Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum.

The Omicron lineage of SARS-CoV-2, which was first described in November 2021, spread rapidly to become globally dominant and has split into a number of sublineages. BA.1 dominated the initial wave but has been replaced by BA.2 in many countries. Recent sequencing from South Africa's Gauteng region uncovered two new sublineages, BA.4 and BA.5, which are taking over locally, driving a new wave. BA.4 and BA.5 contain identical spike sequences, and although closely related to BA.2, they contain further mutations in the receptor-binding domain of their spikes. Here, we study the neutralization of BA.4/5 using a range of vaccine and naturally immune serum and panels of monoclonal antibodies. BA.4/5 shows reduced neutralization by the serum from individuals vaccinated with triple doses of AstraZeneca or Pfizer vaccine compared with BA.1 and BA.2. Furthermore, using the serum from BA.1 vaccine breakthrough infections, there are, likewise, significant reductions in the neutralization of BA.4/5, raising the possibility of repeat Omicron infections.

Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.

Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

On 24th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera.

The race to produce vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began when the first sequence was published, and this forms the basis for vaccines currently deployed globally. Independent lineages of SARS-CoV-2 have recently been reported: UK, B.1.1.7; South Africa, B.1.351; and Brazil, P.1. These variants have multiple changes in the immunodominant spike protein that facilitates viral cell entry via the angiotensin-converting enzyme-2 (ACE2) receptor. Mutations in the receptor recognition site on the spike are of great concern for their potential for immune escape. Here, we describe a structure-function analysis of B.1.351 using a large cohort of convalescent and vaccinee serum samples. The receptor-binding domain mutations provide tighter ACE2 binding and widespread escape from monoclonal antibody neutralization largely driven by E484K, although K417N and N501Y act together against some important antibody classes. In a number of cases, it would appear that convalescent and some vaccine serum offers limited protection against this variant.

Antibody evasion by the P.1 strain of SARS-CoV-2.

Terminating the SARS-CoV-2 pandemic relies upon pan-global vaccination. Current vaccines elicit neutralizing antibody responses to the virus spike derived from early isolates. However, new strains have emerged with multiple mutations, including P.1 from Brazil, B.1.351 from South Africa, and B.1.1.7 from the UK (12, 10, and 9 changes in the spike, respectively). All have mutations in the ACE2 binding site, with P.1 and B.1.351 having a virtually identical triplet (E484K, K417N/T, and N501Y), which we show confer similar increased affinity for ACE2. We show that, surprisingly, P.1 is significantly less resistant to naturally acquired or vaccine-induced antibody responses than B.1.351, suggesting that changes outside the receptor-binding domain (RBD) impact neutralization. Monoclonal antibody (mAb) 222 neutralizes all three variants despite interacting with two of the ACE2-binding site mutations. We explain this through structural analysis and use the 222 light chain to largely restore neutralization potency to a major class of public antibodies.

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera.

SARS-CoV-2 has caused over 2 million deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light-chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.

The antigenic anatomy of SARS-CoV-2 receptor binding domain.

Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50 < 0.1 µg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.

Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition.

Cellular processes are controlled by the thermodynamics of the underlying biomolecular interactions. Frequently, structural investigations use one monomeric binding partner, while ensemble measurements of binding affinities generally yield one affinity representative of a 1:1 interaction, despite the majority of the proteome consisting of oligomeric proteins. For example, viral entry and inhibition in SARS-CoV-2 involve a trimeric spike surface protein, a dimeric angiotensin-converting enzyme 2 (ACE2) cell-surface receptor and dimeric antibodies. Here, we reveal that cooperativity correlates with infectivity and inhibition as opposed to 1:1 binding strength. We show that ACE2 oligomerizes spike more strongly for more infectious variants, while exhibiting weaker 1:1 affinity. Furthermore, we find that antibodies use induced oligomerization both as a primary inhibition mechanism and to enhance the effects of receptor-site blocking. Our results suggest that naive affinity measurements are poor predictors of potency, and introduce an antibody-based inhibition mechanism for oligomeric targets. More generally, they point toward a much broader role of induced oligomerization in controlling biomolecular interactions.

Molecular sandwich-based DNAzyme catalytic reaction towards transducing efficient nanopore electrical detection of antigen proteins.

Despite significant advances in nanopore nucleic acid sequencing and sensing, protein detection remains challenging due to the inherent complexity of protein molecular properties (i.e., net charges, polarity, molecular conformation & dimension) and sophisticated environmental parameters (i.e., biofluids), resulting in unsatisfactory electrical signal resolution for protein detection such as poor accessibility, selectivity and sensitivity. The selection of an appropriate electroanalytical approach is strongly desired which should be capable of offering easily detectable and readable signals regarding proteins particularly depending on the practical application. Herein, a molecular sandwich-based cooperative DNAzyme catalytic reaction nanopore detecting approach was designed. Specifically, this approach uses Mg2+ catalyzed DNAzyme (10-23) toward nucleic acids digestion for efficient antigen protein examination. The proposed strategy operates by initial formation of a molecular sandwich containing capture antibody-antigen-detection antibody for efficient entrapment of target proteins (herein taking the HIV p24 antigen for example) and immobilization on magnetic beads surfaces. After that, the DNAzyme was linked to the detection antibody via a biotin-streptavidin interaction. In the presence of Mg2+, the DNAzyme catalytic reaction was triggered to digest nucleic acid substrates and release unique cleavage fragments as reporters capable of transducing more easily detectable nucleic acids as a substitute for the complicated and hard to yield protein signals, in a nanopore. Notably, experimental validation confirms the detecting stability and sensitivity for the target antigen referenced with other antigen proteins, meanwhile it demonstrates a detection efficacy in a human serum environment at very low concentration (LoD ∼1.24 pM). This cooperative DNAzyme nanopore electroanalytical approach denotes an advance in protein examination, and may benefit in vitro testing of proteinic biomarkers for disease diagnosis and prognosis assessment.

Research on the Postural Stability of Underwater Bottom Platforms with Different Burial Depths.

The bottom platform is an important underwater sensor that can be used in communications, early warning, monitoring, and other fields. It may be affected by earthquakes, winds, waves, and other loads in the working environment, causing changes in posture and affecting its sensing function. Therefore, it is of practical engineering significance to analyze the force conditions and posture changes in the bottom platform. In order to solve the problem of postural stability of the underwater bottom platform, this paper establishes a fluid and structural simulation model of the underwater bottom platform. First, computational fluid dynamics (CFD) technology is used to solve the velocity distribution and forces in the watershed around the bottom platform under a 3 kn ocean current, where the finite element method (FEM) numerical calculation method is used to solve the initial equilibrium state of the bottom platform after it is buried. On this basis, this paper calculates the forces on the bottom platform and the posture of the bottom platform at different burial depths under the action of ocean currents. Additionally, the effects of different burial depths on the maximum displacement, deflection angle, and postural stability of the bottom platform are studied. The calculation results show that when the burial depth is greater than 0.6 m, and the deflection angle of the bottom platform under the action of the 3 kn sea current is less than 5°, the bottom platform can maintain a stable posture. This paper could be used to characterize the postural stability of underwater bottom platforms at different burial depths for the application of underwater sensors in ocean engineering.

Research on Multiple-AUVs Collaborative Detection and Surrounding Attack Simulation.

Due to limitations in operational scope and efficiency, a single Autonomous Underwater Vehicle (AUV) falls short of meeting the demands of the contemporary marine working environment. Consequently, there is a growing interest in the coordination of multiple AUVs. To address the requirements of coordinated missions, this paper proposes a comprehensive solution for the coordinated development of multi-AUV formations, encompassing long-range ferrying, coordinated detection, and surrounding attack. In the initial phase, detection devices are deactivated, employing a path planning method based on the Rapidly Exploring Random Tree (RRT) algorithm to ensure collision-free AUV movement. During the coordinated detection phase, an artificial potential field method is applied to maintain AUV formation integrity and avoid obstacles, dynamically updating environmental probability based on formation movement. In the coordinated surroundings attack stage, predictive capabilities are enhanced using Long Short-Term Memory (LSTM) networks and reinforcement learning. Specifically, LSTM forecasts the target's position, while the Deep Deterministic Policy Gradient (DDPG) method controls AUV formation. The effectiveness of this coordinated solution is validated through an integrated simulation trajectory.

Research Progress on Saccharide Molecule Detection Based on Nanopores.

Saccharides, being one of the fundamental molecules of life, play essential roles in the physiological and pathological functions of cells. However, their intricate structures pose challenges for detection. Nanopore technology, with its high sensitivity and capability for single-molecule-level analysis, has revolutionized the identification and structural analysis of saccharide molecules. This review focuses on recent advancements in nanopore technology for carbohydrate detection, presenting an array of methods that leverage the molecular complexity of saccharides. Biological nanopore techniques utilize specific protein binding or pore modifications to trigger typical resistive pulses, enabling the high-sensitivity detection of monosaccharides and oligosaccharides. In solid-state nanopore sensing, boronic acid modification and pH gating mechanisms are employed for the specific recognition and quantitative analysis of polysaccharides. The integration of artificial intelligence algorithms can further enhance the accuracy and reliability of analyses. Serving as a crucial tool in carbohydrate detection, we foresee significant potential in the application of nanopore technology for the detection of carbohydrate molecules in disease diagnosis, drug screening, and biosensing, fostering innovative progress in related research domains.

Emerging and legacy per- and polyfluoroalkyl substances in house dust from South China: Contamination status and human exposure assessment.

Our study investigated a large variety of per- and polyfluoroalkyl substances (PFASs) in house dust collected from Guangzhou, South China during 2015-2018. The perfluorobutane sulfonic acid (PFBS) exhibited the highest median concentration (17.6 ng/g), followed by linear perfluorooctanoic acid (L-PFOA; 4.8 ng/g), linear perfluorooctane sulfonic acid (L-PFOS; 4.2 ng/g), 6:2 fluorotelomer phosphate diester (6:2 diPAP; 3.4 ng/g), perfluorodecanoic acid (PFDA; 1.2 ng/g) and perfluoroundecanoic acid (PFUdA; 1.2 ng/g), and 6:2 chlorinated perfluoroalkyl ether sulfonic acid (6:2 Cl-PFESA; 1.1 ng/g). Total concentrations of PFASs (median: 53 ng/g) were generally within the 25-50 percentile of the concentration range reported in global studies. However, our samples exhibited composition profiles different from those reported in many other regions. Analysis based on this and previous studies revealed that the compositions in house dust from East Asia, North America, and Europe exhibit a region-specific pattern. This may indicate region-specific market demands, application patterns, as well as associated human exposure risks. Exploration of dwelling characterizations suggested that renovation history appeared to be a significant factor influencing PFAS concentrations in house dust, although other factors may exist and play a role. Estimation of daily intakes via dust ingestion and dermal contact indicates low exposure risks from these two pathways. However, the PFAS chemical-specific biological effects, possible mixture effects, as well as additional exposure pathways, imply that the risk from indoor PFAS exposure should not be overlooked.

Association Between Cardiac Injury and Mortality in Hospitalized Patients Infected With Avian Influenza A (H7N9) Virus.

OBJECTIVES: To evaluate the prevalence of cardiac injury and its association with mortality in hospitalized patients infected with avian influenza A (H7N9) virus. DESIGN: Retrospective cohort study. SETTING: A total of 133 hospitals in 17 provinces, autonomous regions, and municipalities of mainland China that admitted influenza A (H7N9) virus-infected patients between January 22, 2015, and June 16, 2017. PATIENTS: A total of 321 patients with influenza A (H7N9) virus infection were included in the final analysis. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Demographics and clinical characteristics were collected from medical records. Cardiac injury was defined according to cardiac biomarkers, electrocardiography, or echocardiography. Among the 321 patients, 203 (63.2%) showed evidence of cardiac injury. Compared with the uninjured group, the cardiac injury group had lower PaO2/FIO2 (median, 102.0 vs 148.4 mm Hg; p < 0.001), higher Acute Physiology and Chronic Health Evaluation II score (median, 17.0 vs 11.0; p < 0.001), longer stay in the ICU (10.0 vs 9.0 d; p = 0.029), and higher proportion of in-hospital death (64.0% vs 20.3%; p < 0.001). The proportion of virus clearance until discharge or death was lower in the cardiac injury group than in the uninjured group (58.6% vs 86.4%; p < 0.001). Multivariable-adjusted Cox proportional hazards regression analysis showed that cardiac injury was associated with higher mortality (hazards ratio, 2.06; 95% CI, 1.31-3.24) during hospitalization. CONCLUSIONS: Cardiac injury is a frequent condition among hospitalized patients infected with influenza A (H7N9) virus, and it is associated with higher risk of mortality.

Characteristics of H7N9 avian influenza pneumonia: a retrospective analysis of 17 cases.

BACKGROUND: H7N9 avian influenza is an infection of public health concern, in part because of its high mortality rate and pandemic potential. AIMS: To describe the clinical features of H7N9 avian influenza and the response to treatment. METHODS: Clinical, radiological and histopathological data, and treatment-related of H7N9-infected patients hospitalised during 2014-2017 were extracted and analysed. RESULTS: A total of 17 H7N9 patients (three females; mean age, 58.4 ± 13.7 years) was identified; of these six died. All patients presented with fever and productive cough; four patients had haemoptysis and 13 had chest distress and/or shortness of breath. Early subnormal white blood cell count and elevation of serum liver enzymes were common. Multilobar patchy shadows, rapid progression to ground-glass opacities, air bronchograms and consolidation were the most common imaging findings. Histopathological examination of lung tissue of three patients who died showed severe alveolar epithelial cell damage, with inflammatory exudation into the alveolar space and hyaline membrane formation; widened alveolar septae, prominent inflammatory cell infiltration; and hyperplasia of pneumocytes. Viral inclusions were found in the lung tissue of two patients. All patients received antiviral drugs (oseltamivir ± peramivir). Four patients carried the rs12252-C/C interferon-induced transmembrane protein-3 (IFITM3) genotype, while the others had the C/T genotype. CONCLUSIONS: H7N9 virus infection causes human influenza-like symptoms, but may rapidly progress to severe pneumonia and even death. Clinicians should be alert to the possibility of H7N9 infection in high-risk patients. The presence of the IFITM3 rs12252-C genotype may predict severe illness.

Association between polymorphisms in mannose-binding lectin 2 gene with pulmonary tuberculosis susceptibility.

BACKGROUND: Mannose-binding lectin (MBL2) is considered to play a role in the human innate immune response to tuberculosis (TB) infections, and 4 common single nucleotide polymorphisms (SNPs) may be associated with pulmonary tuberculosis (PTB) risk. To examine these potential associations, we performed a comprehensive analysis to assess the relationships between MBL2 polymorphisms and PTB. METHODS: The PubMed, Embase, and SinoMed databases were searched for articles published prior to June 13, 2019. Odds ratios with 95% confidence intervals were calculated to evaluate the strength of the relationships. RESULTS: There were 37 case-control studies examining the effects of the four SNPs in MBL2 on PTB. A positive association between rs11003125 and PTB risk was observed in the hospital-based subgroup. Moreover, for the combined polymorphism and PTB risk, positive associations were detected not only in the total population but also in those with Asian origins across all source of control subgroups. No associations were found for rs7096206 or rs7095891. CONCLUSIONS: Our current study indicated that several SNPs in MBL2 may be associated with susceptibility to PTB.

Slowing down DNA translocation velocity using a LiCl salt gradient and nanofiber mesh.

Solid-state nanopores are considered an attractive basis for single-molecule DNA sequencing. At present, one obstacle to be overcome is the improvement of their temporal resolution, with the DNA molecules remaining in the sensing volume of the nanopore for a long period of time. Here, we used a composite system of a concentration gradient of LiCl in solution and a nanofiber mesh to slow the DNA perforation speed. Compared to different alkali metal solutions with the same concentration, LiCl can extend the dwell time to 20 ms, five times longer than NaCl and KCl. Moreover, as the concentration gradient increases, the dwell time can be tuned from dozens of milliseconds to more than 100 ms. When we introduce a nanofiber mesh layer on top of the pore in the asymmetric solution, the DNA molecules get retarded by 162-185 [Formula: see text]s/nt, which is three orders of magnitude slower than the bare nanopore. At the same time, because the molecule absorption region becomes larger at the pore vicinity, the higher molecule capture rate improves the detection efficiency.

Factors Associated With Prolonged Viral Shedding in Patients With Avian Influenza A(H7N9) Virus Infection.

Background: Data are limited on the impact of neuraminidase inhibitor (NAI) treatment on avian influenza A(H7N9) virus RNA shedding. Methods: In this multicenter, retrospective study, data were collected from adults hospitalized with A(H7N9) infection during 2013-2017 in China. We compared clinical features and A(H7N9) shedding among patients with different NAI doses and combination therapies and evaluated factors associated with A(H7N9) shedding, using Cox proportional hazards regression. Results: Among 478 patients, the median age was 56 years, 71% were male, and 37% died. The median time from illness onset to NAI treatment initiation was 8 days (interquartile range [IQR], 6-10 days), and the median duration of A(H7N9) RNA detection from onset was 15.5 days (IQR, 12-20 days). A(H7N9) RNA shedding was shorter in survivors than in patients who died (P < .001). Corticosteroid administration (hazard ratio [HR], 0.62 [95% confidence interval {CI}, .50-.77]) and delayed NAI treatment (HR, 0.90 [95% CI, .91-.96]) were independent risk factors for prolonged A(H7N9) shedding. There was no significant difference in A(H7N9) shedding duration between NAI combination treatment and monotherapy (P = .65) or between standard-dose and double-dose oseltamivir treatment (P = .70). Conclusions: Corticosteroid therapy and delayed NAI treatment were associated with prolonged A(H7N9) RNA shedding. NAI combination therapy and double-dose oseltamivir treatment were not associated with a reduced A(H7N9) shedding duration as compared to standard-dose oseltamivir.

Precise fabrication of a 5 nm graphene nanopore with a helium ion microscope for biomolecule detection.

We report a scalable method to fabricate high-quality graphene nanopores for biomolecule detection using a helium ion microscope (HIM). HIM milling shows promising capabilities for precisely controlling the size and shape, and may allow for the potential production of nanopores at wafer scale. Nanopores could be fabricated at different sizes ranging from 5 to 30 nm in diameter in few minutes. Compared with the current solid-state nanopore fabrication techniques, e.g. transmission electron microscopy, HIM is fast. Furthermore, we investigated the exposure-time dependence of graphene nanopore formation: the rate of pore expansion did not follow a simple linear relationship with exposure time, but a fast expansion rate at short exposure time and a slow rate at long exposure time. In addition, we performed biomolecule detection with our patterned graphene nanopore. The ionic current signals induced by 20-base single-stranded DNA homopolymers could be used as a basis for homopolymer differentiation. However, the charge interaction of homopolymer chains with graphene nanopores, and the conformations of homopolymer chains need to be further considered to improve the accuracy of discrimination.