Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic.

Antimicrobial resistance is recognized as one of the greatest public health concerns. It is becoming an increasingly threat during the COVID-19 pandemic due to increasing usage of antimicrobials, such as antibiotics and disinfectants, in healthcare facilities or public spaces. To explore the characteristics of airborne antibiotic resistome in public transport systems, we assessed distribution and health risks of airborne antibiotic resistome and microbiome in railway stations before and after the pandemic outbreak by culture-independent and culture-dependent metagenomic analysis. Results showed that the diversity of airborne antibiotic resistance genes (ARGs) decreased following the pandemic, while the relative abundance of core ARGs increased. A total of 159 horizontally acquired ARGs, predominantly confering resistance to macrolides and aminoglycosides, were identified in the airborne bacteria and dust samples. Meanwhile, the abundance of horizontally acquired ARGs hosted by pathogens increased during the pandemic. A bloom of clinically important antibiotic (tigecycline and meropenem) resistant bacteria was found following the pandemic outbreak. 251 high-quality metagenome-assembled genomes (MAGs) were recovered from 27 metagenomes, and 86 genera and 125 species were classified. Relative abundance of ARG-carrying MAGs, taxonomically assigned to genus of Bacillus, Pseudomonas, Acinetobacter, and Staphylococcus, was found increased during the pandemic. Bayesian source tracking estimated that human skin and anthropogenic activities were presumptive resistome sources for the public transit air. Moreover, risk assessment based on resistome and microbiome data revealed elevated airborne health risks during the pandemic.

Brief Report: Supporting Access to HIV Care for Children and Youth During the COVID-19 Pandemic With Telemedicine and Rideshare.

BACKGROUND: In response to the COVID-19 pandemic, we scaled up telemedicine and rideshare services for clinic and laboratory visits for pediatric and adolescent patients with HIV. SETTING: HIV subspecialty program for patients aged 0-24 years at Children's National Hospital, Washington, DC. METHODS: Using the χ2 and Wilcoxon rank sum tests, we compared demographics, visit and laboratory data, and rideshare usage among patients who scheduled telemedicine at least once (telemedicine) versus those who never scheduled telemedicine (no-telemedicine) during the pandemic (April-September 2020). We compared the number and proportion of scheduled and completed clinic visits before the pandemic (April-September 2019) with those during the pandemic. RESULTS: We analyzed 178 pediatric and adolescent patients with HIV (median age 17.9 years, 89.3% Black, 48.9% male patients, 78.7% perinatally infected), of whom 70.2% and 28.6% used telemedicine and rideshare, respectively. Telemedicine patients scheduled more visits (236 vs 179, P < 0.0001) and completed a similar proportion of visits (81.8% vs 86.0%, P = 0.3805) compared with no-telemedicine patients. Laboratory testing rates (81.3% versus 98.5%, P = 0.0005) were lower in telemedicine patients compared with no-telemedicine patients. Rideshare usage (12.4% versus 26.5%, P = 0.0068) was lower in telemedicine versus no-telemedicine patients. During the pandemic, most of the patients (81.0%) had HIV RNA <200 copies/mL. The total number of completed visits and the proportion of visits completed were similar before and during the pandemic. CONCLUSION: Most of the pediatric and adolescent patients with HIV used telemedicine and maintained HIV RNA <200 copies/mL during the pandemic. Despite rideshare usage, laboratory testing rates were lower with telemedicine compared with in-person visits.

Oral Azvudine (FNC) Tablets in Patients infected with SARS-CoV-2 Omicron Variant: A Retrospective Cohort Study (preprint)

BackgroundThere is a lack of data on the efficacy of oral Azvudine in Coronavirus Disease treatment. This study aimed to assess the association between Azvudine treatment and clinical outcomes in a cohort of patients infected with the SARS-CoV-2 Omicron variant. MethodsThis is a retrospective study conducted in two mobile cabin hospitals. All consecutive patients with a diagnosis of COVID-19 admitted from August to October 2022 were included in the study. Linear regression models and Cox proportional hazards models were used to assess the association between Azvudine treatment and time to obtain the first negative nucleic acid test results. ResultsA total of 207 patients were analyzed, of whom 166 patients (80.2%) received Azvudine treatment after hospitalization, and the rest did not. Linear regression models showed that Azvudine treatment was associated with reduced time to obtain the first negative nucleic acid test results after adjusting for age and gender [mean difference = -1.658; 95% CI: -2.772 to -0.544, P = 0.0039]. The multivariable Cox analysis conforms to the results from the linear regression model (hazard ratio = 1.461; 95% CI: 1.01 to 2.11, P = 0.044). ConclusionAzvudine treatment was associated with reduced virus shedding time. Further studies are needed to confirm our findings.

Cancer Evaluations During the COVID-19 Pandemic: An Observational Study Using National Veterans Affairs Data.

INTRODUCTION: Fewer cancer diagnoses have been made during the COVID-19 pandemic. Pandemic-related delays in cancer diagnosis could occur from limited access to care or patient evaluation delays (e.g., delayed testing after abnormal results). Follow-up of abnormal test results warranting evaluation for cancer was examined before and during the pandemic. METHODS: Electronic trigger algorithms were applied to the Department of Veterans Affairs electronic health record data to assess follow-up of abnormal test results before (March 10, 2019-March 7, 2020) and during (March 8, 2020-March 6, 2021) the pandemic. RESULTS: Electronic triggers were applied to 8,021,406 veterans' electronic health records to identify follow-up delays for abnormal results warranting evaluation for 5 cancers: bladder (urinalysis with high-grade hematuria), breast (abnormal mammograms), colorectal (positive fecal occult blood tests/fecal immunochemical tests or results consistent with iron deficiency anemia), liver (elevated alpha-fetoprotein), and lung (chest imaging suggestive of malignancy) cancers. Between prepandemic and pandemic periods, test quantities decreased by 12.6%-27.8%, and proportions of abnormal results lacking follow-up decreased for urinalyses (-0.8%), increased for fecal occult blood tests/fecal immunochemical test (+2.3%) and chest imaging (+1.8%), and remained constant for others. Follow-up times decreased for most tests; however, control charts suggested increased delays at 2 stages: early (pandemic beginning) for urinalyses, mammograms, fecal occult blood tests/fecal immunochemical test, iron deficiency anemia, and chest imaging and late (30-45 weeks into pandemic) for mammograms, fecal occult blood tests/fecal immunochemical test, and iron deficiency anemia. CONCLUSIONS: Although early pandemic delays in follow-up may have led to reduced cancer rates, the significant decrease in tests performed is likely a large driver of these reductions. Future emergency preparedness efforts should bolster essential follow-up and testing procedures to facilitate timely cancer diagnosis.

Effect of the Universal Health Coverage Healthcare System on Stock Returns During COVID-19: Evidence From Global Stock Indices.

The increased uncertainty caused by a sudden epidemic disease has had an impact on the global financial market. We aimed to assess the primary healthcare system of universal health coverage (UHC) during the coronavirus disease (COVID-19) pandemic and its relationship with the financial market. To this end, we employed the abnormal returns of 68 countries from January 2, 2019, to December 31, 2020, to test the impact of the COVID-19 outbreak on abnormal returns in the stock market and determine how a country's UHC changes the impact of a sudden pandemic on abnormal returns. Our findings show that the sudden onset of an epidemic disease results in unevenly distributed medical system resources, consequently diminishing the impact of UHC on abnormal returns.

Genetic screening for hypertension and COVID-19 reveals functional variant of SPEG associated with severe COVID-19 in female (preprint)

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused more than 6.4 million deaths worldwide and is still spreading among global populations. The prevalent comorbidity between hypertension and severe COVID-19 suggests common genetic factors may affect the outcome of both diseases. As both hypertension and severe COVID-19 demonstrate sex-specific prevalence, common genetic factors among the two diseases may display gender-based differential associations. By evaluating COVID-19 association signals of 172-candidate hypertension single nucleotide polymorphisms derived from more than one million European individuals in two severe COVID-19 genome-wide association studies from UK BioBank with European ancestry, we revealed one functional cis expression quantitative trait locus of SPEG (rs12474050) associating with both hypertension and severe COVID-19 in female. The risk allele of rs12474050*T is correlated with lower SPEG expression in muscle-skeletal, heart-atrial appendage, and heart-left ventricle; among these tissues the SPEG expression is higher in female than in male COVID-19 patients. Further analysis revealed SPEG is mainly expressed in cardiomyocytes in heart and is upregulated upon SARS-CoV-2 infection, with significantly higher folder change of SPEG expression observed in female compared to male COVID-19 patients. Taken together, our analyses strongly suggest the involvement of SPEG in both hypertension and severe COVID-19 in female, which provides new insights for sex-specific effect of severe COVID-19 in female.

The mechanism and effects of remdesivir-induced developmental toxicity in zebrafish: Blood flow dysfunction and behavioral alterations.

The antiviral drug remdesivir has been used to treat the growing number of coronavirus disease 2019 (COVID-19) patients. However, the drug is mainly excreted through urine and feces and introduced into the environment to affect non-target organisms, including fish, which has raised concerns about potential ecotoxicological effects on aquatic organisms. Moreover, studies on the ecological impacts of remdesivir on aquatic environments have not been reported. Here, we aimed to explore the toxicological impacts of microinjection of remdesivir on zebrafish early embryonic development and larvae and the associated mechanism. We found that 100 µM remdesivir delayed epiboly and impaired convergent movement of embryos during gastrulation, and dose-dependent increases in mortality and malformation were observed in remdesivir-treated embryos. Moreover, 10-100 µM remdesivir decreased blood flow and swimming velocity and altered the behavior of larvae. In terms of molecular mechanisms, 80 differentially expressed genes (DEGs) were identified by transcriptome analysis in the remdesivir-treated group. Some of these DEGs, such as manf, kif3a, hnf1ba, rgn, prkcz, egr1, fosab, nr4a1, and ptgs2b, were mainly involved in early embryonic development, neuronal developmental disorders, vascular disease and the blood flow pathway. These data reveal that remdesivir can impair early embryonic development, blood flow and behavior of zebrafish embryos/larvae, probably due to alterations at the transcriptome level. This study suggests that it is important to avoid the discharge of remdesivir to aquatic ecosystems and provides a theoretical foundation to hinder remdesivir-induced ecotoxicity to aquatic environments.

Specific Pupylation as IDEntity Reporter (SPIDER) for the identification of Protein-Biomolecule interactions (preprint)

Protein-biomolecule interactions play pivotal roles in almost all biological processes, the identification of the interacting protein is essential. By combining a substrate-based proximity labelling activity from the pupylation pathway of Mycobacterium tuberculosis , and the streptavidin (SA)-biotin system, we developed S pecific P upylation as IDE ntity R eporter (SPIDER) for identifying protein-biomolecular interactions. As a proof of principle, SPIDER was successfully applied for global identification of interacting proteins, including substrates for enzyme (CobB), the readers of m 6 A, the protein interactome of mRNA, and the target proteins of drug (lenalidomide). In addition, by SPIDER, we identified SARS-CoV-2 Omicron variant specific receptors on cell membrane and performed in-depth analysis for one candidate, Protein-g. These potential receptors could explain the differences between the Omicron variant and the Prototype strain, and further serve as target for combating the Omicron variant. Overall, we provide a robust technology which is applicable for a wide-range of protein-biomolecular interaction studies.

Clinical and Virological Features of the First Occurrence of COVID-19 Delta Variant in Anhui Province, China (preprint)

Objectives Since the outbreak of coronavirus disease 2019 (COVID-19), it has caused serious casualties worldwide. In recent months, the virus has mutated into an increasingly infectious form (Delta variant) and spread rapidly.Methods In the current study, we analyzed the clinical, epidemiological and viral genetic characteristics of the first four imported Delta cases in Anhui Province, China.Results The four imported Delta cases developed chest inflammation, tissue damage and recovered after admission, the serum high-sensitivity C-reactive protein (hs-CRP) and CRP levels showed a first increasing and then decreasing trend. The changes of hs-CRP /CRP and serum neutralizing antibodies (Nab) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) levels were associated with the regression of chest lesions. The combination of genetic sequencing and epidemiological analysis suggested that the SARS-CoV-2 delta variant infection of these four patients may originate from Russia.Conclusions Our study found the certain correlations of serum hs-CRP/CRP and Nab levels with the occurrence, development and outcome of COVID-19 delta variant, suggesting that monitoring hs-CRP/CRP and Nab levels of COVID-19 delta variant patients at hospital admission may be useful for understanding the severity of patients’ current conditions.

Potent Neutralization of Omicron and other SARS-CoV-2 Variants of Concern by Biparatopic Human VH Domains (preprint)

The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics that are effective against a variety of strains of the virus. Herein, we characterize a human VH domain, F6, which we generated by sequentially panning large phage displayed VH libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized VH domain, resulted in a construct (F6-ab8-Fc) that neutralized Omicron pseudoviruses with a half-maximal neutralizing concentration (IC50) of 4.8 nM in vitro. Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 VOCs - including the recently emerged Omicron variant - and highlight a vulnerable epitope within the spike protein RBD that may be exploited to achieve broad protection against circulating variants.

Soluble immune checkpoints are dysregulated in COVID-19 and heavy alcohol users with HIV infection (preprint)

Immune checkpoints (ICPs) consist of paired receptor-ligand molecules that exert inhibitory or stimulatory effects on immune defense, surveillance, regulation, and self-tolerance. ICPs exist in both membrane and soluble forms in vivo and in vitro . Imbalances between inhibitory and stimulatory membrane-bound ICPs (mICPs) in malignant cells and immune cells in the tumor immune microenvironment (TIME) have been well documented. Blockades of inhibitory mICPs have emerged as an immense breakthrough in cancer therapeutics. However, the origin, structure, production regulation, and biological significance of soluble ICPs (sICPs) in health and disease largely remains elusive. Soluble ICPs can be generated through either alternative mRNA splicing and secretion or protease-mediated shedding from mICPs. Since sICPs are found in the bloodstream, they likely form a circulating immune regulatory system. In fact, there is increasing evidence that sICPs exhibit biological functions including (1) regulation of antibacterial immunity, (2) interaction with their mICP compartments to positively or negatively regulate immune responses, and (3) competition with their mICP compartments for binding to the ICP blocking antibodies, thereby reducing the efficacy of ICP blockade therapies. Here, we summarize current data of sICPs in cancer and infectious diseases. We particularly focus on sICPs in COVID-19 and HIV infection as they are the two ongoing global pandemics and have created the world’s most serious public health challenges. A “storm” of sICPs occurs in the peripheral circulation of COVID-19 patients and is associated with the severity of COVID-19. Similarly, sICPs are highly dysregulated in people living with HIV (PLHIV) and some sICPs remain dysregulated in PLHIV on antiretroviral therapy (ART), indicating these sICPs may serve as biomarkers of incomplete immune reconstitution in PLHIV on ART. We reveal that HIV infection in the setting of alcohol abuse exacerbates sICP dysregulation as PLHIV with heavy alcohol consumption have significantly elevated plasma levels of many sICPs. Thus, both stimulatory and inhibitory sICPs are present in the bloodstream of healthy people and their balance can be disrupted under pathophysiological conditions such as cancer, COVID-19, HIV infection, and alcohol abuse. There is an urgent need to study the role of sICPs in immune regulation in health and disease.

Emerging SARS-CoV-2 Variants of Concern: Spike Protein Mutational Analysis and Epitope for Broad Neutralization (preprint)

Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we report the discovery of a novel antibody fragment (V H ab6) that neutralizes all major variants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.

Scrutiny of human lung infection by SARS-CoV-2 and associated human immune responses in humanized mice (preprint)

There is an urgent need for animal models of COVID-19 to study immunopathogenesis and test therapeutic intervenes. In this study we showed that NSG mice engrafted with human lung (HL) tissue (NSG-L) could be infected efficiently by SARS-CoV-2, and that live virus capable of infecting Vero cells was found in the HL grafts and multiple organs from infected NSG-L mice. RNA-seq examination identified a series of differentially expressed genes, which are enriched in viral defense responses, chemotaxis, interferon stimulation, and pulmonary fibrosis between HL grafts from infected and control NSG-L mice. Furthermore, when infecting humanized mice with human immune system (HIS) and autologous HL grafts (HISL mice), the mice had bodyweight loss and hemorrhage and immune cell infiltration in HL grafts, which were not observed in immunodeficient NSG-L mice, indicating the development of anti-viral immune responses in these mice. In support of this possibility, the infected HISL mice showed bodyweight recovery and lack of detectable live virus at the later time. These results demonstrate that NSG-L and HISL mice are susceptible to SARS-CoV-2 infection, offering a useful in vivo model for studying SARS-CoV-2 infection and the associated immune response and immunopathology, and testing anti-SARS-CoV-2 therapies.

Effects of Triptolide on Cell Viability, Secretion of Inflammatory Cytokines, and Gene Expression of Severe Coronavirus Disease 2019（COVID-19）Pseudovirus Cell Model (preprint)

Background: Acute respiratory distress syndrome (ARDS), which is caused by severe immune cell response and associated alveolar inflammation, is also a critical complication in hospitalized patients with COVID-19. Triptolide is a powerful anti-inflammatory and immunosuppressive drug and is proved to help relieve the inflammation of ARDS. However, its anti-inflammatory effect on COVID-19 patients with ARDS complications remains uncertain. Methods: : In this study, human normal lung epithelial cells (BEAS-2B), the pseudovirus system of syndrome coronavirus 2(SARS-CoV-2) and lipopolysaccharide (LPS) were used to construct as severe COVID-19-pseudovirus cell model to explore the effects of triptolide on cell viability, secretion of inflammatory cytokines, and gene expression. Results: : The results showed that triptolide increased cell viability, decreased the secretion levels of cytokines IL-6, TNF-a, and increased the expression of IL-10. Furthermore, transcriptome analysis in this cell models showed that the Differentially expressed genes (DEGs) were related to plasma membrane integrity, metabolic activity and mitochondrial function, and were associated with TNF, FOXO, mTOR and MAPK signaling pathways. Conclusion: Take into consideration previous studies on the functions of triptolide in BEAS-2B cells, the current study indicated that triptolide can play a critical role in protecting against inflammatory damage and maintaining the normal physiological function of BEAS-2B cells in response to pseudovirus and LPS infection.

Structural and Biochemical Rationale for Enhanced Spike Protein Fitness in Delta and Kappa SARS-CoV-2 Variants (preprint)

The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a novel head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant.

The Effectiveness of China's Fiscal and Monetary Policy and the Impact of Uncertainty Shocks: From the Perspective of Three Industries (preprint)

Under the influence of major random events such as US-China trade dispute and the coronavirus (COVID-19) outbreak, the uncertainty of macroeconomic regulation has also risen significantly. Then, what role economic policy level shocks and uncertainty shocks play in industrial regulation need to be clarified urgently. This study constructs a large-scale benchmark VAR model including fiscal and monetary policy and three-industry output and inflation, makes a detailed distinction between policy level shocks and uncertainty shocks, and describes the industrial control mechanism of economic policy from a new perspective. The main conclusions are as follows: firstly, compared with the ordinary VAR model, the benchmark VAR model has significant advantages in modeling efficiency, system stability and explanatory power, making it more suitable for describing the transmission mechanism of economic policy. Secondly, in terms of the role of policy uncertainty, its influence sometimes even exceeds the level impact, but in most cases, it is manifested as suppressing the output of the three industries, and the impact on industrial inflation is also dual at the same time. It shows that policy uncertainty is prone to adverse effects, and policy authorities should be more cautious in its use. Finally, from perspective of the adjustment of the three industries, tax and fee reduction are a relatively dominant means to optimize the output of the three industries, while in terms of maintaining price stability, the steady interest rate regulation is more efficient.

Structural Analysis of Receptor Binding Domain Mutations in SARS-CoV-2 Variants of Concern that Modulate ACE2 and Antibody Binding (preprint)

The recently emerged SARS-CoV-2 South African (B. 1.351) and Brazil/Japan (P.1) variants of concern (VoCs) include a key mutation (N501Y) found in the UK variant that enhances affinity of the spike protein for its receptor, ACE2. Additional mutations are found in these variants at residues 417 and 484 that appear to promote antibody evasion. In contrast, the Californian VoCs (B.1.427/429) lack the N501Y mutation, yet exhibit antibody evasion. We engineered spike proteins to express these RBD VoC mutations either in isolation, or in different combinations, and analyzed the effects using biochemical assays and cryo-EM structural analyses. Overall, our findings suggest that the emergence of new SARS-CoV-2 variant spikes can be rationalized as the result of mutations that confer either increased ACE2 affinity, increased antibody evasion, or both, providing a framework to dissect the molecular factors that drive VoC evolution.