Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.

In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.

Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.

Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.

Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.

SARS-CoV-2 rapidly mutates and acquires resistance to neutralizing antibodies. We report an in-silico-designed antibody that restores the neutralizing activity of a neutralizing antibody. Our previously generated antibody, UT28K, exhibited broad neutralizing activity against mutant variants; however, its efficacy against Omicron BA.1 was compromised by the mutation. Using previously determined structural information, we designed a modified-UT28K (VH T28R/N57D), UT28K-RD targeting the mutation site. In vitro and in vivo experiments demonstrated the efficacy of UT28K-RD in neutralizing Omicron BA.1. Although the experimentally determined structure partially differed from the predicted model, our study serves as a successful case of antibody design, wherein the predicted amino acid substitution enhanced the recognition of the previously elusive Omicron BA.1. We anticipate that numerous similar cases will be reported, showcasing the potential of this approach for improving protein-protein interactions. Our findings will contribute to the development of novel therapeutic strategies for highly mutable viruses, such as SARS-CoV-2.

2-thiouridine is a broad-spectrum antiviral nucleoside analogue against positive-strand RNA viruses.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are causing significant morbidity and mortality worldwide. Furthermore, over 1 million cases of newly emerging or re-emerging viral infections, specifically dengue virus (DENV), are known to occur annually. Because no virus-specific and fully effective treatments against these or many other viruses have been approved, there is an urgent need for novel, effective therapeutic agents. Here, we identified 2-thiouridine (s2U) as a broad-spectrum antiviral ribonucleoside analogue that exhibited antiviral activity against several positive-sense single-stranded RNA (ssRNA+) viruses, such as DENV, SARS-CoV-2, and its variants of concern, including the currently circulating Omicron subvariants. s2U inhibits RNA synthesis catalyzed by viral RNA-dependent RNA polymerase, thereby reducing viral RNA replication, which improved the survival rate of mice infected with DENV2 or SARS-CoV-2 in our animal models. Our findings demonstrate that s2U is a potential broad-spectrum antiviral agent not only against DENV and SARS-CoV-2 but other ssRNA+ viruses.

The effect of orthosis management on joint instability in knee joint disease: A systematic review.

INTRODUCTION: Joint instability is a common finding of clinical importance in patients with knee disease. This literature review aimed to examine the evidence regarding the effect of orthosis management on joint instability in knee joint disease. METHODS: The detailed protocol for this study was published in the International Prospective Register of Systematic Reviews in the field of health and social welfare (CRD 42022335360). A literature search was conducted on May 2023, using the following databases: Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, Physiotherapy Evidence Database (PEDro), and Institute of Electrical and Electronics Engineers (IEEE) Xplore. A secondary search was manually conducted using Google Scholar to address publication bias. Each database search strategy was described, and the search was conducted by independent reviewers. RESULTS: A total of 281 studies were retrieved, 11 articles were included in the systematic review. Of the 11 articles selected, the number of included diseases was 2 for osteoarthritis, 7 for anterior cruciate ligament injuries, and 3 for posterior cruciate ligament injuries. In result, orthosis management may improve self-reported instability and functional assessment in patients with osteoarthritis, anterior cruciate ligament injury, and posterior cruciate ligament injury. However, an objective evaluation of anatomical instability did not indicate an improvement in joint instability. CONCLUSION: The effects of orthosis management on knee instability might improve physical function and self-reported instability.

A powered simple walking model explains the decline in propulsive force and hip flexion torque compensation in human gait.

Excessive hip flexion torque to prioritize leg swings in the elderly is likely to be a factor that reduces their propulsive force and gait stability, but the mechanism is not clear. To understand the mechanism, we investigated how propulsive force, hip flexion torque, and margin of stability (MoS) change when only the hip spring stiffness is increased without changing the walking speed in the simple walking model, and verified whether the relationship holds in human walking. The results showed that at walking speeds between 0.50 and 1.75 m/s, increasing hip spring stiffness increased hip flexion torque and decreased the propulsive force and MoS in both the model and human walking. Furthermore, it was found that the increase in hip flexion torque was explained by the increase in spring stiffness, and the decreases in the propulsive force and MoS were explained by the increase in step frequency associated with the increase in spring stiffness. Therefore, the increase in hip flexion torque likely decreased the propulsive force and MoS, and this mechanism was explained by the intervening hip spring stiffness. Our findings may help in the control design of walking assistance devices, and in improving our understanding of elderly walking strategies.

Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.

SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.

In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant.

The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency, but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.

Biomechanical effects of medial meniscus radial tears on the knee joint during gait: A concurrent finite element musculoskeletal framework investigation.

The biomechanical variation in the knee during walking that accompanies medial meniscal radial tears stemming from knee osteoarthritis (OA) has not been explored. This study introduced a finite element musculoskeletal model using concurrent lower limb musculoskeletal dynamics and knee joint finite element analysis in a single framework and expanded the models to include knees with medial meniscal radial tears and total medial meniscectomy. The radial tears involved three locations: anterior horn, midbody, and posterior horn with grades of 33%, 50%, and 83% of the meniscus width. The shear and hoop stresses of the tear meniscus and tibial cartilage contact load, accompanying tears, and postmeniscectomy were evaluated during the stance phase of the gait cycle using the models. In the 83% width midbody tear group, shear stress at the end of the tear was significantly greater than in the intact meniscus and other tear groups, and the maximum shear stress was increased by 310% compared to the intact meniscus. A medial meniscus radial tear has a much smaller effect on the tibial cartilage load (even though in the 83% width tear, the cartilage/total load ratio increased by only 9%). However, the contact force on the tibial cartilage with total postmeniscectomy was increased by 178.93% compared with a healthy intact meniscus, and the peak contact pressure after meniscectomy increased from 11.94 to 12.45 MPa to 17.64 and 13.76 MPa, at the maximum weight acceptance and push-off, respectively. Our study shows that radial tears with larger medial meniscus widths are prone to high stress concentrations at the end of the tears, leading to the potential risk of complete meniscal rupture. Furthermore, although the tears did not change the cartilage load distribution, they disrupted the circumferential stress-transmitting function of the meniscus, thus greatly increasing the likelihood of the onset of knee OA. The significant increase in the tibial cartilage load with total postmeniscectomy indicates a potential risk of OA flare-ups. This study contributes to a better understanding of meniscal tear-induced OA biomechanical changes during human activities and offers some potential directions for surgical guidance of meniscectomies and the prophylaxis and treatment of OA.

Structure of the human galanin receptor 2 bound to galanin and Gq reveals the basis of ligand specificity and how binding affects the G-protein interface.

Galanin is a neuropeptide expressed in the central and peripheral nervous systems, where it regulates various processes including neuroendocrine release, cognition, and nerve regeneration. Three G-protein coupled receptors (GPCRs) for galanin have been discovered, which is the focus of efforts to treat diseases including Alzheimer's disease, anxiety, and addiction. To understand the basis of the ligand preferences of the receptors and to assist structure-based drug design, we used cryo-electron microscopy (cryo-EM) to solve the molecular structure of GALR2 bound to galanin and a cognate heterotrimeric G-protein, providing a molecular view of the neuropeptide binding site. Mutant proteins were assayed to help reveal the basis of ligand specificity, and structural comparison between the activated GALR2 and inactive hß2AR was used to relate galanin binding to the movements of transmembrane (TM) helices and the G-protein interface.

Association between foot posture and tibiofemoral contact forces during barefoot walking in patients with knee osteoarthritis.

BACKGROUND: Accumulating evidence indicates that abnormal foot posture are risk factors for knee osteoarthritis (OA). However, the relationship between foot posture and tibiofemoral contact force (CF) during habitual weight-bearing activities remains unclear. This study aimed to determine the association between tibiofemoral CF and foot posture while walking. METHODS: In total, 18 patients with knee OA and 18 healthy individuals participated in this cross-sectional study. Foot parameters were evaluated by Foot Posture Index (FPI), Staheli Arch Index (SAI), hallux valgus angle, calcaneus inverted angle relative to the floor as a static rearfoot posture, navicular height, and toe grip strength. In addition, all participants underwent kinetic and kinematic measurements during a self-selected speed gait. The measurement device used was the three-dimensional motion analysis system with a sampling rate of 120 Hz. The musculoskeletal model, which has 92 Hill-type muscle-tendon units with 23 degrees of freedom, was used to calculate tibiofemoral CF. Partial correlations was used to investigate the association between foot parameters and total, medial, and lateral tibiofemoral CF of the first and second peaks while controlling for gait speed. RESULTS: A significant negative correlation was observed between Walking SAI and first peak medial tibiofemoral CF in control participants (r = -0.505, p = 0.039). SAI was also significantly positively correlated with first peak medial tibiofemoral CF in patients with knee OA (r = 0.482, p = 0.042). CONCLUSIONS: Our findings revealed a correlation between the medial first peak tibiofemoral CF and the SAI. This study indicates that people with knee OA and flatfoot have excessive first medial tibiofemoral CF during walking.

Effects of flat-flexible shoes on lower limb joint kinetics and kinematics in gait.

Flat-flexible shoes with unique characteristics, such as low pitch and flexibility, can increase the efficiency of ankle energy and running performance. If flat-flexible shoes have the same effect during walking, they could be used for gait training. This study aimed to investigate the effects of flat-flexible shoes on the kinematics and kinetics of the lower limb. Twenty-one healthy young adults (21.8 ± 4.6 years) participated in this study. The participants wore flat-flexible and standard athletic shoes with reflective markers attached according to the Plug-in-Gait model. Walking motion was recorded using infrared cameras and a treadmill embedded with force plates. The angle(s), moment(s), and power(s) of the ankle, knee, and hip joints were calculated. Paired t-test and Wilcoxon's signed-rank test were used to compare the parameters between the two footwear types. The use of flat-flexible shoes increased maximum ankle dorsiflexion and knee flexion angles. The maximum ankle plantar flexion angle was significantly reduced. There was no significant difference in the joint moment between the two footwear types. The peaks of ankle power absorption in late stance, ankle power generation, and hip power generation significantly increased with the use of flat-flexible shoes. These results suggest that flat-flexible shoes have potential as a tool to promote ankle energy storage and release during gait.

Novel super-neutralizing antibody UT28K is capable of protecting against infection from a wide variety of SARS-CoV-2 variants.

Many potent neutralizing SARS-CoV-2 antibodies have been developed and used for therapies. However, the effectiveness of many antibodies has been reduced against recently emerging SARS-CoV-2 variants, especially the Omicron variant. We identified a highly potent SARS-CoV-2 neutralizing antibody, UT28K, in COVID-19 convalescent individuals who recovered from a severe condition. UT28K showed efficacy in neutralizing SARS-CoV-2 in an in vitro assay and in vivo prophylactic treatment, and the reactivity to the Omicron strain was reduced. The structural analyses revealed that antibody UT28K Fab and SARS-CoV-2 RBD protein interactions were mainly chain-dominated antigen-antibody interactions. In addition, a mutation analysis suggested that the emergence of a UT28K neutralization-resistant SARS-CoV-2 variant was unlikely, as this variant would likely lose its competitive advantage over circulating SARS-CoV-2. Our data suggest that UT28K offers potent protection against SARS-CoV-2, including newly emerging variants.

A SARS-CoV-2 antibody broadly neutralizes SARS-related coronaviruses and variants by coordinated recognition of a virus-vulnerable site.

Potent neutralizing SARS-CoV-2 antibodies often target the spike protein receptor-binding site (RBS), but the variability of RBS epitopes hampers broad neutralization of multiple sarbecoviruses and drifted viruses. Here, using humanized mice, we identified an RBS antibody with a germline VH gene that potently neutralized SARS-related coronaviruses, including SARS-CoV and SARS-CoV-2 variants. X-ray crystallography revealed coordinated recognition by the heavy chain of non-RBS conserved sites and the light chain of RBS with a binding angle mimicking the angiotensin-converting enzyme 2 (ACE2) receptor. The minimum footprints in the hypervariable region of RBS contributed to the breadth of neutralization, which was enhanced by immunoglobulin G3 (IgG3) class switching. The coordinated binding resulted in broad neutralization of SARS-CoV and emerging SARS-CoV-2 variants of concern. Low-dose therapeutic antibody treatment in hamsters reduced the virus titers and morbidity during SARS-CoV-2 challenge. The structural basis for broad neutralizing activity may inform the design of a broad spectrum of therapeutics and vaccines.

The effects of trunk endurance training on running kinematics and its variability in novice female runners.

The functional importance of trunk muscle strength for running movement is widely recognised, but the kinematic effects of undertaking specific training are unclear. This study investigated the change in joint angle and its variability during running following trunk muscle training. Eighteen young female and novice runners participated. Using Plug-in-gait model with infrared markers attached to the body surface, the lower limb and lumber angles during running were measured, and the variability was examined by calculating the coefficient variation and Lyapunov exponent. Measurements of trunk endurance were also performed. Over four weeks of training, the subjects performed trunk muscle endurance trainings three times a week. Following this intervention, trunk endurance was found to have significantly increased. The Lyapunov exponent of lumbar flexion-extension angle also significantly increased. Moreover, a decreased range of the ankle angle and increased range of the hip angle were observed following the training. These results demonstrate that the trunk training promoted adjustments to lumbar movement and altered the movement patterns of the participants' lower limbs during running.

Structure, solubility, and permeability relationships in a diverse middle molecule library.

To develop methodology to predict the potential druggability of middle molecules, we examined the structure, solubility, and permeability relationships of a diverse library (HKDL ver.1) consisting of 510 molecules (359 natural product derivatives, 76 non-natural products, 46 natural products, and 29 non-natural product derivatives). The library included peptides, depsipeptides, macrolides, and lignans, and 476 of the 510 compounds had a molecular weight in the range of 500-2000 Da. The solubility and passive diffusion velocity of the middle molecules were assessed using the parallel artificial membrane permeability assay (PAMPA). Quantitative values of solubility of 471 molecules and passive diffusion velocity of 287 molecules were obtained, and their correlations with the structural features of the molecules were examined. Based on the results, we propose a method to predict the passive diffusion characteristics of middle molecules from their three-dimensional structural features.

Efficient preparation of human and mouse CD1d proteins using silkworm baculovirus expression system.

CD1d is a major histocompatibility complex (MHC) class I-like glycoprotein and binds to glycolipid antigens that are recognized by natural killer T (NKT) cells. To date, our understanding of the structural basis for glycolipid binding and receptor recognition of CD1d is still limited. Here, we established a preparation method for the ectodomain of human and mouse CD1d using a silkworm-baculovirus expression system. The co-expression of human and mouse CD1d and ß2-microglobulin (ß2m) in the silkworm-baculovirus system was successful, but the yield of human CD1d was low. A construct of human CD1d fused with ß2m via a flexible GS linker as a single polypeptide was prepared to improve protein yield. The production of this single-chained complex was higher (50 µg/larva) than that of the co-expression complex. Furthermore, differential scanning calorimetry revealed that the linker made the CD1d complex more stable and homogenous. These results suggest that the silkworm-baculovirus expression system is useful for structural and biophysical studies of CD1d in several aspects including low cost, easy handling, biohazard-free, rapid, and high yielding.

Structure of HIV-2 Nef Reveals Features Distinct from HIV-1 Involved in Immune Regulation.

The human immunodeficiency virus (HIV) accessory protein Nef plays a major role in establishing and maintaining infection, particularly through immune evasion. Many HIV-2-infected people experience long-term viral control and survival, resembling HIV-1 elite control. HIV-2 Nef has overlapping but also distinct functions from HIV-1 Nef. Here we report the crystal structure of HIV-2 Nef core. The di-leucine sorting motif forms a helix bound to neighboring molecules, and moreover, isothermal titration calorimetry demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef, ensuring AP-2-mediated endocytosis for CD3. The highly conserved C-terminal region forms a α-helix, absent from HIV-1. We further determined the structure of simian immunodeficiency virus (SIV) Nef harboring this region, demonstrating similar C-terminal α-helix, which may contribute to AP-1 binding for MHC-I downregulation. These results provide insights into the distinct pathogenesis of HIV-2 infection.

Effects of exercise therapy on joint instability in patients with osteoarthritis of the knee: A systematic review.

Objective: Abnormal load stress caused by joint instability has been reported to be one of the factors responsible for the development of osteoarthritis (OA). However, few studies have investigated the efficacy of exercise therapy for patients with knee instability-induced OA, and there are no specific treatment guidelines or effects for this form of OA. Therefore, the purpose of this study was to examine the effect of exercise treatments for joint instability in patients with knee OA by a systematic review. Design: Systematic review. Results: Searches in three databases, PubMed, Cochrane, and the Physiotherapy Evidence Database, yielded 14 articles that were scrutinized, and 6 articles that met the inclusion criteria were selected. Conclusions: Exercise therapy focusing on joint instability, including muscle maintenance and strength training, and specific training targeting knee instability have no additional beneficial effects on knee joint instability. However, because of the benefits of treatment protocols based on patient attributes in exercise treatment focused on joint instability, it is necessary to investigate the effects in more detail in the future.