SARS-CoV-2 Omicron: evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern

Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. Over this time global vaccine programs have been introduced, contributing to lowered COVID-19 hospitalisation and mortality rates, particularly in the first world. In late 2021, the Omicron (B.1.1.529) virus variant emerged, with significant genetic differences and clinical effects from other variants of concern (VOC). This variant a demonstrated higher number of polymorphisms in the gene encoding the Spike (S) protein, and there has been displacement of the dominant Delta variant. We assessed the impact of Omicron infection on the ability of: serum from vaccinated and/or previously infected individuals; concentrated human IgG from plasma donors, and licensed monoclonal antibody therapies to neutralise the virus in vitro. There was a 17 to 27-fold reduction in neutralisation titres across all donors who had a detectable neutralising antibody titre to the Omicron variant. Concentrated pooled human IgG from convalescent and vaccinated donors had greater breadth of neutralisation, although the potency was still reduced 16-fold. Of all therapeutic antibodies tested, significant neutralisation of the Omicron variant was only observed for Sotrovimab, with other monoclonal antibodies unable to neutralise Omicron in vitro. These results have implications for ongoing therapy of individuals infected with the Omicron variant.

Effects of Varying Approaches to Lifting COVID-19 Pandemic Restrictions in the United States

Background Policy approaches to lifting COVID-19 restrictions have varied significantly across the United States. An evaluation of the effects of state reopening policies on population health outcomes can inform ongoing and future pandemic responses. This study evaluates the approaches to lifting social distancing restrictions based on adherence to the Centers for Disease Control and Prevention (CDC) guidance established during the first wave of the COVID-19 pandemic. Methods We performed a retrospective study using difference-in-differences analyses to examine the effects of reopening policies on COVID-19 outcomes with risk-adjustment for population density, temporal changes, and concurrent mask policy implementation. We examined the effects of reopening policies on per capita case rates and rates of severe COVID-19 outcomes, including hospitalizations and deaths. Results Adherence to CDC reopening gating metrics and phased social distancing guidelines resulted in fewer COVID-19 cases, hospitalizations, and deaths. Phase one adherent states exhibited a 50-fold reduction in daily new cases and a 3-fold reduction in daily new deaths after reopening. Phase two adherent states experienced improvements in COVID-19 outcomes after reopening, while non-adherent states had a resurgence of worsening outcomes after lifting restrictions. Conclusions Our study findings indicate that adherence to CDC reopening guidance after implementing social distancing restrictions during the COVID-19 pandemic substantially prevents new cases, hospitalizations, and deaths. Following a stepwise reopening strategy and ensuring a sustained decline in case rates and test positivity rates before lifting restrictions can mitigate on a large scale the negative effects of a pandemic on population health outcomes.

In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate

The emergence and rapid spread of the Omicron variant of SARS-CoV-2, which has more than 30 substitutions in the spike glycoprotein, compromises the efficacy of currently available vaccines and therapeutic antibodies. Using a clinical strain of the Omicron variant, we analyzed the neutralizing power of eight currently used monoclonal antibodies compared to the ancestral B.1 BavPat1 D614G strain. We observed that six of these antibodies have lost their ability to neutralize the Omicron variant. Of the antibodies still having neutralizing activity, Sotrovimab/Vir-7831 shows the smallest reduction in activity, with a factor change of 3.1. Cilgavimab/AZD1061 alone shows a reduction in efficacy of 15.8, resulting in a significant loss of activity for the Evusheld cocktail (42.6 fold reduction) in which the other antibody, Tixagevimab, does not retain significant activity against Omicron. Our results suggest that the clinical efficacy of the initially proposed doses should be rapidly evaluated and the possible need to modify doses or propose combination therapies should be considered.

Experiments And Simulations of Thermometric Lateral Flow Immunoassay For Point-of-Care Testing

Temperature sensing is a promising method of enhancing the detection sensitivity of lateral flow immunoassay for point-of-care testing. A temperature increase of more than 100 °C can be readily achieved by photoexcitation of reporters like gold nanoparticles (GNPs) or colored latex beads (CLBs) on the strips with a laser power below 100 mW. Despite its promise, processes involved in the photothermal detection have not yet been well-characterized. Here, we provide a fundamental understanding of this thermometric assay by combining experiments and simulations using non-fluorescent CLBs as the reporters deposited on nitrocellulose membrane. By measuring the dependence of temperature rises on the number density of membrane-bound CLBs, we determined a 1.5-fold enhancement of the light absorption at 520 nm by the beads (diameter of 0.4 μm). The enhancement, however, was compromised by a 5-fold reduction of the incident laser power due to multiple scattering of the light in this highly porous medium. The limit of detection was measured to be 1 × 105 particles/mm2. In line with previous studies using GNPs as the reporters, the CLB-based thermometric assay provides a 10× higher sensitivity than color visualization, as demonstrated with the immunoassay for nucleocapsid proteins of the SARS-CoV-2 virus.

Neutralization against Omicron SARS-CoV-2 from previous non-Omicron infection

The explosive spread of the Omicron SARS-CoV-2 variant underscores the importance of analyzing the cross-protection from previous non-Omicron infection. We developed a high-throughput neutralization assay for Omicron SARS-CoV-2 by engineering the Omicron spike gene into an mNeonGreen USA-WA1/2020 SARS-CoV-2 (isolated in January 2020). Using this assay, we determined the neutralization titers of patient sera collected at 1- or 6-months after infection with non-Omicron SARS-CoV-2. From 1- to 6-month post-infection, the neutralization titers against USA-WA1/2020 decreased from 601 to 142 (a 4.2-fold reduction), while the neutralization titers against Omicron-spike SARS-CoV-2 remained low at 38 and 32, respectively. Thus, at 1- and 6-months after non-Omicron SARS-CoV-2 infection, the neutralization titers against Omicron were 15.8- and 4.4-fold lower than those against USA-WA1/2020, respectively. The low cross-neutralization against Omicron from previous non-Omicron infection supports vaccination of formerly infected individuals to mitigate the health impact of the ongoing Omicron surge.

mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 Omicron variant

The BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines generate potent neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the global emergence of SARS-CoV-2 variants with mutations in the spike protein, the principal antigenic target of these vaccines, has raised concerns over the neutralizing activity of vaccine-induced antibody responses. The Omicron variant, which emerged in November 2021, consists of over 30 mutations within the spike protein. Here, we used an authentic live virus neutralization assay to examine the neutralizing activity of the SARS-CoV-2 Omicron variant against mRNA vaccine-induced antibody responses. Following the 2nd dose, we observed a 30-fold reduction in neutralizing activity against the omicron variant. Through six months after the 2nd dose, none of the sera from naive vaccinated subjects showed neutralizing activity against the Omicron variant. In contrast, recovered vaccinated individuals showed a 22-fold reduction with more than half of the subjects retaining neutralizing antibody responses. Following a booster shot (3rd dose), we observed a 14-fold reduction in neutralizing activity against the omicron variant and over 90% of boosted subjects showed neutralizing activity against the omicron variant. These findings show that a 3rd dose is required to provide robust neutralizing antibody responses against the Omicron variant.

Single-chain variable fragments of broadly neutralizing antibodies prevent HIV cell-cell transmission

Broadly neutralizing antibodies (bNAbs) are able to prevent HIV infection following passive administration. Single-chain variable fragments (scFv) may have advantages over IgG as their smaller size permits improved diffusion into mucosal tissues. We have previously shown that scFv of bNAbs retain significant breadth and potency against cell-free viral transmission in a TZM-bl assay. However, scFv have not been tested for their ability to block cell-cell transmission, a model in which full-sized bNAbs lose potency. We tested 4 scFv (CAP256.25, PGT121, 3BNC117 and 10E8v4) compared to IgG, in free-virus and cell-cell neutralization assays in A3.01 cells, against a panel of seven heterologous viruses. We show that free-virus neutralization titers in the TZM-bl and A3.01 assays were not significantly different, and confirm that scFv show a 1 to 32-fold reduction in activity in the cell-free model, compared to IgG. However, whereas IgG show 3.4 to 19-fold geometric mean potency loss in cell-cell neutralization compared to free-virus transmission, scFv had more comparable activity in the two assays, with only a 1.3 to 2.3-fold reduction. Geometric mean IC 50 of scFv for cell-cell transmission ranged from 0.65 μg/ml (10E8v4) to 2.3 μg/ml (3BNC117) with IgG and scFv neutralization showing similar potency against cell-associated transmission. Therefore, despite the reduced activity of scFv in cell-free assays, their retention of activity in the cell-cell format may make scFv useful for the prevention of both modes of transmission in HIV prevention studies. Importance Broadly neutralizing antibodies (bNAbs) are a major focus for passive immunization against HIV, with the recently concluded HVTN AMP (Antibody Mediated Protection) trial providing proof of concept. Most studies focus on cell-free HIV, however cell-associated virus may play a significant role in HIV infection, pathogenesis and latency. Single-chain variable fragments (scFv) of antibodies may have increased tissue penetration, and reduced immunogenicity. We previously demonstrated that scFv of four HIV-directed bNAbs (CAP256-VRC26.25, PGT121, 3BNC117 and 10E8v4) retain significant potency and breadth against cell-free HIV. As some bNAbs have been shown to lose potency against cell-associated virus, we investigated the ability of bNAb scFv to neutralize this mode of transmission. We demonstrate that unlike IgG, scFv of bNAbs are able to neutralize cell-free and cell-associated virus with similar potency. These scFv, which show functional activity in the therapeutic range, may therefore be suitable for further development as passive immunity for HIV prevention.

Bacteriomimetic Liposomes Improve Antibiotic Activity of a Novel Energy-Coupling Factor Transporter Inhibitor

Liposomes have been studied for decades as nanoparticulate drug delivery systems for cytostatics, and more recently, for antibiotics. Such nanoantibiotics show improved antibacterial efficacy compared to the free drug and can be effective despite bacterial recalcitrance. In this work, we present a loading method of bacteriomimetic liposomes for a novel, hydrophobic compound (HIPS5031) inhibiting energy-coupling factor transporters (ECF transporters), an underexplored antimicrobial target. The liposomes were composed of DOPG (18:1 (Δ9-cis) phosphatidylglycerol) and CL (cardiolipin), resembling the cell membrane of Gram-positive Staphylococcus aureus and Streptococcus pneumoniae, and enriched with cholesterol (Chol). The size and polydispersity of the DOPG/CL/± Chol liposomes remained stable over 8 weeks when stored at 4 °C. Loading of the ECF transporter inhibitor was achieved by thin film hydration and led to a high encapsulation efficiency of 33.19% ± 9.5% into the DOPG/CL/Chol liposomes compared to the phosphatidylcholine liposomes (DMPC/DPPC). Bacterial growth inhibition assays on the model organism Bacillus subtilis revealed liposomal HIPS5031 as superior to the free drug, showing a 3.5-fold reduction in CFU/mL at a concentration of 9.64 µM. Liposomal HIPS5031 was also shown to reduce B. subtilis biofilm. Our findings present an explorative basis for bacteriomimetic liposomes as a strategy against drug-resistant pathogens by surpassing the drug-formulation barriers of innovative, yet unfavorably hydrophobic, antibiotics.

Pseudotyped SARS-CoV-2 Omicron variant exhibits significant escape from neutralization induced by a third booster dose of vaccination

The Omicron Variant of concern (B.1.1.529) has spread internationally and is raising serious concerns about the reduced vaccine efficacy and the increased risk of reinfection. Here we assessed the serum neutralizing activity using a pseudovirus-based neutralization assay in 292 healthcare workers who had administered a third homologous boosting vaccination 8 to 9 months after completion of the priming two-dose inactivated vaccination to investigate whether the newly identified Omicron variant could escape serum antibody neutralization elicited by the booster vaccination. The third booster dose with BBIBP-CorV lead to a significant rebound in neutralizing immune response against SARS-CoV-2, and the neutralization GMT on day 28 after the third booster dose was 6.1 times higher than the GMT on day 28 after the second dose. The Omicron variant did cause significantly lower neutralization sensitivity compared to the wild-type strain of the booster elicited serum, with about 20.1-fold reduction. Our study demonstrated that a third booster dose of BBIBP-CorV lead to a significant rebound in neutralizing immune response against SARS-CoV-2, while the Omicron variant showed extensive but incomplete escape of the booster elicited neutralization.

Worm Gear Drives with Improved Kinematic Accuracy

This paper presents the fundamentals of the design and applications of new worm gear drive solutions, which enable the minimisation of backlash and are characterised by higher kinematic accuracy. Different types of worm surfaces are briefly outlined. Technological problems concerning the principles of achieving a high degree of precision in machining are also described. Special attention is paid to the shaping of conical helical surfaces. Increasing the manufacturing precision of drive components allows one to achieve both lower backlash values and lower levels of its dispersion. However, this does not ensure that backlash can be eliminated, with its value being kept low during longer periods of operation. This is important in positioning systems and during recurrent operations. Various design solutions for drives in which it is possible to reduce backlash are presented. Results of experiments of a worm gear drive with a worm axially adaptive only locally, in its central section, are presented. In this solution, it is possible to reduce backlash by introducing adjustment settings without disassembling the drive. An important scientific problem concerned defining the principles of achieving a compromise between the effectiveness of reducing backlash and the required load capacity of the drive. In this paper it has been shown that in worm gear drives with a locally axially adaptive worm, as well as with a worm wheel with a deformable rim, it is possible to achieve significant reduction of backlash. In high precision drives—for example, those with an average backlash value of <15 micrometers—this can enable more than a two-fold reduction of the average backlash value and more than a three-fold decrease of the standard deviation of local backlash values.