ABSTRACT
Speed is key during infectious disease outbreaks. It is essential, for example, to identify critical host binding factors to the pathogens as fast as possible. The complexity of host plasma membrane is often a limiting factor hindering fast and accurate determination of host binding factors as well as high-throughput screening for neutralizing antimicrobial drug targets. Here we describe a multi-parametric and high-throughput platform tackling this bottleneck and enabling fast screens for host binding factors as well as new antiviral drug targets. The sensitivity and robustness of our platform was validated by blocking SARS-CoV-2 spike particles with nanobodies and IgGs from human serum samples. TeaserA fast screening platform tackling host-pathogen interactions.
ABSTRACT
The SARS-CoV-2 Omicron1 Variant of Concern (B.1.1.529) has spread rapidly in many countries. With a spike that is highly diverged from that of the pandemic founder, it escapes most available monoclonal antibody therapeutics2,3 and erodes vaccine protection4. A public class of IGHV3-53-using SARS-CoV-2 neutralizing antibodies5,6 typically fails to neutralize variants carrying mutations in the receptor-binding motif7-11, including Omicron. As antibodies from this class are likely elicited in most people following SARS-CoV-2 infection or vaccination, their subsequent affinity maturation is of particular interest. Here, we isolated IGHV3-53-using antibodies from an individual seven months after infection and identified several antibodies capable of broad and potent SARS-CoV-2 neutralization, extending to Omicron without loss of potency. By introducing select somatic hypermutations into a germline-reverted form of one such antibody, CAB-A17, we demonstrate the potential for commonly elicited antibodies to develop broad cross-neutralization through affinity maturation. Further, we resolved the structure of CAB-A17 Fab in complex with Omicron spike at an overall resolution of 2.6 [A] by cryo-electron microscopy and defined the structural basis for this breadth. Thus, public SARS-CoV-2 neutralizing antibodies can, without modified spike vaccines, mature to cross-neutralize exceptionally antigenically diverged SARS-CoV-2 variants.
ABSTRACT
Conventional approaches to isolate and characterize nanobodies are laborious and cumbersome. Here we combine phage display, multivariate enrichment, and novel sequence analysis techniques to annotate an entire nanobody repertoire from an immunized alpaca. We combine this approach with a streamlined screening strategy to identify numerous anti-SARS-CoV-2 nanobodies, and use neutralization assays and Hydrogen/Deuterium exchange coupled to mass spectrometry (HDX-MS) epitope mapping to characterize their potency and specificity. Epitope mapping revealed that the binding site is a key determinant of neutralization potency, rather than affinity alone. The most potent nanobodies bind to the receptor binding motif of the RBD, directly preventing interaction with the host cell receptor ACE2, and we identify two exceptionally potent members of this category (with monomeric IC50s around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD, and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 g/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.
ABSTRACT
The emergence of SARS-CoV-2 Variants of Concern (VOCs) with mutations in key neutralizing antibody epitopes threatens to undermine vaccines developed against the pandemic founder variant (Wu-Hu-1). Widespread vaccine rollout and continued transmission are creating a population that has antibody responses of varying potency to Wu-Hu-1. Against this background, it is critical to assess the outcomes of subsequent immunization with variant antigens. It is not yet known whether heterotypic vaccine boosts would be compromised by original antigenic sin, where pre-existing responses to a prior variant dampen responses to a new one, or whether the primed memory B cell repertoire would bridge the gap between Wu-Hu-1 and VOCs. Here, we show that a single adjuvanted dose of receptor binding domain (RBD) protein from VOC 501Y.V2 (B.1.351) drives an extremely potent neutralizing antibody response capable of cross-neutralizing both Wu-Hu-1 and 501Y.V2 in rhesus macaques previously immunized with Wu-Hu-1 spike protein. Passive immunization with plasma sampled following this boost protected K18-hACE2 mice from lethal challenge with a 501Y.V2 clinical isolate, whereas only partial protection was afforded by plasma sampled after two Wu-Hu-1 spike immunizations.
ABSTRACT
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we isolated a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the B.1.351 variant, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the B.1.351 variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes a novel strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
ABSTRACT
In Sweden, social restrictions to contain SARS-CoV-2 have to date primarily relied upon voluntary adherence to a set of recommendations and strict lockdowns/regulations have not been enforced, potentially affecting viral dissemination. To understand the levels of past SARS-CoV-2 infection in the Stockholm population before the start of mass vaccinations, healthy blood donors and pregnant women (n=5,100) were sampled at random between 14th March 2020-28th February 2021. All individuals (n=200/sampling week) were screened for anti-SARS-CoV-2 spike (S) trimer- and RBD-specific IgG responses and the results were compared with those from historical controls (n=595). Data were modelled using a probabilistic Bayesian framework that considered individual responses to both viral antigens. We found that after a steep rise at the start of the pandemic, the seroprevalence trajectory increased more steadily (over summer) in approach to the winter second-wave of infections, approaching 15% of all adults surveyed by mid-December 2020. The population seropositivity rate again increased more rapidly as cases rose over the winter period. By the end of February 2021, [~]19% ([~]one-in-five) in this study group tested seropositive. Notably, 96% of random seropositive samples screened (n=56), displayed virus neutralizing responses, with titers comparable to those engendered by recently approved mRNA vaccines, supporting that milder infections generally provoke a competent B cell response. These data offer baseline information about the level of seropositivity in this group of active adults in the Stockholm metropolitan area following a full year of SARS-CoV-2 transmission and prior to the introduction of vaccines. Structured abstractO_ST_ABSObjectivesC_ST_ABSSweden did not enforce social lockdown in response to the SARS-CoV-2 pandemic. Therefore, we sought to determine the proportion of seropositive healthy, active adults in Stockholm, the countrys most populous region. Random sampling (of blood donors and pregnant women) was carried out during the first year following virus emergence in the country and prior to vaccination of the general adult population - allowing for an estimate of seroprevalence in response to natural infection. DesignIn this cross-sectional prospective study, otherwise-healthy blood donors (n=2,600) and pregnant women(n=2,500) were sampled at random for consecutive weeks (at four intervals) between 14th March and 28th February 2021. Sera from all participants and a cohort of historical controls (n=595) were screened for IgG responses against trimers of the SARS-CoV-2 spike (S) glycoprotein and the smaller receptor-binding domain (RBD). As a complement to standard analytical approaches, a probabilistic (cut-off-independent) Bayesian framework that assigns likelihood of past infection was used to analyze data over time. The study was carried out in accordance with Swedish Ethical Review Authority: registration number 2020-01807. SettingHealthy participant samples were selected from their respective pools at random through Karolinska University Hospital. ParticipantsNone of the participants were symptomatic at sampling. No additional metadata was available from the samples. ResultsBlood donors and pregnant women showed a similar seroprevalence. After a steep rise at the start of the pandemic, the seroprevalence trajectory increased steadily in approach to the winter second-wave of infections, approaching 15% of all individuals surveyed by 13th December 2020. By the end of February 2021, when deaths were in decline and at low levels following their winter peak, 19% of the population tested seropositive. Notably, 96% of seropositive healthy donors screened (n=56) developed neutralizing antibody responses at titers comparable to, or higher than those observed in clinical trials of SARS-CoV-2 spike mRNA vaccination, supporting that mild infection engenders a competent B cell response. ConclusionsThese data indicate that in the year since the start of community transmission, seropositivity levels in metropolitan Stockholm had reached approximately one-in-five persons, providing important baseline seroprevalence information prior to the start of vaccination.
ABSTRACT
Serological studies are critical for understanding pathogen-specific immune responses and informing public health measures1,2. Here, we evaluate tandem IgM, IgG and IgA responses in a cohort of individuals PCR+ for SARS-CoV-2 RNA (n=105) representing different categories of disease severity, including mild and asymptomatic infections. All PCR+ individuals surveyed were IgG-positive against the virus spike (S) glycoprotein. Elevated Ab levels were associated with hospitalization, with IgA titers, increased circulating IL-6 and strong neutralizing responses indicative of intensive care status. Additional studies of healthy blood donors (n=1,000) and pregnant women (n=900), sampled weekly during the initial outbreak in Stockholm, Sweden (weeks 14-25, 2020), demonstrated that anti-viral IgG titers differed over 1,000-fold between seroconverters, highlighting the need for careful evaluation of assay cut-offs for individual measurements and accurate estimates of seroprevalence (SP). To provide a solution to this, we developed probabilistic machine learning approaches to assign likelihood of past infection without setting an assay cut-off, allowing for more quantitative individual and population-level Ab measures. Using these tools, that considered responses against both S and RBD, we report SARS-CoV-2 S-specific IgG in 6.8% of blood donors and pregnant women two months after the peak of spring COVID-19 deaths, with the SP curve and country death rate following similar trajectories.
ABSTRACT
The COVID-19 pandemic has posed a tremendous challenge for the global community. We established a translational approach combining home blood sampling by finger-pricking with multiplexed serology to assess the exposure to the SARS-CoV-2 virus in a general population. The developed procedure determines the immune response in multiplexed assays against several spike (S, here denoted SPK), receptor binding domain (RBD) and nucleocapsid (NCP) proteins in eluates from dried capillary blood. The seroprevalence was then determined in two study sets by mailing 1000 blood sampling kits to random households in urban Stockholm during early and late April 2020, respectively. After receiving 55% (1097/2000) of the cards back within three weeks, 80% (878/1097) were suitable for the analyses of IgG and IgM titers. The data revealed diverse pattern of immune response, thus seroprevalence was dependent on the antigen, immunoglobulin class, stringency to include different antigens, as well as the required analytical performance. Applying unsupervised dimensionality reduction to the combined IgG and IgM data, 4.4% (19/435; 95% CI: 2.4%-6.3%) and 6.3% (28/443; 95% CI: 4.1%-8.6%) of the samples clustered with convalescent controls. Using overlapping scores from at least two SPK antigens, prevalence rates reached 10.1% (44/435; 95% CI: 7.3%-12.9%) in study set 1 and 10.8% (48/443; 95% CI: 7.9%-13.7%). Measuring the immune response against several SARS-CoV-2 proteins in a multiplexed workflow can provide valuable insights about the serological diversity and improve the certainty of the classification. Combining such assays with home-sampling of blood presents a viable strategy for individual-level diagnostics and towards an unbiased assessment of the seroprevalence in a population and may serve to improve our understanding about the diversity of COVID-19 etiology. One Sentence SummaryA multiplexed serology assay was developed to determine antibodies against SARS-CoV-2 proteins in home-sampled dried blood spots collected by finger pricking.
ABSTRACT
The outbreak and spread of SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), the cause of coronavirus disease 2019 (COVID-19), is a current global health emergency and a prophylactic vaccine is needed urgently. The spike glycoprotein of SARS-CoV-2 mediates entry into host cells, and thus is a target for neutralizing antibodies and vaccine design. Here we show that adjuvanted protein immunization with SARS-CoV-2 spike trimers, stabilized in prefusion conformation 1, results in potent antibody responses in mice and rhesus macaques with neutralizing antibody titers orders of magnitude greater than those typically measured in serum from SARS-CoV-2 seropositive humans. Neutralizing antibody responses were observed after a single dose, with exceptionally high titers achieved after boosting. Furthermore, neutralizing antibody titers elicited by a dose-sparing regimen in mice were similar to those obtained from a high dose regimen. Taken together, these data strongly support the development of adjuvanted SARS-CoV-2 prefusion-stabilized spike protein subunit vaccines.
ABSTRACT
BackgroundSARS-CoV-2 may pose an occupational health risk to health care workers, but the prevalence of infections in this population is unknown. We examined the seroprevalence of SARS-CoV-2 antibodies among health care workers at a large acute care hospital in Stockholm, Sweden. We determined correlations between seroprevalence, self-reported symptoms and occupational exposure to SARS-CoV-2. Methods and findingsAll employees at Danderyd Hospital (n=4375) were invited to participate in a cross-sectional study. 2149 employees from all hospital departments were enrolled in the study between April 14th and May 8th 2020. Study participants completed a questionnaire consisting of symptoms compatible with SARS-CoV-2 infection since January 2020 and occupational exposure to patients infected with SARS-CoV-2. IgG antibodies against SARS-CoV-2 were analyzed using a multiplex assay evaluated to have 99.4% sensitivity and 99.1% specificity. The over-all seroprevalence among 2149 participants was 19.1% (n=410). There was no difference in age or sex between seropositive and seronegative participants. The symptoms with the strongest correlation to seroprevalence were anosmia and ageusia, with odds ratios of 28.4 (p=2.02*10^-120) and 19.2 (p=1.67*10^-99) respectively. Seroprevalence was strongly associated with patient-related work (OR 2.9, p=4.24*10^-8), covid-19 patient contact (OR 1.43, p=0.003), and occupation as assisting nurse (OR 3.67, p=2.16*10^-9). ConclusionThese results demonstrate that anosmia and ageusia should be included in screening guidance and in the recommendations of self-isolation to reduce further spread of SARS-CoV-2. The results furthermore imply an occupational health risk for SARS-CoV-2 infection among hospital workers. Continued measures are warranted to assure healthcare worker safety and reduce transmission from health care settings to the community during the covid-19 outbreak.
ABSTRACT
The current SARS-CoV-2 pandemic has highlighted a need for easy and safe blood sampling in combination with accurate serological methodology. Venipuncture is usually performed by trained staff at health care centers. Long travel distances may introduce a bias of testing towards relatively large communities with close access to health care centers. Rural regions may thus be overlooked. Here, we demonstrate a sensitive method to measure antibodies to the S-protein of SARS-CoV-2. We adapted and optimized this assay for clinical use together with capillary blood sampling to meet the geographical challenges of serosurveillance. Finally, we tested remote at-home capillary blood sampling together with centralized assessment of S-specific IgG in a rural region of northern Scandinavia that encompasses 55,185 sq kilometers. We conclude that serological assessment from capillary blood sampling gives comparable results as analysis of venous blood. Importantly, at-home sampling enabled citizens living in remote rural areas access to centralized and sensitive laboratory antibody tests.
ABSTRACT
The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC50 of 0.6 {micro}g/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed a novel conformation of the spike where two RBDs are in the up ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.
ABSTRACT
SARS-CoV-2 is the etiologic agent of COVID-19, currently causing a devastating pandemic for which pharmacological interventions are urgently needed. The virus enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. The nanobody binds with high affinity in the low nM range to the RBD, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the ‘up’ and ‘down’ conformations and that Ty1 sterically hinders RBD-ACE2 binding. This 12.8 kDa nanobody does not need an Fc domain to neutralize SARS-CoV-2, and can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.Competing Interest StatementThe authors have declared no competing interest.View Full Text
