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Objectives: Data about COVID-19 patients treated with veno-arterial-ECMO (VA-ECMO) is limited. Reported survival rates range from 27.9% to 77.8%, depending on VA-ECMO indication. A subgroup of patients suffers from circulatory failure due to a COVID-19 associated hyperinflammatory state (CovHI). In these patients, differentiation between inflammation and sepsis is difficult but important. In this retrospective case series, differential diagnoses of COVID-19 associated refractory circulatory failure and survival rates in different indications for VA-ECMO are investigated. Method(s): Retrospective analysis of 28 consecutive COVID-19 patients requiring VA-ECMO at the University Hospital Regensburg between March 2020 and May 2022. Specific treatment for COVID-19 was in accordance with respective guidelines. Mycotic infections were either invasive or met current definitions of COVID19-associated-pulmonary aspergillosis. Result(s): At VA-ECMO initiation, median age was 57.3 years (IQR: 51.4 - 61.8), SOFA score 16 (IQR: 13 - 17) and norepinephrine dosing 0.53mug/kg/min (IQR: 0.32 - 0.78). Virus-variants were: 61% wild-type, 14% Alpha, 18% Delta and 7% Omicron. Survival to hospital discharge was 39%. 17 patients were primarily supported with VA-ECMO only (survival 42%), 3 patients were switched from VV to VA-ECMO (survival 0%), and 8 patients were converted from VA to VAV or VV-ECMO (survival 50%). Indications for VA-ECMO support were pulmonary embolism (PE) (n=5, survival 80%), right heart failure due to secondary pulmonary hypertension (n=5, survival 20%), cardiac arrest (n=4, survival 25%), acute left heart failure (ALHF) (n=11, survival 36%) and refractory vasoplegia (n=3, survival 0%). Inflammatory markers at VA-ECMO initiation were higher in patients with ALHF or vasoplegia;in these patients a higher rate of invasive fungal infections (10/14, 71% vs. 4/14, 29%;p=0.023) compared to the other patients was found. Conclusion(s): Survival on VA-ECMO in COVID-19 depends on VA-ECMO indication, which should be considered in further studies and clinical decisions making. Circulatory failure due to vasoplegia should be considered very carefully as indication for VA-ECMO. A high rate of mycotic infections mandates an intense microbiological workup of these patients and must be considered as an important differential diagnosis to CovHI.
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Lung cancer is the leading cause of cancer related deaths worldwide, with a relatively low 5-year survival rate. Although there are some therapies against lung cancer, new effective treatment options are urgently required. Recently during the COVID-19 pandemic, we have seen that SARSCoV-2 binds to its receptor angiotensin-converting enzyme 2 (ACE2) via spike S1 to enter the cells. This study underlines the importance of SARS-CoV-2 spike S1 in inducing death in human lung cancer cells. Interestingly, we have seen that recombinant spike S1 treatment at very low doses led to death of human A549 lung cancer cells. On the other hand, boiled recombinant SARS-CoV-2 spike S1 remained unable to induce death, suggesting that the induction of cell death in A549 cells was due to native SARS-CoV-2 spike S1 protein. SARS-CoV-2 spike S1-induced A549 cell death was also inhibited by neutralizing antibodies against spike S1 and ACE2. Moreover, our newly designed wild type ACE2-interacting domain of SARS-CoV-2 (wtAIDS), but not mAIDS, peptide also attenuated SARS-CoV-2 spike S1-induced cell death, suggesting that SARS-CoV-2 spike S1- induced death in lung cancer cells depends on its interaction with ACE2 receptor. Similarly, recombinant spike S1 treatment also led to death of H1299 and H358 human lung cancer cells. Finally, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) intoxication led to the formation tumors in lungs of A/J mice and alternate day intranasal treatment with low dose of recombinant SARS-CoV-2 spike S1 from 22-weeks of NNK insult (late stage) led to induced apoptosis and tumor regression in the lungs. These studies indicate that recombinant SARS-CoV-2 Spike S1 protein may have implications in the treatment of lung cancer.
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The rapid rate of mutation of the RNA genome of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for the emergence of viral variants, leading to the enhanced survivability of the virus. Hence, searching for new drugs that can restrict new viral infections by interacting with wild-type and mutated viral proteins is important. However, new drug development's economic and time-constraining nature makes drug repurposing a more viable solution to address the problem. In this work, we conducted a computational study to screen 23 Non-Steroidal Anti-Inflammatory Drugs (NSAID) interactions with 5 major viral proteins of SARS-CoV-2 that are mainly involved in host infection. Our in-silico results establish a database that shows that different NSAID ligands interact with the different viral proteins with good binding affinities. Stabilizing point mutations were introduced within the conserved amino acids involved in ligand-protein interactions. Redocking the NSAID ligands with these mutated viral proteins showed that the NSAID ligands could bind with the mutated and wild-type viral proteins with comparable binding affinities. We conclude that the NSAID ligands could be repurposed as therapeutic drugs against the SARS-CoV-2 virus. Additionally, our work generated a repository that includes binding affinities, possible modes of interaction, and specific interacting residues of the protein (wild-type and mutated) ligand complexes that could be used for future validation studies. Further, our results point to the potential of these drugs to treat other viral infections with similar disease etiology.Copyright All © 2023 are reserved by International Journal of Pharmaceutical Sciences and Research.
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Background: The continuous evolution of SARS-CoV-2 in the diverse immune landscape (natural, vaccine, hybrid) is giving rise to novel immune escape mutations. So far, the resulting new variants (BA.1, BA.2, BA.2.12.1) were observed to cause mild infections, however, BA.5 infections are associated with an increased risk of hospitalization.1 Therefore it is essential to investigate the pathogenesis of BA.5. Method(s): Here we compared the pathogenicity of Pre-Omicron (B.1.351) and Omicron (BA.1, BA.2.12.1, and BA.5) variants in wild-type C57BL/6J mice and K18-hACE2 mice. The virus replication kinetics was also studied in human Calu3, pulmonary alveolar type 2 (AT2) cells, and airway organoids (HAO). Cell-to-cell spread of virus was measured by syncytia formation assay and immunohistochemistry (IHC) of infected lungs. Result(s): In the results, infection in C57BL/6J mice showed severe weight loss ( >15%) for B.1.351 infected mice and moderate ( >5%) for BA.5 infected. C57BL/6J mice showed higher virus replication of B.1.351 followed by BA.5, BA.1, and BA.2.12.1. At the peak of virus replication (2 days) plaque-forming units from lung extract of BA.5 infected mice were two, and three logs higher compared to BA.1 and BA.2.12.1 respectively. BA.5 infection was lethal to 80% of infected K18-hACE2 mice, whereas the mice looked normal after infection with BA.1 and BA.2.12.1. BA.5 infected mice showed high virus replication in brain tissue. Surprisingly the syncytia formation assay and IHC for BA.5 was comparable to that of B.1.351, indicating the higher cell-to-cell spread of BA.5 and B.1.351 compared to BA.1 and BA.2.12.1, which is one of the measures of pathogenicity. Calu3 and HAO showed the same trend of virus replication as was observed in-vivo experiments however AT2 cells were found to be resistant to BA.5 replication. Conclusion(s): These results suggest that the BA.5 variant (lineage) of Omicron has the potential to regain the pathogenicity as it shows increased virulence compared to other Omicron sub-variants. Lethal infection of BA.5 in K18-hACE2 mice may be attributed to catastrophic encephalitis and increased cell-to-cell spread.
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Background: Much of the world's population had already been infected with COVID-19 by the time that the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or since, and left a global imprinting of immunity which changed the COVID landscape. In this study, we explore the changing value of vaccines in a landscape of dynamic immunity and rapidly evolving variants of concern. Method(s): We use Covasim, an established agent-based model of COVID-19 enhanced with detailed intra-host dynamics. First, we simulate a vaccine trial over March 2020 - April 2022 within a population resembling that of South Africa, and estimate how both vaccine efficacy (reduction in the risk of severe disease for vaccinated vs unvaccinated individuals) and efficiency (number of doses needed to avert a death) change as the population experiences waves of wild-type, Beta, Delta, and Omicron infections. Next, we introduce six hypothetical variants starting from February 2022 and evaluate the impact of (a) the existing set of vaccines, and (b) vaccines specifically targeted to the new variants. Result(s): We estimate that within our simulated population, vaccine efficacy against severe disease decreased from 80% to 20% in the wake of the first wave of wild-type COVID-19, then increased back to ~70% over the latter half of 2020 as population immunity waned. This pattern repeated following each subsequent wave of infections, with vaccine efficacy falling to its lowest (10%) in the immediate wake of the Omicron wave in December 2021. The efficiency of vaccination decreases over time at an increasing rate: at peak efficiency, fewer than 100 doses would have been required to avert a single death, but by the end of January 2022, we estimate that nearly 4,000 doses would be required to avert a single death. We find that variant-chasing vaccines will only add value above pre-existing vaccines if we can shorten the window between variant introduction and vaccine deployment to under three weeks, an impossible time-frame without significant NPI use. Conclusion(s): Although the vaccines have proven to be remarkably effective, our work demonstrates that the population immunity acquired over the first two years of the pandemic significantly reduced the impact per dose of doses delivered after this time. Next-generation vaccines to fight future COVID variants and/or other respiratory diseases must be delivered rapidly at scale for vaccine strategies to be maximally effective.
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The N protein of the SARS-CoV-2 virion is critical for viral genome packaging via RNA binding and regulation of viral transcription at the replication-transcription complex (RTC). The N protein can be divided into five main domains, and the central region is the linker, which is predicted to be primarily disordered and has not been heavily studied. The linker is Serine-Arginine Rich, which is phosphorylated at multiple sites by host kinases during infection, thereby promoting the N protein's role in viral transcription. Phosphorylation is a critical process for the regulation of many cellular processes and can provide recognition sites for binding complexes. In a study that examined the recognition of the SARS-CoV-2 N protein by the human 14-3-3 protein, the linker was found to contain critical phosphosites for 14-3-3 binding. The goals of this project are to determine the structure, dynamics, and RNA interactions of the Serine-Arginine Rich linker region. To accomplish this, we performed Nuclear Magnetic Resonance spectroscopy (NMR) experiments to analyze the structure of the linker region of the N protein and its ability to bind viral RNA. NMR confirms predictions that the linker is not entirely unstructured and it is able to bind RNA. The linker region of the N protein with phosphoserine incorporated at S188 was also examined via an NMR titration experiment with 1-1000 RNA. Compared to wild type, the incorporation of phosphorylation decreases binding. Other biophysical techniques such as Analytical Ultracentrifugation (AUC) and Multi-Angle Light Scattering (MALS) are used to identify the association state of the linker and the size of the resulting protein-RNA complex. We are currently working to biophysically characterize the structure, dynamics, and viral RNA binding ability of a mutation found in the Delta and Omicron variants: the R203M linker, which have been shown to enhance viral infectivity. This work was supported by the NSF EAGER grant NSF/ MCB 2034446 and URSA Engage. Support to facilities includes the Oregon State University NMR Facility funded in part by NIH, HEI Grant 1S10OD018518, and by the M. J. Murdock Charitable Trust grant # 2014162.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
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The SARS-CoV-2 virus has been the cause of the global pandemic since the end of 2019. Since then, the virus has mutated to create different types of variants with numerous effects on those infected. This has complicated human intervention for prevention. Indonesia was heavily affected by the pandemic, specifically from May to August 2021, and as a country has recorded many distinct isolates. Thus, characterization of the virus strains from Indonesia is important. GISAID, NCBI BLAST, and MAFFT version 7 were used. There were 9,488 isolates in Indonesia as of November 2021, with the majority including the Delta variant. While most of the isolates have mutations common to those from other countries, there are some atypical ones, such as mutation V1264L in the Delta variant that was suspected to play a role in worsening the pandemic. The Delta variant had the most mutations in the spike protein when compared to the Alpha and Beta variants, giving it important roles in infectivity and vigorous entry into cells, with some general clinical manifestations like fever and sore throat;however, the severity of the Delta variant is attributable to its rapid growth. This is why, from May to November 2021 in Indonesia, cases of the Delta variant rocketed, unlike the other variants. Copyright © 2023 THE AUTHOR(S).
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Background: Next-generation SARS-CoV-2 vaccines demonstrated that nanoparticle messenger ribonucleic acid (mRNA) delivery is effective and safe for in vivo delivery in humans. Current treatments for cystic fibrosis (CF) primarily focus on modulator drug therapies designed to correct malfunctioning CF transmembrane conductance regulator (CFTR) protein, but these modulators are ineffective for the 10% of people with CF with variants that do not allow protein production. Among these is the splice variant 3120 + 1G >A, the most common CF-causing mutation in native Africans. Gene editing would allow production of CFTR protein and enhancement of function using available CFTR modulators. We have demonstrated that electroporation of a modified CRISPR-Cas9 base editor to primary human bronchial epithelial cells carrying 3120 + 1G >A and F508del mutant alleles achieved 75% genome editing of the splice variant, resulting in approximately 40% wild-type (WT) CFTR function [1]. Here,we evaluate the effectiveness of several new nanoparticle formulations at delivering green fluorescent protein (GFP) mRNA to CF bronchial epithelial (CFBE41o-) cells. Using the optimal formulation,we then tested the efficacy correction of the 3120 + 1G >Avariant in a CFTR expression minigene (EMG) integrated into the genome of isogenic CFBE cells using mRNA and plasmid deoxyribonucleic acid (DNA) encoding adenine base editor (ABE) and guide (g)RNA. Method(s): GFP served as a reporter to evaluate transfection efficiency, cell viability, and mean fluorescence intensity (MFI) for three dosages (150, 75, 32.5 ng of mRNA), four polymer-to-mRNA to weight (w/w) ratios (60, 40, 30, 20), and four polymers (R, Y, G, B). 7-AAD served as a live/dead stain to quantify viability, with flow cytometry results analyzed using FlowJo software. CFBE cells stably expressing the 3120 + 1G >A EMG were transfected with the optimized nanoparticle formulation to deliver ABE and gRNA at two dosages (150, 75 ng) of mRNA and DNA. CFTR function in CFBE cellswas measured by short circuit current, forskolin stimulation, and inh-172 inhibition as a measure of editing efficiency. Result(s): Flow cytometry showed that polymer R achieved more than 85% GFP transfection, compared with a maximum of approximately 35% for the other three polymers at the maximum 150-ng dose, with approximately 80% viability normalized to untreated cells. In addition, polymer R achieved GFP MFI more than one order of magnitude as high as other formulations (~30 000 vs 2700 MFI) for the other three polymers at 150-ng dose and 40 w/w ratio. CFBE cells transfected with polymer R nanoparticles containing ABE and guide RNA at 75 ng and 150 ng showed mean CFTR function increase to 10 muA 6 (standard error of the mean [SEM] 1.1 muA) (~10% of WT) and 6.3 muA (SEM 0.9 muA) (~6% of WT), respectively. Greater toxicity at the higher dose could explain the larger increase in CFTR current at the lower dose. DNA-encoded ABE plasmid and gRNA showed a less robust increase in CFTR function (2.9 muA [SEM 0.4 muA] for 75-ng dose;3.0 muA [SEM 0.4 muA] for 150-ng dose), which was probably a result of the nanoparticle formulation being optimized for RNA instead of DNA cargo or the additional intracellular barriers that must be overcome for successful DNA delivery. Conclusion(s): We demonstrated that an optimized nanoparticle formulation containing ABE and gRNA can correct splicing of isogenic cells bearing the 3120 + 1G >A CFTR variant, resulting in recovery of CFTR function. In ongoing work, we are adapting these nanoparticles for RNA- and DNAencoded ABE and gRNA delivery to primary human bronchial epithelial cells.Copyright © 2022, European Cystic Fibrosis Society. All rights reserved
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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the current global pandemic of the COVID-19, which has persisted partly through the emergence of new variants. A non-infectious, convenient, and reproducible in vitro system is needed to assess drug susceptibility of new variants of concern and potential drug resistance mutations. Method(s): The SARS-CoV-2 replicon protocol was adapted and optimized based on {Zhang 2021}. The replicon RNA was produced by in vitro transcription of full-length replicon DNA assembled by ligation of plasmid fragments encoding for the SARS-CoV-2 non-structural proteins (Nsps), nucleoprotein and gaussia luciferase reporter protein. Wild-type and mutant replicon RNAs were transfected into Huh7-1CN cells by electroporation and treated with remdesivir (RDV). To determine EC50 values, luciferase activity was determined at 48 hours post transfection. A recombinant SARS-CoV-2 virus rescue system {Xie 2020} was used to generate matching Nsp mutants for comparison with the replicon system. Result(s): The selected substitutions reflective of Omicron BA.5 sub-lineage BF.7 variant: the triple mutants (Nsp12 (P323L) +Nsp13 (R392C) + Nsp14 (I42V), and a single Nsp12 L247F mutant as well as several specific Nsp12 mutations identified by in vitro resistance selection with RDV or RDV parent nucleoside analog GS-441524 were cloned into the replicon and tested for susceptibility to RDV. RDV inhibited the SARS-CoV-2 wild-type replicon with a mean EC50 value of 14.7 +/- 3.5 nM (N=9). The Nsp12 P323L substitution, a common polymorphism in all major variants of concern including Omicron, was fully susceptible to RDV with a 0.6-fold change in EC50 from the wild-type. The Omicron BF.7 triple mutants and L247F were also fully susceptible to RDV with 0.5- and 0.4-fold changes, respectively. Nsp12 substitutions F480L, V557L, V792I, S759A+V792I, and C799F resulting from in vitro resistance selections with RDV showed minimal to moderate levels of reduced susceptibility to RDV (1.8 to 18.3-fold change) (Table 1). The RDV EC50 fold changes correlated between the noninfectious replicon and recombinant infection virus system (Table 1). Conclusion(s): The replicon system is a convenient and reproducible model to test the susceptibility of SARS-CoV-2 mutant variants to RDV and potentially other antivirals. The common Nsp12 polymorphisms in all variants including the highly transmissible Omicron variant were fully susceptible to RDV.
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Pregnancy is a physiological state that predisposes women to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, a disease that can cause adverse maternal and perinatal outcomes. The severity of coronavirus disease 2019 (COVID-19) disease is known to vary by viral strain;however, evidence for the effects of this virus in pregnant women has yet to be fully elucidated. In this review, we describe maternal and perinatal outcomes, vaccination, and vertical transmission, among pregnant women infected with the different SARS-CoV-2 variants identified to date. We also summarize existing evidence for maternal and perinatal outcomes in pregnant women with specific information relating to SARS-CoV-2 variants. Our analysis showed that Omicron infection was associated with fewer severe maternal and perinatal adverse outcomes while the Delta variant was associated with worse pregnancy outcomes. Maternal deaths arising from COVID-19 were found to be rare (<1.0%), irrespective of whether the virus was a wild-Type strain or a variant. Severe maternal morbidity was more frequent for the Delta variant (10.3%), followed by the Alpha (4.7%), wild-Type (4.5%), and Omicron (2.9%) variants. The rates of stillbirth were 0.8%, 4.1%, 3.1%, and 2.3%, respectively, in pregnancies infected with the wild-Type strain, Alpha, Delta, and Omicron variants, respectively. Preterm birth and admission to neonatal intensive care units were more common for cases with the Delta infection (19.0% and 18.62%, respectively), while risks were similar for those infected with the wild-Type (14.7% and 11.2%, respectively), Alpha (14.9% and 13.1%), and Omicron variants (13.2% and 13.8%, respectively). As COVID-19 remains a global pandemic, and new SARS-CoV-2 variants continue to emerge, research relating to the specific impact of new variants on pregnant women needs to be expanded.Copyright © Wolters Kluwer Health, Inc. All rights reserved.
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Background: Limited data exist regarding the immune benefits of fourth COVID-19 vaccine doses in people with HIV (PWH) receiving antiretroviral therapy (ART), particularly given that most have now experienced SARS-CoV-2 infection. We measured the effect of fourth doses on SARS-CoV-2 neutralization in 63 PWH, including 19 SARS-CoV-2-naive and 44 SARS-CoV-2-experienced participants. Method(s): Wild-type (WT)-, Omicron-BA.5 and Omicron-BQ.1-specific neutralization activities were longitudinally quantified using live virus assays up to one month post-fourth vaccine dose. Multiple linear regression was used to investigate the relationship between sociodemographic, health and vaccinerelated variables and SARS-CoV-2 neutralization. Result(s): Participants (54 male;9 female) received monovalent (44%) or bivalent (56%) mRNA fourth doses. In COVID-19-naive PWH, a fourth dose enhanced WT- and BA.5-specific neutralization modestly above three-dose levels (p=0.1). In COVID-19-experienced PWH, a fourth dose enhanced WT neutralization modestly (p=0.1) and BA.5 neutralization significantly (p=0.002). Consistent with the humoral benefits of 'hybrid' immunity, the highest neutralization was observed in COVID-19-experienced PWH after a fourth dose. Of note, PWH with Omicron-era infections exhibited higher WT-specific (p=0.04), but comparable BA.5- or BQ.1-specific neutralization, compared to PWH with pre-Omicron-era infections. Overall, BA.5 neutralization was significantly lower than WT in all participants regardless of COVID-19 experience, and BQ.1 neutralization was significantly lower than BA.5 (all p< 0.0001). In multivariable analyses, fourth dose valency did not significantly affect neutralization magnitude, nor did sex, age nor CD4+ T-cell count (neither recent nor nadir). Rather, an mRNA-1273 fourth dose (versus a BNT162b2 one) was the strongest correlate of WT-specific neutralization, while prior COVID-19, regardless of infection era, was the strongest correlate of BA.5 and BQ.1-specific neutralization post-fourth dose. Conclusion(s): Fourth COVID-19 vaccine doses, irrespective of valency, benefit PWH regardless of prior SARS-CoV-2 infection, but the highest neutralization of Omicron-BA.5 and BQ.1 variants post-fourth dose occurred in PWH with hybrid immunity. These results support existing recommendations that all adults receive a fourth immunization within 6 months of their third vaccine dose (or their most recent SARS-CoV-2 infection). (Figure Presented).
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OBJECTIVES: Waning vaccine-induced immunity and emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants which may lead to immune escape, pose a major threat to the COVID-19 pandemic. Currently, enhanced efficacy of the neutralization antibodies (NAb) produced after the booster dose of vaccinations against the Omicron variant is the main focus of vaccine strategy research. In this study we have analyzed the potency of the NAbs and IgGs produced after the third vaccine dose in patients infected with Omicron variant and wild-type (WT) SARS-CoV-2. METHODS: We enrolled 75 patients with Omicron variant breakthrough infections, and 87 patients with WT infections. We recorded the clinical characteristics and vaccination information of all patients and measured the NAb and anti-S1 (spike protein) + N (nucleocapsid protein) IgG-binding antibodies against SARS-CoV-2 in serum samples of Omicron variant-infected patients at admission, and patients with WT COVID-19 infection from the time of admission and discharge, and one-year to two-years follow-ups. RESULTS: Our results demonstrated higher NAb levels, fewer clinical symptoms, and faster viral shedding in Omicron variant infected patients vaccinated with the booster dose. Hybrid immunity (natural infection plus vaccination) induces higher NAb levels than vaccine-only immunity. NAb and IgG levels decreased significantly at one-year follow-up in WT convalescents with natural infection. The NAb and IgG levels in booster-vaccinated COVID-19 patients were higher than those in two-dose-vaccinated patients. CONCLUSION: Our results suggest that booster vaccinations are required to improve the level of protective NAbs. Moreover, our data provide important evidence for vaccination strategies based on existing vaccines.
Subject(s)
Antibodies, Neutralizing , COVID-19 , Humans , SARS-CoV-2 , Pandemics , Immunoglobulin G , Antibodies, Viral , VaccinationABSTRACT
BACKGROUND: Quantitative models leveraging non-clinical data to predict clinical vaccine efficacy provide a translational framework to rapidly develop vaccines/ boosters against new strains of SARS-CoV- 2. METHOD(S): Previously, based on a systematic literature review, we performed a translational Model-Based Meta-Analysis (MBMA)1 integrating data of wild-type (WT) SARS-CoV- 2 from 13 rhesus macaques (RM) studies and eight clinical trials. The model is here updated with data from 32 additional RM studies including newer strains of SARS-CoV- 2 (e.g., omicron). Non-linear mixed-effects modeling was used to quantify the relationship in RM between serum neutralizing (SN) titers after vaccination and peak viral load (VL) post challenge in relevant tissue matrices. RESULT(S): The plot2 shows the model describes the relationship between SN titers and peak VL across all specimens well. The overlap between the confidence intervals across virus strains suggests that the model can be leveraged to describe RM data across viral SARS-CoV- 2 strains. CONCLUSION(S): The previous work1 demonstrated that RM VL is quantitatively predictive of clinical efficacy, and so this update provides a framework to predict clinical vaccine efficacy against newer variants using only RM data (Figure Presented).
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Rationale: To establish a novel SARS-CoV-2 human challenge model enabling controlled investigation of pathogenesis, correlates of protection and efficacy testing of interventions. Method(s): Thirty-six healthy 18-29-year-old subjects, without evidence of previous infection or vaccination, received 10 TCID50 of a wild-type virus (SARS-CoV-2/human/GBR/484861/2020) intranasally. Following inoculation, subjects resided in a high-containment quarantine, with 24-hour medical monitoring. The study's main objectives were to identify a virus dose that induced well-tolerated infection in >50% of subjects and assess virus and symptoms over time. AEs and longitudinal disease profiles are presented. Result(s): Eighteen of thirty-four evaluable (~53%) subjects became infected and developed serum antibodies. Viral load rose steeply and peaked ~5 days post-inoculation (PI). Virus was first detected in the throat but rose to significantly higher levels in the nose, peaking at ~8.87 log10 copies/ml (median, 95% CI [8.41,9.53]). Viable virus was recoverable from the nose up to ~10 days PI, on average. Mild-to-moderate symptoms were reported by 16 (89%) infected subjects, beginning 2-4 days PI. Anosmia or dysosmia developed in 15 (83%) subjects. Results from lateral flow tests were associated with viable virus and modelling showed that twice-weekly rapid antigen tests could diagnose infection before 70-80% of viable virus had been generated. There were no overt lung function changes, CT abnormalities, or SAEs. Conclusion(s): This novel SARS-CoV-2 challenge of 18-29-year-olds was considered safe. Viral kinetics over the course of primary infection was established, with implications for public health recommendations and strategies to impact transmission.
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Background: Anti-tumour necrosis factor drugs such as infliximab are associated with attenuated antibody responses after COVID-19 vaccination It is unknown how infliximab impacts vaccine-induced serological responses against highly transmissible Omicron variants, which possess the ability to evade host immunity and are now the dominating variants causing current waves of infection Methods: In this prospective, multicentre, observational cohort study we investigated neutralising antibody responses against SARS-CoV-2 wild-type and Omicron BA.1 and BA.4/5 variants after three doses of COVID-19 vaccination in 1288 patients with IBD without prior COVID-19 infection, who were established on either infliximab (n=871) or vedolizumab (n=417). Cox proportional hazards models were constructed to investigate the risk of breakthrough infection in relation to neutralising antibody titres Results: Following three doses of COVID-19 vaccine, neutralising titre NT50 (half-inhibitory neutralising titre) was significantly diminished in patients treated with infliximab as compared to patients treated with vedolizumab, against wild-type, BA.1 and BA.4/5 variants (Fig 1). Patients with Crohn's disease showed lower antibody NT50 compared to patients with ulcerative colitis against wild-type strain and BA.4/5 (Fig 2). Older age and thiopurine were independently associated with lower NT50 against wild-type strain and BA.4/5 (Fig 2). Non-white ethnicity was associated with higher NT50 compared to white ethnicity against wild-type strain, BA.1 and BA.4/5 (Fig 2). Breakthrough infection was significantly more frequent in patients treated with infliximab compared to patients treated with vedolizumab (Fig 3). Cox proportional hazards models of time to breakthrough infection after the third dose showed infliximab treatment to be associated with a higher hazard risk (HR) of 1.71 (95% CI [1.08 to 2.71], p=0.022) compared to vedolizumab (Fig 4). Higher neutralising antibody titres against BA.4/5 were associated with a lower hazard risk and a longer time to breakthrough infection (HR 0.87 [0.79 to 0.95] p=0.0028) (Fig 4) Conclusion(s): Following a third COVID-19 vaccine dose, patients established on infliximab treatment have significantly lower neutralising titres against SARS-CoV-2, which were especially low against Omicron variants. Increased breakthrough infection in infliximab recipients was associated with lower neutralising antibody titres against BA.4/5. These data underline the importance of continued COVID-19 vaccination programs, including second-generation bivalent vaccines, especially in patient subgroups where vaccine immunogenicity and efficacy may be reduced.
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Background: Patients with Inflammatory bowel disease (IBD) receiving anti-TNF or JAK-inhibitor therapy have attenuated responses to COVID-19 vaccination. We aimed to determine how IBD treatments affect neutralising antibody responses against the currently dominant Omicron BA.4/5 variants. Method(s): We prospectively recruited 329 adults (68 healthy controls (HC) and 261 IBD) who had received three doses of COVID-19 vaccine at nine UK centres. The IBD population was established (>12 weeks therapy) on either thiopurine (n=60), infliximab (IFX) (n=43), thiopurine and IFX combination (n=46), ustekinumab (n=43), vedolizumab (n=46) or tofacitinib (n=23). Pseudoneutralisation assays were performed and the half maximal inhibitory concentration (NT50) of participant sera was calculated. The primary outcome was anti-SARSCoV-2 neutralising response against wild-type (WT) virus and the BA.4/5 variant after the second and third doses of anti-SARS-CoV-2 vaccine, stratified by immunosuppressive therapy, adjusting for prior infection, ethnicity, vaccine type and age. Result(s): Heterologous (two doses adenovirus vaccine, third dose mRNA vaccine) and homologous (three doses mRNA vaccine) vaccination strategies significantly increased neutralising titres against both WT SARS-CoV-2 virus and the BA.4/5 variants in HCs and IBD (fig 1). Antibody titres against BA.4/5 were significantly lower than antibodies against WT virus in both groups (Geometric Mean Ratio (GMR) [95% CI], 0.11 [0.09, 0.15], P<0.0001 in healthy participants;GMR 0.07 [0.06, 0.08], P<0.0001 in IBD patients). Multivariable models showed that neutralising antibodies against BA.4/5 after three doses of vaccine were significantly lower in IBD patients on IFX (GMR 0.44 [0.20, 0.97], P=0.042), IFX and thiopurine combination (GMR 0.34 [0.15, 0.77], P=0.0098) or tofacitinib (GMR 0.37 [0.15, 0.92], P=0.032), but not in patients on thiopurine monotherapy, ustekinumab or vedolizumab. Breakthrough infection was associated with lower neutralising antibodies against WT and BA.4/5 (P<0.05). Conclusion(s): A third dose of COVID-19 vaccine based on the WT spike glycoprotein boosts neutralising antibody titres in patients with IBD. However, responses are lower against the currently dominant variant BA.4/5, particularly in patients taking anti-TNF or JAK-inhibitor therapy. Breakthrough infections are associated with lower neutralising antibodies and immunosuppressed IBD patients may receive additional benefit from bivalent vaccine boosters which target Omicron variants. .
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Background: Little is known about the induction of mucosal Ab after the 3rd dose. We reported that two doses of BNT162b2 induced mucosal Abs as early as 14-days after the 1st dose. As BNT162b2 only provides the RNA encoding a full-length spike (S) protein, a mixed-vaccine regime with a vaccine that provides inactivated but intact viral particles was executed in some countries to expand the diversity of SARS-CoV-2 Abs. Aim and objectives: To examine the mucosal and plasma Ab induction in vaccine recipients receiving their 3rd vaccine dose with single or mixed vaccine type. Method(s): 46 healthy subjects who had BNT162b2 (B) or CoronaVac (C) in a sequence of either BBB, BBC, CCC or CCB were recruited for a longitudinal sampling of nasal fluid and blood. The S1-specific Ab and neutralizing Ab against SARS-CoV-2 VOCs were measured. Result(s): All BBB recipients (n=28) had nasal specific S1-IgA and IgG after two doses, and the Abs lasted six months and were readily induced after the 3rd dose. In BBC recipients (n=4), though they had prior induction of nasal Abs after two doses of B, the inactivated vaccine did not boost their nasal Abs. In CCC recipients (n=5), there was no induction on nasal Abs. If they adopted the CCB regime (CCB, n=11), they acquired nasal Ab after the 3rd dose. The nasal neutralizing antibodies against the wild type were boosted in 20/28 of the BBB recipients and induced in 8/11 of the CCB recipients but not in CCC or BBC recipients. Lastly, all 46 subjects had a boosted specific S1-IgA and S1IgG in plasma. Conclusion(s): Our findings highlighted the uniqueness of BNT162b2 in induing nasal Ab regardless of the vaccination history.
ABSTRACT
This study aims to fill a knowledge gap in our understanding of Omicron variant receptor-binding domain (RBD) interactions with host cell receptor, angiotensin-converting enzyme 2 (ACE2). Protein-protein docking, scoring, and filtration were all performed using the HDOCK server. A coarse-grained prediction of the changes in binding free energy caused by point mutations in Omicron RBD was requested from the Binding Affinity Changes upon Mutation (BeAtMuSiC) tools. GROMACS was utilized to perform molecular dynamics simulations (MD). Within the 15 mutations in Omicron RBD, several mutations have been linked to increased receptor affinity, immunological evasion, and inadequate antibody response. Wild-type (wt) SARS-CoV-2 and its Omicron variant have 92.27% identity. Nonetheless, Omicron RBD mutations resulted in a slight increase in the route mean square deviations (RMSD) of the Omicron structural model during protein-protein docking, as evidenced by RMSDs of 0.47 and 0.85 A for the wt SARS-CoV-2 and Omicron RBD-ACE2 complexes, respectively. About five-point mutations had essentially an influence on binding free energy, namely G6D, S38L, N107K, E151A, and N158Y. The rest of the mutations were expected to reduce the binding affinity of Omicron RBD and ACE2. The MD simulation supports the hypothesis that Omicron RBD is more stably bound to ACE2 than wt SARS-CoV-2 RBD. Lower RMSD and greater radius of gyration (Rg) imply appropriate Omicron structure 3D folding and stability. However, the increased solvent accessible surface area (SASA) with a greater Omicron shape may have a different interaction with receptor binding and regulate virus entrance. Omicron RBD's mutations help it maintain its structural stability, compactness, ACE2 binding, and immune evasion.Copyright © 2022 AEPress, s.r.o.. All rights reserved.
ABSTRACT
Background: The effects of immunosuppressive medications on immune responses to COVID-19 vaccination in patients with inflammatory bowel diseases (IBD) have been reported. However there is little data on immune responses in naturally infected SARS-CoV-2 patients compared with vaccination. We compared in a longitudinal study SARS-CoV-2 antibody and T cell responses in naturally-infected vs. vaccinated IBD patients Methods: 110 IBD patients enrolled at the Icahn School of Medicine at Mount Sinai were prospectively followed with serial blood collection between May 2020, and February 2022. Samples were screened by ELISA to determine seropositivity, and stratified by infection, vaccination status, and IBD medications. Subsequently, ELISA-based inhibition assay and pseudotyped SARS-CoV-2 microneutralization assays were used to determine the inhibition and neutralization capacity of the seropositive individuals for wild type (WT) delta variant (Dv) and Omicron. Cellular responses were measured by IFN-gamma ELIspot using nucleocapsid and spike peptide libraries Results: Overall, 64 patients had Crohn's Disease and 46 had Ulcerative Colitis (UC), 69 were naturally infected. Only Anti-TNF (N=52), Ustekinumab (N=16), and Vedolizumab (VDZ) (N=33) treatment groups were considered. Only US-available vaccinations were included. Double-vaccinated IBD patients showed greater neutralizing responses to SARS-CoV-2 WT and Dv than naturally-infected individuals (p=0.0003, p=0.0025). Moreover, double-vaccinated individuals had greater neutralizing reactions against WT than DV (p 0.017) and Omicron (p 0.001) variants. Following natural infection, there were no differences between treatment groups in neutralization response, however those double-vaccinated on anti-TNF had lower neutralization than VDZ (p=0.008). Neutralization responses were maintained for a period of 8 months following natural infection and double vaccination SARS-CoV-2 spike T cell responses were significantly higher in naturally infected (p=0.009) and double vaccinated individuals (p=0.005) with no significant differences between treatment groups (p<0.999) Conclusion(s): After a second vaccine dose, IBD patients showed stronger neutralizing antibody titers than naturally infected patients. Those on anti-TNF exhibited lower neutralizing responses than VDZ. T-cell responses were similar in infected and double-vaccinated subjects after vaccination or infection. These data imply COVID-19 immunization provides additional serological protection over natural infection.
ABSTRACT
Background: IgG anti-spike (S) antibodies arise after SARS-CoV-2 infection aswellas vaccination. LevelsofIgG anti-S are linked to neutralizing antibody titers and protection against (re)infection. Method(s): We measured IgG anti-S and surrogate neutralizing antibody kinetics against Wild Type (WT) and 4 Variants of Concern (VOC) in health care workers (HCW) 3 and 10 months after natural infection ("infection", n=83) or vaccination (2 doses of BNT162b2) with ("hybrid immunity", n=17) or without prior SARS-CoV-2 infection ("vaccination", n=97). Result(s): The humoral immune response in the "vaccination" cohort was higher at 3 months, but lower at 10 months, compared to the "infection" cohort due to a faster decline. The "hybrid immunity" cohort had the highest antibody levels at 3 and 10 months with a slower decline compared to the "vaccination" cohort (figure 1). Surrogate neutralizing antibody levels (expressed as %inhibition of ACE-2 binding) showed a linear relation with log10 of IgG anti-S against WT and four VOC. IgG anti-S corresponding to 90% inhibition ranged from 489 BAU/mL for WT to 1756 BAU/mL for Beta variant. Broad pseudoneutralization predicted live virus neutralization of Omicron BA.1 in 20 randomly selected high titer samples. Conclusion(s): Hybrid immunity resulted in the strongest humoral immune response. Antibodies induced by natural infection decreased more slowly than after vaccination, resulting in higher antibody levels at 10 months compared to vaccinated HCW without prior infection. There was a linear relationship between surrogate neutralizing activity and log10 IgG anti-S for WT and 4 VOC, although some VOC showed reduced sensitivity to pseudoneutralization.