ABSTRACT
The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics that are effective against a variety of strains of the virus. Herein, we characterize a human VH domain, F6, which we generated by sequentially panning large phage displayed VH libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized VH domain, resulted in a construct (F6-ab8-Fc) that neutralized Omicron pseudoviruses with a half-maximal neutralizing concentration (IC50) of 4.8 nM in vitro. Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 VOCs - including the recently emerged Omicron variant - and highlight a vulnerable epitope within the spike protein RBD that may be exploited to achieve broad protection against circulating variants.
ABSTRACT
Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we report the discovery of a novel antibody fragment (VH ab6) that neutralizes all major variants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.
ABSTRACT
ObjectivesImmunocompromised patients were excluded from COVID-19 vaccine clinical trials. The objectives of the study were to measure antibody responses, levels, and neutralization capability after COVID-19 vaccination among immunocompromised patients and compare these variables to those of immunocompetent healthcare workers. MethodsThis is an interim analysis of an ongoing observational, prospective cohort study which launched on April 14, 2021 across Western Pennsylvania. Participants were healthy healthcare workers (HCW) and immunocompromised patients who had completed their COVID-19 vaccination series. Individuals with a history of COVID-19 were not eligible. Serum was collected to measure for the presence of IgG against the SARS-CoV-2 Spike protein using a semi-quantitative assay; antibody levels were available for comparisons. A quasi-random subset of patients was selected for pseudovirus neutralization assays. Seropositivity with 95% Clopper-Pearson exact confidence intervals and distribution of antibody levels were measured. To identify risk factors for seronegativity, clinical characteristics were univariately compared between antibody reactive and non-reactive individuals within the immunocompromised group. Results107 HCW and 489 immunocompromised patients were enrolled. Compared to HCWs, seropositivity was significantly lower (p<.001) among immunocompromised patients with Solid organ transplant (SOT), autoimmune, hematological malignancies, and solid tumors (HCW=98.1%; SOT=37.2%; autoimmune=83.8%; hematological malignancies=54.7%; and solid tumor=82.4%, p < 0.05). Over 94% of patients with Human Immunodeficiency Virus were seropositive. Among seropositive patients, antibody levels were much lower among SOT (4.5 [2.1,13.1], p=.020). Neutralization titers tightly correlated with antibody levels (Spearman r = 0.91, p < 0.0001). ConclusionOur findings demonstrate the heterogeneity of the humoral immune response to COVID-19 vaccines based on underlying immunosuppressive condition and highlight an urgent need to optimize and individualize COVID-19 prevention in these patients. These findings also have implications on public health guidance, particularly given revised Centers for Disease Control and Prevention recommendations permitting vaccinated individuals to abandon masking and social distancing in most settings. Future studies are warranted to determine assessment of cellular immunity, longitudinal measurement of immune responses, and the safety and efficacy of revaccination.
ABSTRACT
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission with several emerging variants remain uncontrolled in many countries, indicating the pandemic remains severe. Recent studies showed reduction of neutralization against these emerging SARS-CoV-2 variants by vaccine-elicited antibodies. Among those emerging SARS-CoV-2 variants, a panel of amino acid mutations was characterized including those in the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. In the present study, we evaluated our previously identified antibody and antibody domains for binding to these RBD variants with the emerging mutations, and neutralization of pseudo typed viruses carrying spike proteins with such mutations. Our results showed that one previously identified antibody domain, ab6, can bind 32 out of 35 RBD mutants tested in an ELISA assay. All three antibodies and antibody domains can neutralize pseudo typed B.1.1.7 (UK variant), but only the antibody domain ab6 can neutralize the pseudo typed virus with the triple mutation (K417N, E484K, N501Y). This domain and its improvements have potential for therapy of infections caused by SARS-CoV-2 mutants.
ABSTRACT
Background/Aims: We reviewed demographic and clinical profiles, along with measures of hospital-based clinical practice to identify temporal changes in clinical practice that may have affected in-hospital outcomes of patients with COVID-19. Methods: Data consisted of sociodemographic and clinical data captured in University of Pittsburgh Medical Center (UPMC) electronic medical record (EMR) systems, linked by common variables (deidentified). The analysis population included hospitalized patients (across 21 hospitals) with a primary diagnosis of COVID-19 infection during the period March 14-August 31, 2020. The primary outcome was a composite of in-hospital mechanical ventilation/mortality. We compared temporal trends in patient characteristics, clinical practice, and hospital outcomes using 4 time-defined epochs for calendar year 2020: March 14-March 31 (epoch 1); April 1-May 15, (epoch 2), May 16-June 28 (epoch 3); and June 29-August 31 (epoch 4). We report unadjusted survival estimates, followed by propensity score analyses to adjust for differences in patient characteristics, to compare in-hospital outcomes of epoch 4 patients (recently treated) to epoch 1-3 patients (earlier treated). Results: Mean number of hospital admissions was 9.9 per day during epoch 4, which was ~2- to 3-fold higher than the earlier epochs. Presenting characteristics of the 1,076 COVID-19 hospitalized patients were similar across the 4 epochs, including mean age. The crude rate of mechanical ventilation/mortality was lower in epoch 4 patients (17%) than in epoch 1-3 patients (23% to 35%). When censoring for incomplete patient follow-up, the rate of mechanical ventilation/mortality was lower in epoch 4 patients (p<0.0001), as was the individual component of mechanical ventilation (p=0.0002) and mortality (p=0.02). In propensity score adjusted analyses, the in-hospital relative risk (RR) of mechanical ventilation/mortality was lower in epoch 4 patients (RR=0.67, 95% CI: 0.48, 0.93). For the outcome being discharged alive within 3, 5, or 7 days of admission, adjusted odds ranged from 1.6- to 1.7-fold higher among epoch 4 patients compared to earlier treated patients. The better outcomes in epoch 4 patients were principally observed in patients under the age of 75 years. Patient level dexamethasone use was 55.6% in epoch 4 compared to 15% or less of patients in the earlier epochs. Most patients across epochs received anticoagulation drugs (principally heparin). Overall steroid (81.7% vs. 54.3%, p<0.0001) and anticoagulation use (90.4% vs. 80.7%, p=0.0001) was more frequent on the day or day after hospitalization in epoch 4 patients compared to earlier treated patients. Conclusions: In our large system, recently treated hospitalized COVID-19 patients had lower rates of in-hospital mechanical ventilation/mortality and shorter length of hospital stay. Alongside of this was a change to early initiation of glucocorticoid therapy and anticoagulation. The extent to which the improvement in patient outcomes was related to changes in clinical practice remains to be established.
ABSTRACT
Effective therapies are urgently needed for the SARS-CoV-2/COVID19 pandemic. We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. One high affinity mAb, IgG1 ab1, specifically neutralized replication competent SARS-CoV-2 with exceptional potency as measured by two different assays. There was no enhancement of pseudovirus infection in cells expressing Fc{gamma} receptors at any concentration. It competed with human angiotensin-converting enzyme 2 (hACE2) for binding to RBD suggesting a competitive mechanism of virus neutralization. IgG1 ab1 potently neutralized mouse ACE2 adapted SARS-CoV-2 in wild type BALB/c mice and native virus in hACE2 expressing transgenic mice. The ab1 sequence has relatively low number of somatic mutations indicating that ab1-like antibodies could be quickly elicited during natural SARS-CoV-2 infection or by RBD-based vaccines. IgG1 ab1 does not have developability liabilities, and thus has potential for therapy and prophylaxis of SARS-CoV-2 infections. The rapid identification (within 6 days) of potent mAbs shows the value of large antibody libraries for response to public health threats from emerging microbes.
