A Thermostable mRNA Vaccine against COVID-19.

There is an urgent need for vaccines against coronavirus disease 2019 (COVID-19) because of the ongoing SARS-CoV-2 pandemic. Among all approaches, a messenger RNA (mRNA)-based vaccine has emerged as a rapid and versatile platform to quickly respond to this challenge. Here, we developed a lipid nanoparticle-encapsulated mRNA (mRNA-LNP) encoding the receptor binding domain (RBD) of SARS-CoV-2 as a vaccine candidate (called ARCoV). Intramuscular immunization of ARCoV mRNA-LNP elicited robust neutralizing antibodies against SARS-CoV-2 as well as a Th1-biased cellular response in mice and non-human primates. Two doses of ARCoV immunization in mice conferred complete protection against the challenge of a SARS-CoV-2 mouse-adapted strain. Additionally, ARCoV is manufactured as a liquid formulation and can be stored at room temperature for at least 1 week. ARCoV is currently being evaluated in phase 1 clinical trials.

Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals.

The World Health Organization has declared SARS-CoV-2 virus outbreak a worldwide pandemic. However, there is very limited understanding on the immune responses, especially adaptive immune responses to SARS-CoV-2 infection. Here, we collected blood from COVID-19 patients who have recently become virus-free, and therefore were discharged, and detected SARS-CoV-2-specific humoral and cellular immunity in eight newly discharged patients. Follow-up analysis on another cohort of six patients 2 weeks post discharge also revealed high titers of immunoglobulin G (IgG) antibodies. In all 14 patients tested, 13 displayed serum-neutralizing activities in a pseudotype entry assay. Notably, there was a strong correlation between neutralization antibody titers and the numbers of virus-specific T cells. Our work provides a basis for further analysis of protective immunity to SARS-CoV-2, and understanding the pathogenesis of COVID-19, especially in the severe cases. It also has implications in developing an effective vaccine to SARS-CoV-2 infection.

Human Virus-Derived Small RNAs Can Confer Antiviral Immunity in Mammals.

RNA interference (RNAi) functions as a potent antiviral immunity in plants and invertebrates; however, whether RNAi plays antiviral roles in mammals remains unclear. Here, using human enterovirus 71 (HEV71) as a model, we showed HEV71 3A protein as an authentic viral suppressor of RNAi during viral infection. When the 3A-mediated RNAi suppression was impaired, the mutant HEV71 readily triggered the production of abundant HEV71-derived small RNAs with canonical siRNA properties in cells and mice. These virus-derived siRNAs were produced from viral dsRNA replicative intermediates in a Dicer-dependent manner and loaded into AGO, and they were fully active in degrading cognate viral RNAs. Recombinant HEV71 deficient in 3A-mediated RNAi suppression was significantly restricted in human somatic cells and mice, whereas Dicer deficiency rescued HEV71 infection independently of type I interferon response. Thus, RNAi can function as an antiviral immunity, which is induced and suppressed by a human virus, in mammals.

25-Hydroxycholesterol Protects Host against Zika Virus Infection and Its Associated Microcephaly in a Mouse Model.

Zika virus (ZIKV) has become a public health threat due to its global transmission and link to severe congenital disorders. The host immune responses to ZIKV infection have not been fully elucidated, and effective therapeutics are not currently available. Herein, we demonstrated that cholesterol-25-hydroxylase (CH25H) was induced in response to ZIKV infection and that its enzymatic product, 25-hydroxycholesterol (25HC), was a critical mediator of host protection against ZIKV. Synthetic 25HC addition inhibited ZIKV infection in vitro by blocking viral entry, and treatment with 25HC reduced viremia and conferred protection against ZIKV in mice and rhesus macaques. 25HC suppressed ZIKV infection and reduced tissue damage in human cortical organoids and the embryonic brain of the ZIKV-induced mouse microcephaly model. Our findings highlight the protective role of CH25H during ZIKV infection and the potential use of 25HC as a natural antiviral agent to combat ZIKV infection and prevent ZIKV-associated outcomes, such as microcephaly.

Observation of anti-damping spin-orbit torques generated by in-plane and out-of-plane spin polarizations in MnPd3.

Large spin-orbit torques (SOTs) generated by topological materials and heavy metals interfaced with ferromagnets are promising for next-generation magnetic memory and logic devices. SOTs generated from y spin originating from spin Hall and Edelstein effects can realize field-free magnetization switching only when the magnetization and spin are collinear. Here we circumvent the above limitation by utilizing unconventional spins generated in a MnPd3 thin film grown on an oxidized silicon substrate. We observe conventional SOT due to y spin, and out-of-plane and in-plane anti-damping-like torques originated from z spin and x spin, respectively, in MnPd3/CoFeB heterostructures. Notably, we have demonstrated complete field-free switching of perpendicular cobalt via out-of-plane anti-damping-like SOT. Density functional theory calculations show that the observed unconventional torques are due to the low symmetry of the (114)-oriented MnPd3 films. Altogether our results provide a path toward realization of a practical spin channel in ultrafast magnetic memory and logic devices.

Does COVID-19 affect sperm quality in males? the answer may be yes, but only temporarily.

BACKGROUND: The Corona Virus Disease 2019 (COVID-19) pandemic has raised concerns regarding its potential impact on male reproductive health. However, the impact of COVID-19 on sperm quality remains uncertain. This retrospective study aimed to investigate the short-term and relatively long-term effects of COVID-19 infection on sperm quality. METHODS: A total of 85 males with fertility requirements, who underwent semen evaluation at Guilin People's Hospital between June 2022 and July 2023, were included in the study. Changes in semen parameters were analyzed across three specific timeframes: within 6 months before COVID-19 infection, within 3 months after COVID-19 infection, and 3-6 months after COVID-19 recovery. RESULTS: The results revealed that the sperm concentration and total sperm number were significantly lower after infection compared to before, while in the recovery period, the sperm concentration, total sperm count, progressive motility, and normal morphology significantly increased. Comparing the three periods, the most significant difference was observed in sperm concentration, which exhibited a significant decrease after infection but returned to normal levels after recovery from COVID-19. CONCLUSIONS: These findings suggest that COVID-19 may exert some impact on sperm quality, particularly evidenced by decreased sperm concentration post-infection. Fortunately, these effects on semen parameters appear to be temporary, with gradual restoration of semen parameters within 3-6 months after recovery. However, further research is needed to explore the underlying mechanisms and long-term implications of these observed changes in semen parameters.

Metabolic self-feeding in HBV-associated hepatocarcinoma centered on feedback between circulation lipids and the cellular MAPK/mTOR axis.

INTRODUCTION: Hepatitis B Virus (HBV) is widely recognized as a "metabolic virus" that disrupts hepatic metabolic homeostasis, rendering it one of the foremost risk factors for hepatocellular carcinoma (HCC). Except for antiviral therapy, the fundamental principles underlying HBV- and HBV+ HCC have remained unchanged, limiting HCC treatment options. OBJECTIVES: In this study, we aim to identify the distinctive metabolic profile of HBV-associated HCC, with the promise of identifying novel metabolic targets that confer survival advantages and ultimately impede cancer progression. METHODS: We employed a comprehensive methodology to evaluate metabolic alterations systematically. Initially, we analyzed transcriptomic and proteomic data obtained from a public database, subsequently validating these findings within our test cohort at both the proteomic and transcriptomic levels. Additionally, we conducted a comprehensive analysis of tissue metabolomics profiles, lipidomics, and the activity of the MAPK and AKT signaling pathway to corroborate the abovementioned changes. RESULTS: Our multi-omics approach revealed distinct metabolic dysfunctions associated with HBV-associated HCC. Specifically, we observed upregulated steroid hormone biosynthesis, primary bile acid metabolism, and sphingolipid metabolism in HBV-associated HCC patients' serum. Notably, metabolites involved in primary bile acid and sphingolipids can activate the MAPK/mTOR pathway. Tissue metabolomics and lipidomics analyses further validated the serum metabolic alterations, particularly alterations in lipid composition and accumulation of unsaturated fatty acids. CONCLUSION: Our findings emphasize the pivotal role of HBV in HCC metabolism, elucidating the activation of a unique MAPK/mTOR signaling axis by primary bile acids and sphingolipids. Moreover, the hyperactive MAPK/mTOR signaling axis transduction leads to significant reprogramming in lipid metabolism within HCC cells, further triggering the activation of the MAPK/mTOR pathway in turn, thereby establishing a self-feeding circle driven by primary bile acids and sphingolipids.

The evolution of indium precipitation in gallium focused ion beam prepared samples of InGaAs/InAlAs quantum wells under electron beam irradiation.

Gallium ion (Ga+ ) beam damage induced indium (In) precipitation in indium gallium arsenide (InGaAs)/indium aluminium arsenide (InAlAs) multiple quantum wells and its corresponding evolution under electron beam irradiation was investigated by valence electron energy loss spectroscopy (VEELS) and high-angle annular dark-field imaging (HAADF) in scanning transmission electron microscopy (STEM). Compared with argon ion milling for sample preparation, the heavier projectiles of Ga+ ions pose a risk to trigger In formation in the form of tiny metallic In clusters. These are shown to be sensitive to electron irradiation and can increase in number and size under the electron beam, deteriorating the structure. Our finding reveals the potential risk of formation of In clusters during focused ion beam (FIB) preparation of InGaAs/InAlAs quantum well samples and their subsequent growth under STEM-HAADF imaging, where initially invisible In clusters of a few atoms can move and swell during electron beam exposure.

Long-term re-intervention after USgHIFU and prediction of NPVR in different ages of patients with uterine fibroids.

OBJECTIVE: Long-term re-intervention after ultrasound-guided high intensity focused ultrasound (USgHIFU) ablation was reported, and the prediction of non-perfusion volume ratio (NPVR) in differently aged patients with uterine fibroids (UFs) was explored. MATERIALS AND METHODS: Patients with UFs who underwent USgHIFU ablation from January 2012 to December 2019 were enrolled and divided into < 40-year-old and ≥ 40-year-old groups. Cox regression was used to analyze the influencing factors of re-intervention rate, and receiver operating characteristic (ROC) curve was used to analyze the correlation between NPVR and re-intervention rate. RESULTS: A total of 2141 patients were enrolled, and 1558 patients were successfully followed up. The 10-year cumulative re-intervention rate was 21.9%, and the < 40-year-old group had a significantly higher rate than the ≥ 40-year-old group (30.8% vs. 19.1%, p < 0.001). NPVR was an independent risk factor in both two groups. When the NPVR reached 80.5% in the < 40-year-old group and 75.5% in the ≥ 40-year-old group, the risk of long-term re-intervention was satisfactory. CONCLUSION: The long-term outcome of USgHIFU is promising. The re-intervention rate is related to NPVR in differently aged patients. Young patients need a high NPVR to reduce re-intervention risk.

Disease-induced changes in bacterial and fungal communities from plant below- and aboveground compartments.

The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture. KEY POINTS: • Different recruitment strategies between plant bacterial and fungal communities. • Bacterial community was more sensitive to PVY infection than fungal community. • pH and WC drove the microbial community assembly under PVY infection.

Assisted reproductive technology and physical activity among Chinese pregnant women at high risk for gestational diabetes mellitus in early pregnancy: A cross-sectional study.

Currently, the number of pregnant women at high risk for gestational diabetes mellitus (GDM) and using assisted reproductive technology (ART) is increasing. The present study aims to explore the relationship between ART and physical activity in Chinese pregnant women at high risk for GDM in early pregnancy. A cross-sectional study was conducted in a regional teaching hospital in Guangzhou, China, between July 2022 and March 2023. Three hundred fifty-five pregnant women at high risk for GDM in early pregnancy completed the Chinese version of the Pregnant Physical Activity Questionnaire (PPAQ), the Pregnancy Physical Activity Knowledge Scale, the Pregnancy Physical Activity Self-Efficacy Scale, the Pregnancy Physical Activity Social Support Scale, and a sociodemographic and obstetric characteristics data sheet. Compared to women who conceived naturally, women who used ART were more likely to be 35 years or older, unemployed, primigravidae, and to have intentionally planned their pregnancies. Women who used ART had significantly lower levels of physical activity and self-efficacy compared to their counterparts who conceived naturally. Over half (55.6%) of women who used ART reported being physically inactive, and those with lower self-efficacy, as well as the unemployed, were significantly more likely to be inactive. Physical inactivity is a critical clinical issue among women who use ART, especially in the context of GDM risk. Future research should develop and test physical activity programs, including enhancing physical activity self-efficacy for women who use ART. Patient or public contribution: In this study, survey questionnaires were completed by participants among Chinese pregnant women at high risk for GDM in early pregnancy.

An advance in novel intelligent sensory technologies: From an implicit-tracking perspective of food perception.

Food sensory evaluation mainly includes explicit and implicit measurement methods. Implicit measures of consumer perception are gaining significant attention in food sensory and consumer science as they provide effective, subconscious, objective analysis. A wide range of advanced technologies are now available for analyzing physiological and psychological responses, including facial analysis technology, neuroimaging technology, autonomic nervous system technology, and behavioral pattern measurement. However, researchers in the food field often lack systematic knowledge of these multidisciplinary technologies and struggle with interpreting their results. In order to bridge this gap, this review systematically describes the principles and highlights the applications in food sensory and consumer science of facial analysis technologies such as eye tracking, facial electromyography, and automatic facial expression analysis, as well as neuroimaging technologies like electroencephalography, magnetoencephalography, functional magnetic resonance imaging, and functional near-infrared spectroscopy. Furthermore, we critically compare and discuss these advanced implicit techniques in the context of food sensory research and then accordingly propose prospects. Ultimately, we conclude that implicit measures should be complemented by traditional explicit measures to capture responses beyond preference. Facial analysis technologies offer a more objective reflection of sensory perception and attitudes toward food, whereas neuroimaging techniques provide valuable insight into the implicit physiological responses during food consumption. To enhance the interpretability and generalizability of implicit measurement results, further sensory studies are needed. Looking ahead, the combination of different methodological techniques in real-life situations holds promise for consumer sensory science in the field of food research.

Prevalence and risk factors of cognitive frailty among pre-frail and frail older adults in nursing homes.

BACKGROUND: The purpose of this research was to stratify the level of frailty to examine the risk factors associated with reversible cognitive frailty (RCF) and potentially reversible cognitive frailty (PRCF) in nursing homes to provide a basis for hierarchical management in different stages of frailty. METHODS: The study was a cross-sectional study conducted from September to November 2022; 504 people were selected by stratified random sampling after convenience selection from the Home for the Aged Guangzhou. The structured questionnaire survey was conducted through face-to-face interviews using the general data questionnaire, Fried Frailty Phenotype, Montreal Cognitive Assessment Scale. RESULTS: In total, 452 individuals were included for analysis. A total of 229 cases (50.7%) were PRCF, 70 (15.5%) were RCF. Multivariate logistic regression analysis showed that in pre-frailty, the Geriatric Depression Scale (GDS-15) score (odds ratio (OR) 1.802; 95% CI 1.308-2.483), Instrumental Activities of Daily Living Scale (IADL) score (0.352; 0.135-0.918) and energy (0.288; 0.110-0.755) were influencing factors of RCF. GDS-15 score (1.805; 1.320-2.468), IADL score (0.268; 0.105-0.682), energy (0.377; 0.150-0.947), lack of intellectual activity (6.118; 1.067-35.070), admission time(>3 years) (9.969; 1.893-52.495) and low education (3.465; 1.211-9.912) were influencing factors of PRCF. However, RCF with frailty was associated with the Short-Form Mini-Nutritional Assessment (MNA-SF) score (0.301; 0.123-0.739) and low education time (0 ~ 12 years) (0.021; 0.001-0.826). PRCF with frailty was associated with age (1.327; 1.081-1.629) and weekly exercise time (0.987; 0.979-0.995). CONCLUSIONS: The prevalence of RCF and PRCF was high among pre-frail and frail older adults in nursing homes. Different levels of frailty had different influencing factors for RCF and PRCF. Depression, daily living ability, energy, intellectual activity, admission time, education level, nutrition status, age and exercise time were associated with RCF and PRCF. Hierarchical management and intervention should be implemented for different stages of frailty to prevent or delay the progression of cognitive frailty.

Regular Medications in the Emergency Department Short Stay Unit (ReMedIES): Can Prescribing be Improved Without Increasing Resources?

Background: Hospital medication errors are frequent and may result in adverse events. Data on non-prescription of regular medications to emergency department short stay unit patients is lacking. In response to local reports of regular medication omissions, a multi-disciplinary team was tasked to introduce corrective emergency department (ED) process changes, but with no additional financing or resources. Aim: To reduce the rate of non-prescription of regular medications for patients admitted to the ED Short Stay Unit (SSU), through process change within existing resource constraints. Methods: A pre- and post-intervention observational study compared regular medication omission rates for patients admitted to the ED SSU. Included patients were those who usually took regular home medications at 08:00 or 20:00. Omissions were classified as clinically significant medications (CSMs) or non-clinically significant medications (non-CSMs). The intervention included reinforcement that the initially treating acute ED doctor was responsible for prescription completion, formal checking of prescription presence at SSU handover rounds, double-checking of prescription completeness by the overnight SSU lead nurse and junior doctor, and ED pharmacist medication reconciliation for those still identified as having regular medication non-prescription at 07:30. Results: For the 110 and 106 patients in the pre- and post-intervention periods, there was a non-significant reduction in the CSM omission rate of -11% (95% CI: -23 to 2), from 41% (95% CI: 32-50) to 30% (95% CI: 21-39). Conclusion: Non-prescription of regular CSMs for SSU patients was not significantly reduced by institution of work practice changes within existing resource constraints.

Improving the Hydrogen Oxidation Reaction Rate of Ru by Active Hydrogen in the Ultrathin Pd Interlayer.

Enhancing the catalytic activity of Ru metal in the hydrogen oxidation reaction (HOR) potential range, improving the insufficient activity of Ru caused by its oxophilicity, is of great significance for reducing the cost of anion exchange membrane fuel cells (AEMFCs). Here, we use Ru grown on Au@Pd as a model system to understand the underlying mechanism for activity improvement by combining direct in situ surface-enhanced Raman spectroscopy (SERS) evidence of the catalytic reaction intermediate (OHad) with in situ X-ray diffraction (XRD), electrochemical characterization, as well as DFT calculations. The results showed that the Au@Pd@Ru nanocatalyst utilizes the hydrogen storage capacity of the Pd interlayer to "temporarily" store the activated hydrogen enriched at the interface, which spontaneously overflows at the "hydrogen-deficient interface" to react with OHad adsorbed on Ru. It is the essential reason for the enhanced catalytic activity of Ru at anodic potential. This work deepens our understanding of the HOR mechanism and provides new ideas for the rational design of advanced electrocatalysts.

Genetic engineering of complex feed enzymes into barley seed for direct utilization in animal feedstuff.

Currently, feed enzymes are primarily obtained through fermentation of fungi, bacteria, and other microorganisms. Although the manufacturing technology for feed enzymes has evolved rapidly, the activities of these enzymes decline during the granulating process and the cost of application has increased over time. An alternative approach is the use of genetically modified plants containing complex feed enzymes for direct utilization in animal feedstuff. We co-expressed three commonly used feed enzymes (phytase, ß-glucanase, and xylanase) in barley seeds using the Agrobacterium-mediated transformation method and generated a new barley germplasm. The results showed that these enzymes were stable and had no effect on the development of the seeds. Supplementation of the basal diet of laying hens with only 8% of enzyme-containing seeds decreased the quantities of indigestible carbohydrates, improved the availability of phosphorus, and reduced the impact of animal production on the environment to an extent similar to directly adding exogenous enzymes to the feed. Feeding enzyme-containing seeds to layers significantly increased the strength of the eggshell and the weight of the eggs by 10.0%-11.3% and 5.6%-7.7% respectively. The intestinal microbiota obtained from layers fed with enzyme-containing seeds was altered compared to controls and was dominated by Alispes and Rikenella. Therefore, the transgenic barley seeds produced in this study can be used as an ideal feedstuff for use in animal feed.

Pathogenicity and Structural Basis of Zika Variants with Glycan Loop Deletions in the Envelope Protein.

The glycan loop of Zika virus (ZIKV) envelope protein (E) contains the glycosylation site and has been well documented to be important for viral pathogenesis and transmission. In the present study, we report that deletions in the E glycan loop, which were recorded in African ZIKV strains previously, have re-emerged in their contemporary Asian lineages. Here, we generated recombinant ZIKV containing specific deletions in the E glycan loop by reverse genetics. Extensive in vitro and in vivo characterization of these deletion mutants demonstrated an attenuated phenotype in an adult A129 mouse model and reduced oral infections in mosquitoes. Surprisingly, these glycan loop deletion mutants exhibited an enhanced neurovirulence phenotype, and resulted in a more severe microcephalic brain in neonatal mouse models. Crystal structures of the ZIKV E protein and a deletion mutant at 2.5 and 2.6 Å, respectively, revealed that deletion of the glycan loop induces encephalitic flavivirus-like conformational alterations, including the appearance of perforations on the surface and a clear change in the topology of the loops. Overall, our results demonstrate that the E glycan loop deletions represent neonatal mouse neurovirulence markers of ZIKV. IMPORTANCE Zika virus (ZIKV) has been identified as a cause of microcephaly and acquired evolutionary mutations since its discovery. Previously deletions in the E glycan loop were recorded in African ZIKV strains, which have re-emerged in the contemporary Asian lineages recently. The glycan loop deletion mutants are not glycosylated, which are attenuated in adult A129 mouse model and reduced oral infections in mosquitoes. More importantly, the glycan loop deletion mutants induce an encephalitic flavivirus-like conformational alteration in the E homodimer, resulting in a significant enhancement of neonatal mouse neurovirulence. This study underscores the critical role of glycan loop deletion mutants in ZIKV pathogenesis, highlighting a need for global virological surveillance for such ZIKV variants.

Characterization and phylogenetic analysis of a neurovirulent Zika virus isolated from Cambodia in 2019.

The geographic range of Zika virus (ZIKV) has expanded from Asia to the Americas, leading to the 2015-2016 pandemic with enhanced neurovirulence. At present, ZIKV is continuously circulating in many Southeast Asian countries. Unfortunately, the persistent evolution of ZIKV in Southeast Asia and its influence on the biological characteristics of the virus remain incompletely understood. In this study, the in vitro and in vivo properties of a new ZIKV isolate obtained from Cambodia in 2019 (CAM/2019) were characterized and compared with those of the Cambodian strain (CAM/2010). Compared with CAM/2010, the CAM/2019 virus showed similar plaque morphology and growth curves in cell cultures and induced comparable viremia and organ viral loads profiles in both BALB/c and A129 (IFNAR1-/- ) mice upon intraperitoneal (i.p.) inoculation. Remarkably, the CAM/2019 virus exhibited enhanced neurovirulence in neonatal mice compared with CAM/2010, with a 74-fold reduction in the 50% lethal dose (LD50 ). Consistently, CAM/2019 produced higher viral loads in the brains of BALB/c neonatal mice than CAM/2010 did. Sequence alignment showed that the CAM/2019 virus has acquired 12 amino acid substitutions, several of which were found to be associated with neurovirulence. In particular, the CAM/2019 virus shared an A1204T substitution in NS2A with the Thai isolate SI-BKK02 that was isolated from a microcephaly case. Taken together, our results indicate that a ZIKV strain isolated with specific mutations has emerged in Cambodia, highlighting the need for extensive molecular and disease surveillance in Cambodia and other Asian countries.

Competitive fitness and homologous recombination of SARS-CoV-2 variants of concern.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge and cocirculate in humans and wild animals. The factors driving the emergence and replacement of novel variants and recombinants remain incompletely understood. Herein, we comprehensively characterized the competitive fitness of SARS-CoV-2 wild type (WT) and three variants of concern (VOCs), Alpha, Beta and Delta, by coinfection and serial passaging assays in different susceptible cells. Deep sequencing analyses revealed cell-specific competitive fitness: the Beta variant showed enhanced replication fitness during serial passage in Caco-2 cells, whereas the WT and Alpha variant showed elevated fitness in Vero E6 cells. Interestingly, a high level of neutralizing antibody sped up competition and completely reshaped the fitness advantages of different variants. More importantly, single clone purification identified a significant proportion of homologous recombinants that emerged during the passage history, and immune pressure reduced the frequency of recombination. Interestingly, a recombination hot region located between nucleotide sites 22,995 and 28,866 of the viral genomes could be identified in most of the detected recombinants. Our study not only profiled the variable competitive fitness of SARS-CoV-2 under different conditions, but also provided direct experimental evidence of homologous recombination between SARS-CoV-2 viruses, as well as a model for investigating SARS-CoV-2 recombination.

Deep background-mismodeling-learned reconstruction for high-accuracy fluorescence diffuse optical tomography.

We present a deep background-mismodeling-learned reconstruction framework for high-accuracy fluorescence diffuse optical tomography (FDOT). A learnable regularizer incorporating background mismodeling is formulated in the form of certain mathematical constraints. The regularizer is then learned to obtain the background mismodeling automatically using a physics-informed deep network implicitly. Here, a deep-unrolled FIST-Net for optimizing L1-FDOT is specially designed to obtain fewer learning parameters. Experiments show that the accuracy of FDOT is significantly improved via implicitly learning the background mismodeling, which proves the validity of the deep background-mismodeling-learned reconstruction. The proposed framework can also be used as a general method to improve a class of image modalities based on linear inverse problems with unknown background modeling errors.