The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute ...respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein
show promise therapeutically and are being evaluated clinically
. Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies
in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs
. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.
Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the ...receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.
X-ray fluorescence (XRF) scanning of unlithified, untreated sediment cores is becoming an increasingly common method used to obtain paleoproxy data from lake records. XRF-scanning is fast and ...delivers high-resolution records of relative variations in the elemental composition of the sediment. However, lake sediments display extreme variations in their organic matter content, which can vary from just a few percent to well over 50%. As XRF scanners are largely insensitive to organic material in the sediment, increasing levels of organic material effectively dilute those components that can be measured, such as the lithogenic material (the closed-sum effect). Consequently, in sediments with large variations in organic material, the measured variations in an element will to a large extent mirror the changes in organic material. It is therefore necessary to normalize the elements in the lithogenic component of the sediment against a conservative element to allow changes in the input of the elements to be addressed. In this study we show that Al, which is the lightest element that can be measured using the Itrax XRF-scanner, can be used to effectively normalize the elements of the lithogenic fraction of the sediment against variations in organic content. We also show that care must be taken when choosing resolution and exposure time to ensure optimal output from the measurements.
Loneliness is associated with increased morbidity and mortality. Deeper understanding of neurobiological mechanisms underlying loneliness is needed to identify potential intervention targets. We did ...not find any systematic review of neurobiology of loneliness. Using MEDLINE and PsycINFO online databases, we conducted a search for peer-reviewed publications examining loneliness and neurobiology. We identified 41 studies (n = 16,771 participants) that had employed various methods including computer tomography (CT), structural magnetic resonance imaging (MRI), functional MRI (fMRI), electroencephalography (EEG), diffusion tensor imaging (DTI), single-photon emission computed tomography (SPECT), positron emission tomography (PET), and post-mortem brain tissue RNA analysis or pathological analysis. Our synthesis of the published findings shows abnormal structure (gray matter volume or white matter integrity) and/or activity (response to pleasant versus stressful images in social versus nonsocial contexts) in the prefrontal cortex (especially medial and dorsolateral), insula (particularly anterior), amygdala, hippocampus, and posterior superior temporal cortex. The findings related to ventral striatum and cerebellum were mixed. fMRI studies reported links between loneliness and differential activation of attentional networks, visual networks, and default mode network. Loneliness was also related to biological markers associated with Alzheimer's disease (e.g., amyloid and tau burden). Although the published investigations have limitations, this review suggests relationships of loneliness with altered structure and function in specific brain regions and networks. We found a notable overlap in the regions involved in loneliness and compassion, the two personality traits that are inversely correlated in previous studies. We have offered recommendations for future research studies of neurobiology of loneliness.
Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding ...domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD β sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.
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•Donor-derived antibodies C118 and C022 recognize a highly conserved RBD epitope•Both antibodies cross-react and neutralize sarbecoviruses and SARS-CoV-2 VOCs•C118-RBD and C022-RBD crystal structures show long CDRH3s that extend RBD β sheet•C118-S cryo-EM structure suggests intra- and inter-spike crosslinking by C118 IgG
Jette et al. characterize antibodies derived from convalescent COVID-19 donors that broadly recognize sarbecoviruses and neutralize ACE2-tropic strains, including all SARS-CoV-2 variants of concern. Structures reveal binding to a highly conserved RBD epitope using long CDRH3 loops, with an orientation that inhibits ACE2 binding to the RBD and allows IgG avidity.
To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic ...nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.
Summary
Objective
To investigate whether the live birth rate following in vitro fertilization (IVF) is affected by thyroid autoimmunity (TAI) and/or subclinical hypothyroidism in subfertile women.
...Design and setting
Retrospective study in a university infertility clinic.
Patients
A total of 627 women without past or current history of thyroid disorder undergoing their first IVF cycle.
Intervention
Pre‐IVF archived blood serum samples were tested for TAI and thyroid function tests.
Main outcome measure
Live birth rate.
Results
The clinical pregnancy rate, live birth rate and miscarriage rate were similar among women with or without TAI and/or subclinical hypothyroidism using a TSH threshold 4·5 mIU/l. Thyroid autoantibody level did not affect these IVF outcomes.
Conclusion
The live birth rate and miscarriage rate of women with TAI and/or subclinical hypothyroidism following IVF were not impaired.
Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV ...envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.
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•Pre-existing antibodies to DENV1 correlate with high ZIKV neutralizing responses•Antibodies to the EDIII lateral ridge correlate with serum neutralization of ZIKV•Recurrent VH3-23/VK1-5 antibodies to the EDIII potently neutralize ZIKV and DENV1•The structures of VH3-23/VK1-5 antibodies with the EDIIIs of DENV1 and ZIKV were solved
Individuals with high neutralizing antibody response against Zika virus have expanded clones of B cells that express the same heavy and light immunoglobulin genes and that are cross-reactive against dengue 1 virus.
SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor-binding domain (RBD) and the N-terminal domain (NTD) of the ...spike trimer (S) constitute the two major neutralizing targets for antibodies. Here, we use NTD-specific probes to capture anti-NTD memory B cells in a longitudinal cohort of infected individuals, some of whom were vaccinated. We found 6 complementation groups of neutralizing antibodies. 58% targeted epitopes outside the NTD supersite, 58% neutralized either Gamma or Omicron, and 14% were broad neutralizers that also neutralized Omicron. Structural characterization revealed that broadly active antibodies targeted three epitopes outside the NTD supersite including a class that recognized both the NTD and SD2 domain. Rapid recruitment of memory B cells producing these antibodies into the plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants, including Omicron.
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•Vaccination boosts anti-NTD responses against Omicron in convalescent individuals•Natural SARS-CoV-2 infection induces variant-reactive memory B cell responses to NTD•Anti-NTD neutralizing antibodies form 6 complementation groups•Structures of anti-NTD broad neutralizing antibodies reveal epitopes outside supersite
Most neutralizing antibodies to SARS-CoV-2 NTD characterized to date bind a single supersite, but these antibodies were obtained by methods that were not NTD-specific. Wang et al. analyzed SARS-CoV-2 NTD-specific memory B cell responses in a longitudinal cohort of infected individuals, some of whom were vaccinated. Structural analysis revealed neutralizing epitopes conserved among variants of concern outside the NTD supersite.
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