralizing yet mostly strain-specific antibodies. Here, we evaluate the ability of several immunofocusing techniques to enhance the functional breadth of vaccine-elicited immune responses against the HA RBD. We present a series of "trihead" nanoparticle immunogens that display native-like closed trimeric RBDs from the HAs of several H1N1 influenza viruses. The series includes hyperglycosylated and hypervariable variants that incorporate natural and designed sequence diversity at key positions in the receptor-binding site periphery. Nanoparticle immunogens displaying triheads or hyperglycosylated triheads elicit higher hemagglutination inhibition (HAI) and neutralizing activity than the corresponding immunogens lacking either trimer-stabilizing mutations or hyperglycosylation. By contrast, mosaic nanoparticle display and antigen hypervariation do not significantly alter the magnitude or breadth of vaccine-elicited antibodies. Our results yield important insights into antibody responses against the RBD and the ability of several structure-based immunofocusing techniques to influence vaccine-elicited antibody responses.

mRNA-based VP8* nanoparticle vaccines against rotavirus are highly immunogenic in rodents

Despite the availability of live-attenuated oral vaccines, rotavirus remains a major cause of severe childhood diarrhea worldwide. Due to the growing demand for parenteral rotavirus vaccines, we developed mRNA-based vaccine candidates targeting the viral spike protein VP8*. Our monomeric P2 (universal T cell epitope)-VP8* mRNA design is equivalent to a protein vaccine currently in clinical development, while LS (lumazine synthase)-P2-VP8* was designed to form nanoparticles. Cyro-electron microscopy and western blotting-based data presented here suggest that proteins derived from LS-P2-VP8* mRNA are secreted in vitro and self-assemble into 60-mer nanoparticles displaying VP8*. mRNA encoded VP8* was immunogenic in rodents and introduced both humoral and cellular responses. LS-P2-VP8* induced superior humoral responses to P2-VP8* in guinea pigs, both as monovalent and trivalent vaccines, with encouraging responses detected against the most prevalent P genotypes. Overall, our data provide evidence that trivalent LS-P2-VP8* represents a promising mRNA-based next-generation rotavirus vaccine candidate.

De novo design of monomeric helical bundles for pH-controlled membrane lysis

Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.

An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting

The existence of broadly cross-reactive antibodies that can neutralize diverse HIV-1 isolates (bnAbs) has been appreciated for more than a decade. Many high-resolution structures of bnAbs, typically with one or two well-characterized HIV-1 Env glycoprotein trimers, have been reported. However, an understanding of how such antibodies grapple with variability in their antigenic targets across diverse viral isolates has remained elusive. To achieve such an understanding requires first characterizing the extent of structural and antigenic variation embodied in Env, and then identifying how a bnAb overcomes that variation at a structural level. Here, using hydrogen/deuterium-exchange mass spectrometry (HDX-MS) and quantitative measurements of antibody binding kinetics, we show that variation in structural ordering in the V1/V2 apex of Env across a globally representative panel of HIV-1 isolates has a marked effect on antibody association rates and affinities. We also report cryo-EM reconstructions of the apex-targeting PGT145 bnAb bound to two divergent Env that exhibit different degrees of structural dynamics throughout the trimer structures. Parallel HDX-MS experiments demonstrate that PGT145 bnAb has an exquisitely focused footprint at the trimer apex where binding did not yield allosteric changes throughout the rest of the structure. These results demonstrate that structural dynamics are a cryptic determinant of antigenicity, and mature antibodies that have achieved breadth and potency in some cases are able to achieve their broad cross-reactivity by "threading the needle" and binding in a highly focused fashion, thus evading and overcoming the variable properties found in Env from divergent isolates.

hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics

SARS-CoV and SARS-CoV-2 cell entry begins when spike glycoprotein (S) docks with the human ACE2 (hACE2) receptor. While the two coronaviruses share a common receptor and architecture of S, they exhibit differences in interactions with hACE2 as well as differences in proteolytic processing of S that trigger the fusion machine. Understanding how those differences impact S activation is key to understand its function and viral pathogenesis. Here, we investigate hACE2-induced activation in SARS-CoV and SARS-CoV-2 S using hydrogen/deuterium-exchange mass spectrometry (HDX-MS). HDX-MS revealed differences in dynamics in unbound S, including open/closed conformational switching and D614G-induced S stability. Upon hACE2 binding, notable differences in transduction of allosteric changes were observed extending from the receptor binding domain to regions proximal to proteolytic cleavage sites and the fusion peptide. Furthermore, we report that dimeric hACE2, the native oligomeric form of the receptor, does not lead to any more pronounced structural effect in S compared to saturated monomeric hACE2 binding. These experiments provide mechanistic insights into receptor-induced activation of Sarbecovirus spike proteins.

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection

The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor-binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are unique in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.

Structural dynamics reveal subtype-specific activation and inhibition of influenza virus hemagglutinin

Influenza hemagglutinin (HA) is a prototypical class 1 viral entry glycoprotein, responsible for mediating receptor binding and membrane fusion. Structures of its prefusion and postfusion forms, embodying the beginning and endpoints of the fusion pathway, have been extensively characterized. Studies probing HA dynamics during fusion have begun to identify intermediate states along the pathway, enhancing our understanding of how HA becomes activated and traverses its conformational pathway to complete fusion. HA is also the most variable, rapidly evolving part of influenza virus, and it is not known whether mechanisms of its activation and fusion are conserved across divergent viral subtypes. Here, we apply hydrogen-deuterium exchange mass spectrometry to compare fusion activation in two subtypes of HA, H1 and H3. Our data reveal subtype-specific behavior in the regions of HA that undergo structural rearrangement during fusion, including the fusion peptide and HA1/HA2 interface. In the presence of an antibody that inhibits the conformational change (FI6v3), we observe that acid-induced dynamic changes near the epitope are dampened, but the degree of protection at the fusion peptide is different for the two subtypes investigated. These results thus provide new insights into variation in the mechanisms of influenza HA's dynamic activation and its inhibition.

Combinatorial immune refocusing within the influenza hemagglutinin head elicits cross-neutralizing antibody responses

The head domain of influenza hemagglutinin (HA) elicits potently neutralizing yet mostly strain-specific antibodies during infection and vaccination. Here we evaluated a series of immunogens that combined several immunofocusing techniques for their ability to enhance the functional breadth of vaccine-elicited immune responses. We designed a series of "trihead" nanoparticle immunogens that display native-like closed trimeric heads from the HAs of several H1N1 influenza viruses, including hyperglycosylated variants and hypervariable variants that incorporate natural and designed sequence diversity at key positions in the periphery of the receptor binding site (RBS). Nanoparticle immunogens displaying triheads or hyperglycosylated triheads elicited higher HAI and neutralizing activity against vaccine-matched and -mismatched H1 viruses than corresponding immunogens lacking either trimer-stabilizing mutations or hyperglycosylation, indicating that both of these engineering strategies contributed to improved immunogenicity. By contrast, mosaic nanoparticle display and antigen hypervariation did not significantly alter the magnitude or breadth of vaccine-elicited antibodies. Serum competition assays and electron microscopy polyclonal epitope mapping revealed that the trihead immunogens, especially when hyperglycosylated, elicited a high proportion of antibodies targeting the RBS, as well as cross-reactive antibodies targeting a conserved epitope on the side of the head. Our results yield important insights into antibody responses against the HA head and the ability of several structure-based immunofocusing techniques to influence vaccine-elicited antibody responses.

Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection

The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs, including recently circulating BA.4/BA.5, in both pseudovirus-based and live virus assays, and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.

Exploring adherence to an early rule-out pathway for myocardial infarction in the emergency department using mixed-methods

Background

Incorporating a high-sensitivity cardiac troponin assay into a care pathway for the assessment of suspected acute coronary syndrome has enabled myocardial infarction to be ruled out earlier.

Purpose

Using mixed methods, we explored adherence to an early rule-out pathway in the HiSTORIC (High-Sensitivity Cardiac Troponin on Presentation to Rule Out Myocardial Infarction) randomised controlled trial.

Methods

In 16,972 consecutive patients we evaluated clinician adherence to an early rule-out pathway for the assessment of suspected acute coronary syndrome. Adherence was defined in patients with presentation cardiac troponin I concentrations <5ng/L and symptom onset >2 hours from presentation without serial troponin testing (type 1 adherence); presentation troponin <5ng/L and symptom onset ≤2 hours from presentation with serial testing (type 2 adherence); or presentation troponin between 5ng/L and sex-specific 99th centile with serial testing (type 3 adherence). Semi-structured interviews were conducted with 23 clinicians to aid interpretation of the quantitative analysis. Qualitative data were coded and organized into themes.

Results

In patients with troponin <5ng/L presenting >2hr from symptom onset, adherence was achieved in 81% of patients. In patients presenting ≤2hr from symptom onset, 35% of patients had a second troponin test. In patients with an initial troponin concentration between 5ng/L and the 99th centile, 65% of patients had a second troponin test. Compared to patients managed by clinicians who were adherent to the pathway, patients with troponin over-testing (type 1 non-adherence) were more likely to be older (mean age 52±16 years versus 58±14, P<0.001) and have a history of coronary disease (11% versus 27%, P<0.001). In contrast, patients with under testing (type 2 non-adherence) tended to be younger (mean age 49±16 versus 63±15, P<0.001), female (50% versus 37%, P<0.001) and have lower presentation troponin levels (median concentration 1.0ng/L IQR 1.0 to 2.0, versus 5.0ng/L IQR 2.0–10.0) compared to those in whom testing was performed according to pathway recommendations. Semi-structured interview data revealed how pathway adherence was influenced by five main themes: guideline characteristics, patient characteristics, the healthcare practitioner, the healthcare system and scientific evidence. Clear visual pathway layout was fundamental in achieving optimal adherence. Strong clinical suspicion of acute coronary syndrome promoted repeat troponin testing and deviation from the pathway was felt to be justifiable by more senior clinicians.

Conclusion

This analysis revealed successful implementation of the early rule-out pathway with interview data aiding interpretation of trial data. Younger patients with lower troponin concentrations were less likely to receive pathway recommended serial troponin testing. Clinical judgement is one of the main reasons for discontinuation of pathway recommendations.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): British Heart Foundation

Machine learning to optimise use of cardiac troponin in the diagnosis of acute myocardial infarction

Background

Guidelines recommend fixed cardiac troponin thresholds for the assessment of patients with suspected acute coronary syndrome, however, performance varies in important patient groups as concentrations are influenced by age, sex and comorbidities. This limitation can be addressed using machine learning algorithms.

Methods

Machine learning algorithms were developed that integrate cardiac troponin concentrations at presentation or on serial testing with age, sex and clinical features in 10,038 consecutive emergency patients with suspected acute coronary syndrome. The primary outcome was an adjudicated diagnosis of type 1, type 4b or type 4c myocardial infarction. The best performing algorithm was selected for the CoDE-ACS (Collaboration for the Diagnosis and Evaluation of Acute Coronary Syndrome) decision-support tool, and performance was externally validated in 3,035 patients pooled from three prospective studies.

Findings

CoDE-ACS had excellent discrimination and calibration using cardiac troponin at presentation (area under curve [AUC] 0.959, 95% confidence interval 0.948–0.971, Brier score 0.040), in the pooled external validation cohort. At presentation, the rule-out score identified 62.1% (1,885/3,035) of all patients as low-probability of myocardial infarction with a 99.5% (99.1–99.7%) negative predictive value and 97.0% (96.3–97.6%) sensitivity. The rule-in score identified 8.3% (252/3,035) of patients as high-probability with an 83.7% (82.4–85.0%) positive predictive value and 98.5% (98.0–98.9%) specificity. Performance of the rule-out and rule-in scores was consistent across patient subgroups (Figure 1 and Figure 2). CoDE-ACS incorporating a second cardiac troponin measurement also had excellent discrimination and calibration (AUC 0.971 [0.962–0.980], Brier score 0.039) and refined the individualised probabilities in the 29.5% (898/3,035) of patients neither ruled-out or ruled-in at presentation to guide further investigation.

Conclusions

We developed and externally validated the CoDE-ACS decision-support tool using machine learning to aid in the diagnosis of myocardial infarction. CoDE-ACS had excellent diagnostic performance to rule-out and rule-in myocardial infarction at presentation, performed consistently across patient subgroups, and provided individualised probabilities to guide further care in those who require serial troponin measurements.

Conclusions

We developed and externally validated the CoDE-ACS decision-support tool using machine learning to aid in the diagnosis of myocardial infarction. CoDE-ACS had excellent diagnostic performance to rule-out and rule-in myocardial infarction at presentation, performed consistently across patient subgroups, and provided individualised probabilities to guide further care in those who require serial troponin measurements.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): National Institute for Health ResearchBritish Heart Foundation

Impact of patient selection on performance of an early rule-out pathway for myocardial infarction: from research to the real world

Background

Early rule-out pathways for myocardial infarction using high-sensitivity cardiac troponin are widely recommended in the assessment of patients with suspected acute coronary syndrome. Although developed in selected patients participating in research studies, these pathways are applied more widely in clinical practice where the diagnostic performance and effectiveness of these pathways may differ.

Purpose

To evaluate the performance of an early rule-out pathway for myocardial infarction using high-sensitivity cardiac troponin in selected and consecutive unselected patients with suspected acute coronary syndrome.

Methods

Presentation and serial high-sensitivity cardiac troponin I concentrations were measured in two cohorts of patients with suspected acute coronary syndrome presenting to the Emergency Departments across three acute care hospitals in Scotland. In the unselected cohort, electronic health record data were collected on consecutive patients in whom the usual care clinician measured cardiac troponin for suspected acute coronary syndrome. In the selected cohort, patients with suspected acute coronary syndrome were approached between 8am and 8pm by research staff and written informed consent obtained. In both cohorts, the performance of the High-STEACS early rule-out pathway was evaluated for an adjudicated diagnosis of myocardial infarction (type 1, type 4b or type 4c) during the index hospital admission.

Results

The unselected and selected patient cohorts comprised of 1,242 (median age 60 [interquartile range 47–75] years, 46% women) and 1,695 (median age 61 [52–73] years, 40% women) patients respectively. Myocardial infarction was diagnosed in 6% (74/1,242) and 14% (232/1,695) of patients in the unselected and selected patient cohorts respectively. More patients had myocardial infarction ruled-out in the unselected (74% [828/1,112] versus 66% [1,102/1,678]; P<0.001), with similar negative predictive value (99.9% [95% CI 99.7%-100%] versus 99.7% [95% CI 99.4%-99.0%) and sensitivity (99.3% [95% CI 97.4%-100%] versus 98.9% [95% CI 97.6%-99.9%]; Figure 1). In the selected cohort, more patients had intermediate troponin concentrations requiring serial testing (36% versus 29%) or had myocardial infarction diagnosed (34% versus 26%; P<0.001 for both). In contrast, the positive predictive value for myocardial infarction was lower in unselected patients (26.1% [95% CI 21.2%-31.4%] versus 39.9% [95% CI 35.9%-44.0%]).

Conclusion

The prevalence of myocardial infarction is lower in patients with suspected acute coronary syndrome evaluated in routine practice compared to those selected to participate in a research study. Whilst more patients have myocardial infarction accurately ruled out, the positive-predictive value in those ruled in is lower resulting in more hospital admissions with elevated cardiac troponin due to other conditions.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): British Heart FoundationMedical Research Council

Vaccination with a structure-based stabilized version of malarial antigen Pfs48/45 elicits ultra-potent transmission-blocking antibody responses

Malaria transmission-blocking vaccines (TBVs) aim to elicit human antibodies that inhibit sporogonic development of Plasmodium falciparum in mosquitoes, thereby preventing onward transmission. Pfs48/45 is a leading clinical TBV candidate antigen and is recognized by the most potent transmission-blocking monoclonal antibody (mAb) yet described; still, clinical development of Pfs48/45 antigens has been hindered, largely by its poor biochemical characteristics. Here, we used structure-based computational approaches to design Pfs48/45 antigens stabilized in the conformation recognized by the most potently inhibitory mAb, achieving >25°C higher thermostability compared with the wild-type protein. Antibodies elicited in mice immunized with these engineered antigens displayed on liposome-based or protein nanoparticle-based vaccine platforms exhibited 1-2 orders of magnitude superior transmission-reducing activity, compared with immunogens bearing the wild-type antigen, driven by improved antibody quality. Our data provide the founding principles for using molecular stabilization solely from antibody structure-function information to drive improved immune responses against a parasitic vaccine target.

Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery

Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV's complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein's post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.

Structural dynamics reveal isolate-specific differences at neutralization epitopes on HIV Env

The envelope glycoprotein (Env) is the sole target for neutralizing antibodies against HIV and the most rapidly evolving, variable part of the virus. High-resolution structures of Env trimers captured in the pre-fusion, closed conformation have revealed a high degree of structural similarity across diverse isolates. Biophysical data, however, indicate that Env is highly dynamic, and the level of dynamics and conformational sampling is believed to vary dramatically between HIV isolates. Dynamic differences likely influence neutralization sensitivity, receptor activation, and overall trimer stability. Here, using hydrogen/deuterium-exchange mass spectrometry (HDX-MS), we have mapped local dynamics across native-like Env SOSIP trimers from diverse isolates. We show that significant differences in epitope order are observed across most sites targeted by broadly neutralizing antibodies. We also observe isolate-dependent conformational switching that occurs over a broad range of timescales. Lastly, we report that hyper-stabilizing mutations that dampen dynamics in some isolates have little effect on others.

Structure-based design of stabilized recombinant influenza neuraminidase tetramers

Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across non-bat subtypes adopt various tetrameric conformations, including an “open” state that may help explain poorly understood variations in NA stability across viral strains and subtypes. We use homology-directed protein design to uncover the structural principles underlying these distinct tetrameric conformations and stabilize multiple recombinant NAs in the “closed” state, yielding two near-atomic resolution structures of NA by cryo-EM. In addition to enhancing thermal stability, conformational stabilization improves affinity to protective antibodies elicited by viral infection, including antibodies targeting a quaternary epitope and the broadly conserved catalytic site. Stabilized NAs can also be integrated into viruses without affecting fitness. Our findings provide a deeper understanding of NA structure, stability, and antigenicity, and establish design strategies for reinforcing the conformational integrity of recombinant NA proteins.

Influenza virus neuraminidase (NA) is a drug target and a potential vaccine antigen. Here, the authors provide a detailed analysis of the conformational stability of NA, and show how expression and stability of recombinant NA antigens can be strengthened through structure-based design.

Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies

HIV-1 clade C envelope immunogens that elicit both neutralizing and non-neutralizing V1V2-scaffold-specific antibodies (protective correlates from RV144 human trial) are urgently needed due to the prevalence of this clade in the most impacted regions worldwide. To achieve this, we introduce structure-guided changes followed by consensus-C-sequence-guided optimizations at the V2 region to generate UFO-v2-RQH¹⁷³ trimer. This improves the abundance of well-formed trimers. Following the immunization of rabbits, the wild-type protein fails to elicit any autologous neutralizing antibodies, but UFO-v2-RQH¹⁷³ elicits both autologous neutralizing and broad V1V2-scaffold antibodies. The variant with a 173Y modification in the V2 region, most prevalent among HIV-1 sequences, shows decreased ability in displaying a native-like V1V2 epitope with time in vitro and elicited antibodies with lower neutralizing and higher V1V2-scaffold activities. Our results identify a stabilized clade C trimer capable of eliciting improved neutralizing and V1V2-scaffold antibodies and reveal the importance of the V2 region in tuning this.

Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice

HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed characterization. Here, we used cryo-electron tomography to analyze Env in mature and immature HIV-1 particles. Immature particles showed distinct Env positioning relative to the underlying Gag lattice, providing insights into long-standing questions about Env incorporation. A 9.1-Å sub-tomogram-averaged reconstruction of virion-bound Env in conjunction with structural mass spectrometry revealed unexpected features, including a variable central core of the gp41 subunit, heterogeneous glycosylation between protomers, and a flexible stalk that allows Env tilting and variable exposure of neutralizing epitopes. Together, our results provide an integrative understanding of HIV assembly and structural variation in Env antigen presentation.

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Structural analysis of immature HIV shows Env position on Gag hexameric rim

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HIV Env has a flexible stalk that allows tilting and variation in stalk exposure

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Env’s fusion peptide is dynamic and exposed to solvent in membrane-bound Env

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Glycans in unliganded Env shield antigenic sites and vary between protomers

Mannose-binding lectin and complement mediate follicular localization and enhanced immunogenicity of diverse protein nanoparticle immunogens

Nanoparticle (NP) vaccine formulations promote immune responses through multiple mechanisms. We recently reported that mannose-binding lectin (MBL) triggers trafficking of glycosylated HIV Env-immunogen NPs to lymph node follicles. Here, we investigate effects of MBL and complement on NP forms of HIV and other viral antigens. MBL recognition of oligomannose on gp120 nanoparticles significantly increases antigen accumulation in lymph nodes and antigen-specific germinal center (GC) responses. MBL and complement also mediate follicular trafficking and enhance GC responses to influenza, HBV, and HPV particulate antigens. Using model protein nanoparticles bearing titrated levels of glycosylation, we determine that mannose patches at a minimal density of 2.1 × 10^-3 mannose patches/nm² are required to trigger follicular targeting, which increases with increasing glycan density up to at least ∼8.2 × 10^-3 patches/nm². Thus, innate immune recognition of glycans has a significant impact on humoral immunity, and these findings provide a framework for engineering glycan recognition to optimize vaccine efficacy.

How a broadly neutralizing antibody grapples with antigenic and conformational diversity in dengue virus

In this issue of Cell, two studies apply powerful structural approaches to probe the modes of interaction between a broadly neutralizing antibody and a conserved epitope found on four dengue virus serotypes and Zika virus. These findings offer new insights into how a broadly neutralizing antibody surmounts antigenic and conformational variation.

Machine learning to aid in the diagnosis of acute heart failure in the emergency department

Background

B-type natriuretic peptide (BNP) and mid-regional pro-atrial natriuretic peptide (MRproANP) testing are recommended to aid in the diagnosis of acute heart failure. However, the application of these biomarkers for optimal diagnostic performance is uncertain.

Methods

We performed a systematic review and harmonised individual patient-level data to evaluate the diagnostic performance of BNP and MRproANP for the diagnosis of acute heart failure using random-effects meta-analysis. We subsequently developed and externally validated a decision-support tool called CoDE-HF for both BNP and MRproANP that combines the natriuretic peptide concentrations with clinical variables using machine learning to report the probability of acute heart failure for an individual patient.

Results

Fourteen studies from 12 countries provided individual patient-level data in 8,493 patients for BNP and 3,847 patients for MRproANP, in whom, 48.3% (4,105/8,493) and 41.3% (1,611/3899) had an adjudicated diagnosis of acute heart failure, respectively. The negative and positive predictive values of guideline-recommended thresholds for BNP (100 pg/mL) and MR-proANP (120 pg/mL) were 93.6% (95% confidence interval 88.4–96.6%) and 68.8% (62.9–74.2%), and 95.6% (92.2–97.6%) and 64.8% (56.3–72.5%), respectively. However, we observed significant heterogeneity in the diagnostic performance across important patient subgroups (Figure 1). In the external validation cohort, CoDE-HF was well calibrated with excellent discrimination in those without prior acute heart failure for both BNP and MRproANP (area under the curve of 0.946 [0.933–0.958] and 0.943 [0.921–0.964], and Brier scores of 0.105 and 0.073, respectively). CoDE-HF performed consistently across all subgroups for both BNP and MRproANP, and identified 30% and 65.7% at low-probability (negative predictive value of 99.1% [98.8–99.3%] and 99.1% [98.8–99.4%]), and 30% and 17.3% at high-probability (positive predictive value of 91.3% [90.7–91.9%] and 70.0% [68.5–71.4%]) in those without prior heart failure, respectively (Figure 2).

Conclusion

In an international collaborative analysis, we observed that guideline-recommended thresholds for BNP and MRproANP to diagnose acute heart failure varied significantly across patient subgroups. A decision-support tool using machine learning to combine natriuretic peptides as a continuous measure and other clinical variables provides a more accurate and individualised approach.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): Medical Research Council and British Heart Foundation Figure 1. NPV of BNP threshold (100 pg/mL)Figure 2. NPV of the CoDE-HF rule-out score

Mechanisms of myocardial injury and clinical outcomes in patients hospitalised with suspected COVID-19

Background

Myocardial injury is associated with adverse outcomes in patients with COVID-19. However, the prognostic role of myocardial injury in COVID-19 compared to other acute illnesses and the underlying mechanisms of injury are poorly understood.

Methods

In a prospective, multi-centre, cohort study conducted in secondary and tertiary care hospitals in Scotland, all consecutive patients with suspected COVID-19 underwent cardiac troponin (ARCHITECTSTAT high-sensitive troponin I (hs-cTnI) assay; Abbott Laboratories) testing in plasma that was surplus to clinical requirements. The results were not reported unless required by the attending clinician. We evaluated the prevalence of myocardial injury, mechanisms and outcomes in all patients. In those with any hs-cTnI concentration above the sex-specific 99th centile the diagnosis was adjudicated according to the 4th Universal Definition of Myocardial Infarction. The primary outcome of all-cause mortality was compared in those with and without myocardial injury and COVID-19 by cox regression adjusted for age, sex, renal function and co-morbidities.

Results

A total of 2,916 (median age 69 [interquartile range, IQR 54–79] years, 53% women) consecutive patients with suspected COVID-19 were followed up for 228 [IQR 203–249] days. Myocardial injury occurred in 26% (750/2,916) with a median troponin concentration of 66 [35–178] ng/L; the prevalence was 41% (46/112) and 25% (704/2,804) in those with and without COVID-19, respectively. The most common mechanism was acute non-ischaemic myocardial injury occurring in 80% (37/46) and 71% (502/704) of patients with and without COVID-19, respectively. Type 1 myocardial infarction (2% and 4%), type 2 myocardial infarction (7% and 14%) and chronic myocardial injury (11% and 11%) were less common and only one patient had confirmed myocarditis. In patients with myocardial injury mortality was increased compared to those without (P<0.001 log rank), whether they had COVID-19 (54% [25/46] versus 26% [17/66]) or not (35% [248/704] versus 14% [294/2100]). Myocardial injury was an independent predictor of death in all patients (adjusted hazard ratio [aHR] 2.04, 95% confidence interval [CI] 1.71 to 2.43), but this excess risk was not higher in patients with COVID-19 (aHR 1.58, 95% CI 0.75 to 3.15) compared to those without the condition (aHR 2.01, 95% CI 1.81 to 2.49).

Conclusion

Myocardial injury is common in hospitalised patients with suspected COVID-19 whether or not COVID-19 was the cause of their presentation. The majority of patients had acute non-ischaemic myocardial injury rather than a defined cardiac condition. Despite this the presence of myocardial injury was an independent predictor of death in all hospitalised patients.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): British Heart Foundation Kaplan-Meier curve for all-cause death

Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization

Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 μg/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a β-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184-186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.

Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection

Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.

Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design

The unprecedented global demand for SARS-CoV-2 vaccines has demonstrated the need for highly effective vaccine candidates that are thermostable and amenable to large-scale manufacturing. Nanoparticle immunogens presenting the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein (S) in repetitive arrays are being advanced as second-generation vaccine candidates, as they feature robust manufacturing characteristics and have shown promising immunogenicity in preclinical models. Here, we used previously reported deep mutational scanning (DMS) data to guide the design of stabilized variants of the RBD. The selected mutations fill a cavity in the RBD that has been identified as a linoleic acid binding pocket. Screening of several designs led to the selection of two lead candidates that expressed at higher yields than the wild-type RBD. These stabilized RBDs possess enhanced thermal stability and resistance to aggregation, particularly when incorporated into an icosahedral nanoparticle immunogen that maintained its integrity and antigenicity for 28 days at 35-40°C, while corresponding immunogens displaying the wild-type RBD experienced aggregation and loss of antigenicity. The stabilized immunogens preserved the potent immunogenicity of the original nanoparticle immunogen, which is currently being evaluated in a Phase I/II clinical trial. Our findings may improve the scalability and stability of RBD-based coronavirus vaccines in any format and more generally highlight the utility of comprehensive DMS data in guiding vaccine design.

Quadrivalent influenza nanoparticle vaccines induce broad protection

Influenza vaccines that confer broad and durable protection against diverse virus strains would have a major impact on global health¹. Here we show that computationally designed, two-component nanoparticle immunogens² induce potently neutralizing and broadly protective antibody responses against a wide variety of influenza viruses. The nanoparticle immunogens display 20 hemagglutinin (HA) trimers in an ordered array, and their assembly in vitro enables precisely controlled co-display of multiple distinct HAs in defined ratios. Nanoparticle immunogens co-displaying the four HAs of licensed quadrivalent influenza vaccines (QIV) elicited antibody responses against vaccine-matched strains that were equivalent or superior to commercial QIV, and simultaneously induced broadly protective antibody responses to heterologous viruses by targeting the subdominant yet conserved HA stem. The combination of potent receptor-blocking and cross-reactive stem-directed antibodies induced by the nanoparticle immunogens make them attractive candidates for a supraseasonal influenza vaccine candidates with potential to replace conventional seasonal vaccines³.

Simple Platform for Automating Decoupled LC-MS Analysis of Hydrogen/Deuterium Exchange Samples

Hydrogen/deuterium exchange with mass spectrometry (HDX-MS) is capable of providing unique insight into complex biological systems that are difficult to study by other techniques. Due to arduous sample handling requirements, automating HDX experimentation for higher throughput requires specialized equipment. While recent advances have enabled automation of sample preparation and analysis, several proteins of interest and types of HDX experiments remain incompatible with automated workflows and require manual sample preparation that greatly limits experimental throughput. To expand throughput and increase the precision of HDX-MS for systems requiring manual preparation, we have developed an inexpensive autosampler capable of thawing and injecting frozen HDX-MS samples in a highly reproducible manner.

Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies

A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naive antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of broadly active ADCC antibodies may require mutations that enable high-affinity antigen recognition along with mutations that optimize factors contributing to functional ADCC activity.

Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2

A safe, effective, and scalable vaccine is needed to halt the ongoing SARS-CoV-2 pandemic. We describe the structure-based design of self-assembling protein nanoparticle immunogens that elicit potent and protective antibody responses against SARS-CoV-2 in mice. The nanoparticle vaccines display 60 SARS-CoV-2 spike receptor-binding domains (RBDs) in a highly immunogenic array and induce neutralizing antibody titers 10-fold higher than the prefusion-stabilized spike despite a 5-fold lower dose. Antibodies elicited by the RBD nanoparticles target multiple distinct epitopes, suggesting they may not be easily susceptible to escape mutations, and exhibit a lower binding:neutralizing ratio than convalescent human sera, which may minimize the risk of vaccine-associated enhanced respiratory disease. The high yield and stability of the assembled nanoparticles suggest that manufacture of the nanoparticle vaccines will be highly scalable. These results highlight the utility of robust antigen display platforms and have launched cGMP manufacturing efforts to advance the SARS-CoV-2-RBD nanoparticle vaccine into the clinic.

Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2

A safe, effective, and scalable vaccine is needed to halt the ongoing SARS-CoV-2 pandemic. We describe the structure-based design of self-assembling protein nanoparticle immunogens that elicit potent and protective antibody responses against SARS-CoV-2 in mice. The nanoparticle vaccines display 60 SARS-CoV-2 spike receptor-binding domains (RBDs) in a highly immunogenic array and induce neutralizing antibody titers 10-fold higher than the prefusion-stabilized spike despite a 5-fold lower dose. Antibodies elicited by the RBD nanoparticles target multiple distinct epitopes, suggesting they may not be easily susceptible to escape mutations, and exhibit a lower binding:neutralizing ratio than convalescent human sera, which may minimize the risk of vaccine-associated enhanced respiratory disease. The high yield and stability of the assembled nanoparticles suggest that manufacture of the nanoparticle vaccines will be highly scalable. These results highlight the utility of robust antigen display platforms and have launched cGMP manufacturing efforts to advance the SARS-CoV-2-RBD nanoparticle vaccine into the clinic.

Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2

A safe, effective, and scalable vaccine is urgently needed to halt the ongoing SARS-CoV-2 pandemic. Here, we describe the structure-based design of self-assembling protein nanoparticle immunogens that elicit potent and protective antibody responses against SARS-CoV-2 in mice. The nanoparticle vaccines display 60 copies of the SARS-CoV-2 spike (S) glycoprotein receptor-binding domain (RBD) in a highly immunogenic array and induce neutralizing antibody titers roughly ten-fold higher than the prefusion-stabilized S ectodomain trimer despite a more than five-fold lower dose. Antibodies elicited by the nanoparticle immunogens target multiple distinct epitopes on the RBD, suggesting that they may not be easily susceptible to escape mutations, and exhibit a significantly lower binding:neutralizing ratio than convalescent human sera, which may minimize the risk of vaccine-associated enhanced respiratory disease. The high yield and stability of the protein components and assembled nanoparticles, especially compared to the SARS-CoV-2 prefusion-stabilized S trimer, suggest that manufacture of the nanoparticle vaccines will be highly scalable. These results highlight the utility of robust antigen display platforms for inducing potent neutralizing antibody responses and have launched cGMP manufacturing efforts to advance the lead RBD nanoparticle vaccine into the clinic.

New Biophysical Approaches Reveal the Dynamics and Mechanics of Type I Viral Fusion Machinery and Their Interplay with Membranes

Protein-mediated membrane fusion is a highly regulated biological process essential for cellular and organismal functions and infection by enveloped viruses. During viral entry the membrane fusion reaction is catalyzed by specialized protein machinery on the viral surface. These viral fusion proteins undergo a series of dramatic structural changes during membrane fusion where they engage, remodel, and ultimately fuse with the host membrane. The structural and dynamic nature of these conformational changes and their impact on the membranes have long-eluded characterization. Recent advances in structural and biophysical methodologies have enabled researchers to directly observe viral fusion proteins as they carry out their functions during membrane fusion. Here we review the structure and function of type I viral fusion proteins and mechanisms of protein-mediated membrane fusion. We highlight how recent technological advances and new biophysical approaches are providing unprecedented new insight into the membrane fusion reaction.

Bridging protein structure, dynamics, and function using hydrogen/deuterium-exchange mass spectrometry

Much of our understanding of protein structure and mechanistic function has been derived from static high-resolution structures. As structural biology has continued to evolve it has become clear that high-resolution structures alone are unable to fully capture the mechanistic basis for protein structure and function in solution. Recently Hydrogen/Deuterium-exchange Mass Spectrometry (HDX-MS) has developed into a powerful and versatile tool for structural biologists that provides novel insights into protein structure and function. HDX-MS enables direct monitoring of a protein's structural fluctuations and conformational changes under native conditions in solution even as it is carrying out its functions. In this review, we focus on the use of HDX-MS to monitor these dynamic changes in proteins. We examine how HDX-MS has been applied to study protein structure and function in systems ranging from large, complex assemblies to intrinsically disordered proteins, and we discuss its use in probing conformational changes during protein folding and catalytic function. STATEMENT FOR A BROAD AUDIENCE: The biophysical and structural characterization of proteins provides novel insight into their functionalities. Protein motions, ranging from small scale local fluctuations to larger concerted structural rearrangements, often determine protein function. Hydrogen/Deuterium-exchange Mass Spectrometry (HDX-MS) has proven a powerful biophysical tool capable of probing changes in protein structure and dynamic protein motions that are often invisible to most other techniques.

De novo design of tunable, pH-driven conformational changes

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

247Safety and efficacy of high-sensitivity cardiac troponin for risk stratification in patients with suspected acute coronary syndrome

Background

Guidelines acknowledge the emerging role of high-sensitivity cardiac troponin (hs-cTn) assays for the risk stratification and rapid rule-out of myocardial infarction, but multiple approaches have been described. We previously demonstrated the utility of a single hs-cTnI concentration <5 ng/L at presentation to risk stratify patients with suspected acute coronary syndrome (ACS).

Purpose

To assess the safety and efficacy of a hs-cTnI concentration <5 ng/L at presentation in consecutive patients included in the High-STEACS (High-SensitivityTroponin in the Evaluation of patients with Acute Coronary Syndrome) randomised controlled trial.

Methods

The High-STEACS trial was a stepped wedge cluster randomised controlled trial in ten hospitals across Scotland that included 48,282 patients in whom high-sensitivity cardiac troponin was requested by the attending clinician for evaluation of suspected ACS. Patients with ST-segment elevation myocardial infarction (STEMI) were excluded. We evaluated the negative predictive value (NPV) and sensitivity of a presentation hs-cTnI <5 ng/L for a composite outcome of type 1 myocardial infarction, or subsequent type 1 myocardial infarction or cardiac death at 30 days. To assess safety, we report the one-year risk of type 1 myocardial infarction or cardiac death. To assess efficacy, we report the proportion of patients with cardiac troponin <5 ng/L at presentation.

Results

We included 47,101 consecutive patients in the analysis (mean 61±17 years old, 47% female). Of these patients, 27,500 (58%) had a cardiac troponin <5 ng/L at presentation. Overall, 4,313/47,101 (9%) patients had a composite outcome at 30 days, but the event rate was only 0.4% in those with troponin <5 ng/L (98/27,500). The NPV for the composite outcome in those <5 ng/L was 99.7% (95% confidence intervals [CI] 99.6–99.7) and the sensitivity was 98.0% (95% CI 97.6–98.4). In those without evidence of myocardial injury at presentation (hs-cTnI <99thcentile), type 1 myocardial infarction or cardiac death at one year occurred in 197 (0.7%) patients with cardiac troponin <5 ng/L, compared to 647 (5.5%) of those ≥5 ng/L. The NPV was unchanged across all age groups, although efficacy fell as fewer older patients had hs-cTnI concentrations below the risk stratification threshold (see Figure).

Conclusion

A hs-cTnI concentration <5 ng/L at presentation identifies the majority of patients with suspected ACS as low-risk of early or late cardiac events. Although the proportion identified as low risk is reduced in older populations, the safety of this risk stratification approach is maintained across patients of all ages.

Acknowledgement/Funding

British Heart Foundation

3325Incidence, outcomes and microbiology in patients with infective endocarditis

Introduction

Despite recent improvements in management, infective endocarditis remains associated with high morbidity and mortality. Over the last few decades, several factors have impacted on both the incidence and outcomes following infective endocarditis.

Purpose

Using a national linkage approach, we describe the changing age- and sex-stratified incidence and outcomes of infective endocarditis in Scotland over the last 25 years.

Methods

We conducted a consecutive retrospective individual patient linkage study across multiple national databases. Using data extracted from the Scottish hospital discharge dataset held by the Information Services Division of NHS National Services Scotland, we extracted episodes for all patients aged 20 years or older who were admitted with infective endocarditis between January 1, 1990, and December 31, 2014 in Scotland, UK. Patient episodes with infective endocarditis were linked to national prescribing and microbiology databases. The primary outcome was 1-year mortality following the index presentation. Generalised additive models were constructed to estimate the crude and age- and sex-stratified incidence rates (using a poison distribution) as well as trends in mortality (using a binomial distribution) adjusted for age, sex and comorbidity.

Results

Across 12,446 individual patients, there were a total of 12,667 hospitalisations (mean age 68±17 years, 55% females) with infective endocarditis using a 5-year look back period. The estimated crude rate of hospitalisation increased from 7.38 per 100,000 (95% CI 6.58 to 8.28) in 1990 to 15.09 per 100,000 (95% CI 13.90 to 16.39) in 2014 (p<0.001). Over the period of the study, 31% (3,877/12,667) of people admitted to hospital with infective endocarditis died within one year of admission. Case fatality fell markedly in both men and women from 1990 to 2014 (Figure). Microbiology was status was available for 34% of all hospitalisations with staphylococcus cultures associated with worse outcomes.

Conclusions

Despite the crude incidence of infective endocarditis doubling over the last 25 years and case fatality remaining high, the risk of death has markedly fallen over the last two decades. Staphylococcus cultures remain an independent marker of poor prognosis in this cohort.

Acknowledgement/Funding

British Heart Foundation

P1578Outcomes in patients with renal impairment and myocardial injury or infarction identified by high-sensitivity cardiac troponin testing: a secondary analysis of the High-STEACS trial

Background

Patients with renal impairment are at increased risk of myocardial infarction (MI), but the interpretation of cardiac troponin is challenging in this setting. The use of high-sensitivity cardiac troponin (hs-cTn) assays increases the detection of myocardial injury, yet may contribute to uncertainty in the diagnosis of MI in those with renal impairment.

Purpose

To describe the diagnosis and outcomes of patients with myocardial injury or infarction identified using a hs-cTnI assay, stratified by renal function.

Methods

In a pre-specified secondary analysis of a stepped-wedge cluster-randomised controlled trial, we identified consecutive patients with a hs-cTnI concentration greater than the sex-specific 99th centile between June 2013 and March 2016. The diagnoses of type 1 or type 2 MI were adjudicated and classified according to the 4th Universal Definition of Myocardial Infarction. Renal impairment was defined as an estimated glomerular filtration rate (eGFR) of <60 mL/min/1.73m2.The primary outcome of type 1 or type 4b MI or cardiovascular death was compared in patients with and without renal impairment at 1 year.

Results

A measure of renal function was available in 47,334 (98.0%) patients, of whom 7,933 (16.8%) had renal impairment (mean age 76±12 years; 54% female). Plasma hs-cTnI concentrations were >99th centile in 47.9% (3,800/7,933) of patients with renal impairment and 16.3% (6,439/39,401) of patients with normal renal function. In those with and without renal impairment, the adjudicated diagnosis was type 1 MI in 35.2% (1,336/3,800) and 55.8% (3,596/6,439) of patients, and type 2 MI in 12.6% (480/3,800) and 9.7% (626/6,439) of patients, respectively (P<0.001 for both). In patients with hs-cTnI concentrations >99th centile, the primary outcome occurred in 24.9% (945/3,800) of patients with renal impairment, compared to 12.1% (779/6,439) of patients with normal renal function (P<0.001). In patients with type 1 MI, the primary outcome occurred in 32.6% (436/1,336) of those with renal impairment and 11.7% (419/3,596) of those without (P<0.001). In patients with type 2 MI, the primary outcome occurred in 20.4% (98/480) and 9.9% (62/626) of patients with and without renal impairment, respectively (P<0.001).

Conclusion

Almost half of all patients with suspected acute coronary syndrome and renal impairment have hs-cTnI concentrations greater than the sex-specific 99th centile. Whilst only one in three had a diagnosis of type 1 MI, an elevated troponin concentration was associated with a poorer prognosis in those with concomitant renal impairment compared to those without, irrespective of the index diagnosis.

Acknowledgement/Funding

British Heart Foundation

P1731High-sensitivity troponin with sex-specific thresholds in suspected acute coronary syndrome

Background/Introduction

Major disparities between women and men in the diagnosis, management and outcome of acute coronary syndrome are well recognised. Whether sex-specific diagnostic thresholds for myocardial infarction will address these differences is uncertain.

Purpose

To evaluate the impact of implementing a high-sensitivity cardiac troponin I (hs-cTnI) assay with sex-specific diagnostic thresholds for myocardial infarction in women and men with suspected acute coronary syndrome.

Methods

In a stepped-wedge, cluster-randomized controlled trial across ten hospitals we evaluated the implementation of a hs-cTnI assay in 48,282 (47% women) consecutive patients with suspected acute coronary syndrome. During a validation phase the hs-cTnI assay results were suppressed and a contemporary cTnI assay with a single threshold was used to guide care. Myocardial injury was defined as any hs-cTnI concentration >99th centile of 16 ng/L in women and 34 ng/L in men. The primary outcome was myocardial infarction after the initial presentation or cardiovascular death at 1 year. In this prespecified analysis, we evaluated outcomes in men and women before and after implementation of the hs-cTnI assay.

Results

Use of the hs-cTnI assay with sex-specific thresholds increased myocardial injury in women by 42% (from 3,521 (16%) to 4,991 (22%)) and by 6% in men (from 5,068 (20%) to 5,369 (21%)). Whilst treatment increased in both sexes, women with myocardial injury remained less likely than men to undergo coronary revascularisation (15% versus34%), or to receive dual anti-platelet (26% versus43%), statin (16% versus26%) or other preventative therapies (P<0.001 for all). The primary outcome occurred in 18% (369/2,072) and 17% (488/2,919) of women with myocardial injury during the validation and implementation phase respectively (adjusted hazard ratio 1.11, 95% confidence interval 0.92 to 1.33), compared to 18% (370/2,044) and 15% (513/3,325) of men (adjusted hazard ratio 0.85, 95% confidence interval 0.71 to 1.01).

Patient management

Conclusion

Use of sex-specific thresholds identified five-times more additional women than men with myocardial injury, such that the proportion of women and men with myocardial injury is now similar. Despite this increase, women received approximately half the number of treatments for coronary artery disease as men and their outcomes were not improved.

Acknowledgement/Funding

The British Heart Foundation

P3593Improving the performance of high-sensitivity cardiac troponin for the diagnosis of myocardial infarction

Background

The Universal Definition of Myocardial Infarction (UDMI) mandates a rise and/or fall in high-sensitivity cardiac troponin (hs-cTn) concentration with at least one measure above the 99th centile of a healthy reference population. However, the 99th centile varies by age, sex, and prevalence of comorbid disease within reference populations, and the application of a single threshold may create diagnostic uncertainty in unselected patients attending the Emergency Department.

Purpose

To compare performance of hs-cTnI at the 99th centile with a model that includes additional clinical variables, for the diagnosis of type 1 myocardial infarction.

Methods

The High-Sensitivity Troponin in the Evaluation of patients with Acute Coronary Syndrome (High-STEACS trial) was a stepped wedge cluster randomised controlled trial of 48,282 consecutive patients across 10 hospitals in Scotland. We evaluated the positive predictive value (PPV) of a hs-cTnI >99th centile for a diagnosis of type 1 myocardial infarction. Patients with ST-segment elevation myocardial infarction (STEMI) were excluded, and all were adjudicated according to the 4th UDMI. The study population was randomly divided into derivation (80%) and internal validation (20%) cohorts. Using generalised additive modelling, we tested the effect of adding clinically relevant variables to hs-cTnI for the prediction of type 1 myocardial infarction in the derivation cohort, and assessed performance of the final model in the validation cohort.

Results

We included 47,101 consecutive patients (61±17 years, 47% female), of whom 9,057 (19%) had at least one hs-cTnI >99th centile (7,207 in derivation and 1,850 in validation cohorts). There were 4,087 (45%) patients with type 1 myocardial infarction, with 3239 (45%) and 848 (46%) in the derivation and validation cohorts, respectively. Across the study population, PPV for type 1 myocardial infarction reduced markedly with increasing age (Figure). Age, sex, chest pain, ischaemia on the electrocardiogram, creatinine and rate of change of hs-cTnI were included in the model. Comorbidities (ischaemic heart disease, diabetes, stroke and hyperlipidaemia) did not improve model performance. In the validation cohort, the area under the curve (AUC) for type 1 myocardial infarction using the 99th centile alone was 0.72 (95% CI 0.70–0.74), whereas the AUC for the optimised model was 0.84 (95% CI 0.82–0.85) (p<0.001 by DeLong's test for difference, see Figure).

Figure 1

Conclusion

The diagnostic performance of the 99th centile for type 1 myocardial infarction is poor, particularly in older populations. A simple model including readily available clinical features improves diagnostic performance and with further external validation could support more individualised treatment decisions.

Acknowledgement/Funding

British Heart Foundation

249High-sensitivity cardiac troponin and the universal definition of myocardial infarction: a randomised controlled trial

Background

The Universal Definition of Myocardial Infarction recommends the 99th centile diagnostic threshold using a high-sensitivity cardiac troponin (hs-cTn) assay and the classification of patients by the etiology of myocardial injury. Whether implementation of this definition improves risk stratification, treatment or outcomes is unknown.

Methods

In a stepped-wedge cluster randomized controlled trial, we implemented a high-sensitivity troponin assay and the recommendations of the Universal Definition in 48,282 consecutive patients with suspected acute coronary syndrome across ten hospitals. In a pre-specified secondary analysis, we compared the primary outcome of myocardial infarction or cardiovascular death, and secondary outcome of non-cardiovascular death at one year across diagnostic categories as per the Fourth Universal Definition. We applied competing risks methodology in all analyses, using a cumulative incidence function and determining the cause-specific hazard ratio (csHR) for competing outcomes.

Results

Cardiac troponin concentrations were elevated in 21.5% (10,360/48,282) of all trial participants. Implementation increased the diagnosis of type 1 myocardial infarction by 11% (510/4,471), type 2 myocardial infarction by 22% (205/916), acute myocardial injury by 36% (443/1,233) and chronic myocardial injury by 43% (389/898). The risk and rate of the primary outcome was highest in those with type 1 myocardial infarction, whereas the risk and rate of non-cardiovascular death was highest in those with acute myocardial injury (Table, Figure). Despite increases in anti-platelet therapy and coronary revascularization after implementation, the primary outcome was unchanged in patients with type 1 myocardial infarction (csHR 1.00, 95% CI 0.82 to 1.21), or in any other category.

Adjusted csHR for competing outcomes Myocardial infarction or cardiovascular death Non-cardiovascular death Adjusted csHR (95% CI) Adjusted csHR (95% CI) Type 1 myocardial infarction 5.64 (5.12 to 6.22) 0.83 (0.72 to 0.96) Type 2 myocardial infarction 3.50 (2.94 to 4.15) 1.72 (1.44 to 2.06) Acute myocardial injury 4.38 (3.80 to 5.05) 2.65 (2.33 to 3.00) Chronic myocardial injury 3.88 (3.31 to 4.55) 2.06 (1.77 to 2.40) Cox regression models adjusted for age, sex, diabetes, ischaemic heart disease, season, days since trial onset and site of recruitment (as a random effect).

Cumulative incidence and number at risk

Conclusions

Implementation of the recommendations of the Universal Definition identified patients with different risks of future cardiovascular and non-cardiovascular events, but did not improve outcomes. Greater understanding of the underlying mechanisms and effective strategies for the investigation and treatment of patients with myocardial injury and infarction are required if we are to improve outcomes.

Acknowledgement/Funding

British Heart Foundation

Superinfection Drives HIV Neutralizing Antibody Responses from Several B Cell Lineages that Contribute to a Polyclonal Repertoire

Eliciting broad and potent HIV-specific neutralizing antibody responses represents the holy grail of HIV vaccine efforts. Data from singly infected individuals with broad and potent plasma neutralizing activity targeting one epitope have guided our understanding of how these responses develop. However, far less is known about responses developed by super-infected individuals who acquire two distinct HIV strains. Here, we isolated HIV-specific mAbs from a superinfected individual with a broad plasma response. In this superinfection case, neutralizing activity resulted from multiple distinct B cell lineages that arose in response to either the initial or the superinfecting virus, including an antibody that targets the N332 supersite. This nAb, QA013.2, was specific to the superinfecting virus and was associated with eventual reemergence of the initial infecting virus. The complex dynamic between viruses in superinfection may drive development of a unique collection of polyclonal nAbs that present a higher barrier to escape than monoclonal responses.

Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance

Influenza A virus matrix protein M1 is involved in multiple stages of the viral infectious cycle. Despite its functional importance, our present understanding of this essential viral protein is limited. The roles of a small subset of specific amino acids have been reported, but a more comprehensive understanding of the relationship between M1 sequence, structure, and virus fitness remains elusive. In this study, we used deep mutational scanning to measure the effect of every amino acid substitution in M1 on viral replication in cell culture. The map of amino acid mutational tolerance we have generated allows us to identify sites that are functionally constrained in cell culture as well as sites that are less constrained. Several sites that exhibit low tolerance to mutation have been found to be critical for M1 function and production of viable virions. Surprisingly, significant portions of the M1 sequence, especially in the C-terminal domain, whose structure is undetermined, were found to be highly tolerant of amino acid variation, despite having extremely low levels of sequence diversity among natural influenza virus strains. This unexpected discrepancy indicates that not all sites in M1 that exhibit high sequence conservation in nature are under strong constraint during selection for viral replication in cell culture.IMPORTANCE The M1 matrix protein is critical for many stages of the influenza virus infection cycle. Currently, we have an incomplete understanding of this highly conserved protein's function and structure. Key regions of M1, particularly in the C terminus of the protein, remain poorly characterized. In this study, we used deep mutational scanning to determine the extent of M1's tolerance to mutation. Surprisingly, nearly two-thirds of the M1 sequence exhibits a high tolerance for substitutions, contrary to the extremely low sequence diversity observed across naturally occurring M1 isolates. Sites with low mutational tolerance were also identified, suggesting that they likely play critical functional roles and are under selective pressure. These results reveal the intrinsic mutational tolerance throughout M1 and shape future inquiries probing the functions of this essential influenza A virus protein.

Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage

HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.

Single-Molecule Analysis of a Viral Fusion Protein Illuminates a Fusion-Active Intermediate State

The influenza virus hemagglutinin (HA) fusion glycoprotein mediates viral entry into host cells through its receptor binding and membrane fusion activities. In this issue of Cell, Das et al. use single-molecule Förster resonance energy transfer (smFRET) to monitor HA conformational dynamics. Their study reveals this prototypical class I fusion protein to be a highly dynamic molecule capable of reversibly sampling multiple states, including on-pathway fusion intermediates between pre-fusion and post-fusion endpoints. These findings challenge long-held ideas for how HA functions and move the field closer to obtaining a mechanistic understanding of how class I fusion proteins mediate membrane fusion.

Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein

BACKGROUND

Recent advances in structural characterization of the HIV envelope glycoprotein (Env) have provided a high-resolution glimpse of the architecture of this target for neutralizing antibodies and the machinery responsible for mediating receptor binding and membrane fusion. These structures primarily capture the detailed organization of the receptor-naive, prefusion conformation of Env, but under native solution conditions Env is highly dynamic, sampling multiple conformational states as well as exhibiting local protein flexibility.

METHODS

Special emphasis is placed on the use of biophysical methods, including single-molecule fluorescence microscopy and hydrogen/deuterium-exchange mass spectrometry.

RESULTS

Using novel biophysical approaches, striking isolate-specific differences in Env's dynamic profile have been revealed that appear to underlie phenotypic differences of the viral isolates such as neutralization sensitivity and CD4 receptor reactivity.

CONCLUSION

Structural studies are complemented by novel biophysical investigations that enable visualization of the dynamics of HIV-1 Env under native conditions. These approaches will also enable us to gain new insights into the mechanisms of action of antibodies and drugs.

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus

Respiratory syncytial virus (RSV) is a worldwide public health concern for which no vaccine is available. Elucidation of the prefusion structure of the RSV F glycoprotein and its identification as the main target of neutralizing antibodies have provided new opportunities for development of an effective vaccine. Here, we describe the structure-based design of a self-assembling protein nanoparticle presenting a prefusion-stabilized variant of the F glycoprotein trimer (DS-Cav1) in a repetitive array on the nanoparticle exterior. The two-component nature of the nanoparticle scaffold enabled the production of highly ordered, monodisperse immunogens that display DS-Cav1 at controllable density. In mice and nonhuman primates, the full-valency nanoparticle immunogen displaying 20 DS-Cav1 trimers induced neutralizing antibody responses ∼10-fold higher than trimeric DS-Cav1. These results motivate continued development of this promising nanoparticle RSV vaccine candidate and establish computationally designed two-component nanoparticles as a robust and customizable platform for structure-based vaccine design.