A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265-269. [PMID: 32015508 PMCID: PMC7094943 DOI: 10.1038/s41586-020-2008-3]

The recombinant immunodominant regions 179-344 and 550-670 from SARS-COV2 spike protein can efficiently react with patients' sera

SARS-COV2 is related to the COVID-19 pandemic that emerged in 2019. It caused severe criticism of world health care and the economic system. Its high mutation rate increases contagiousness and gives rise to new variants, causing recurrent epidemic waves. One of the effective strategies for prevention and controlling infections is evaluating antibody existence against SARS-CoV2 to know how much individuals are protected against new infection. Therefore, it can be helpful to conduct health care strategies for vaccination and healing infected patients. In this study, we identified two immunodominant linear B cell epitopes (S179-344 and S550-670) within the S1 subunit of the spike protein using bioinformatics tools (ABCpred and BepiPred). These regions were subsequently cloned into the pET28a(+) vector, expressed in E. coli BL21 (DE3), and then purified. The recombinant antigens were then assessed for their seroreactivity using a variety of diagnostic techniques, including Western blot, dot blot, and ELISA. The study population for this assessment included 68 positive sera from patients infected with SARS-CoV2 and 63 negative control samples, both of which were screened by standard PCR. The results obtained from the ELISA assay indicated that both antigens demonstrated strong seroreactivity with high sensitivity (91-98 %) and specificity (82 %), suggesting their potential as diagnostic tools. The combination of both antigens exhibited diagnostic accuracy, further supporting their utility in clinical settings. The results of this study underscore the remarkable antigenicity of these epitopes and underscore the suitability of the assay for evaluating community immunity levels against SARS-CoV2 and vaccine efficacy.

A Novel Toolkit of SARS-CoV-2 Sub-Genomic Replicons for Efficient Antiviral Screening

SARS-CoV-2 is classified as a containment level 3 (CL3) pathogen, limiting research access and antiviral testing. To address this, we developed a non-infectious viral surrogate system using reverse genetics to generate sub-genomic replicons. These replicons contained the nsp1 mutations K164A and H165A and had the spike, membrane, ORF6, and ORF7a coding sequences replaced with various reporter and selectable marker genes. Replicons based on the ancestral Wuhan Hu-1 strain and the Delta variant of concern were replication-competent in multiple cell lines, as assessed by Renilla luciferase activity, fluorescence, immunofluorescence staining, and single-molecule fluorescent in situ hybridization. Antiviral assays using transient replicon expression showed that remdesivir effectively inhibited both replicon and viral replication. Ritonavir and cobicistat inhibited Delta variant replicons similarly to wild-type virus but did not inhibit Wuhan Hu-1 replicon replication. To further investigate the impact of nsp1 mutations, we generated a recombinant SARS-CoV-2 virus carrying the K164A and H165A mutations. The virus exhibited attenuated replication across a range of mammalian cell lines, was restricted by the type I interferon response, and showed reduced cytopathic effects. These findings highlight the utility of sub-genomic replicons as reliable CL2-compatible surrogates for studying SARS-CoV-2 replication and drug activity mechanisms.

A distinctive IGHV3-66 SARS-CoV-2 neutralizing antibody elicited by primary infection with an Omicron variant

SARS-CoV-2 Omicron sub-variants continuously evolve under the pressure of neutralizing antibodies (nAbs), eliminating numerous potential elite monoclonal nAbs. The IGHV3-53/3-66 public nAbs have great potential for neutralizing SARS-CoV-2. However, it has been unclear whether a primary Omicron infection could also induce IGHV3-53/3-66 nAbs. In this study, we report an IGHV3-66-encoding monoclonal nAb, ConBA-998, that was elicited by primary infection with BA.1. ConBA-998 is an Omicron-dependent nAb with high binding affinity that triggers the shedding of the S1 subunit from the spike protein. The cryo-electron microscopy (cryo-EM) structure revealed the interactions between ConBA-998 and the Omicron BA.1 spike protein. ConBA-998 has a distinctive binding mode to receptor-binding domain (RBD) that differs from canonical IGHV3-53/3-66 nAbs. Overall, our findings indicate that Omicron may elicit unique specific nAbs distinct from those induced by pre-Omicron variants, providing further insights into SARS-CoV-2 variant-specific antibody responses.

Monitoring SARS-CoV-2 Nsp13 helicase binding activity using expanded genetic code techniques

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) non-structural protein 13 (Nsp13) helicase is a multi-functional protein that can unwind dsDNA and dsRNA in an NTP-dependent manner. Given that this viral helicase is essential for viral replication and highly conserved among coronaviruses, a thorough understanding of the helicase's unwinding and binding activity may allow for the development of more effective pan-coronavirus therapeutics. Herein, we describe the use of genetic code expansion techniques to site-specifically incorporate the non-canonical amino acid (ncAA) p-azido-l-phenylalanine (AzF) into Nsp13 for fluorescent labelling of the enzyme with a conjugated Cy5 fluorophore. This Cy5-labelled Nsp13-AzF can then be used in Förster resonance energy transfer (FRET) experiments to investigate the dynamics of enzyme translocation on its substrate during binding and unwinding. Five sites (F81, F90, Y205, Y246, and Y253) were identified for AzF incorporation in Nsp13 and assessed for fluorescent labelling efficiency. The incorporation of AzF was confirmed to not interfere with the unwinding activity of the helicase. Subsequently, FRET-based binding assays were conducted to monitor the binding of Cy5-labelled Nsp13-AzF constructs to a series of fluorescently-labelled nucleic acid substrates in a distance-dependent manner. Overall, this approach not only allows for the direct monitoring of Nsp13's binding activity on its substrate, it may also introduce a novel method to screen for compounds that can inhibit this essential enzymatic activity during viral replication.

Viral Infections in Elderly Individuals: A Comprehensive Overview of SARS-CoV-2 and Influenza Susceptibility, Pathogenesis, and Clinical Treatment Strategies

As age increases, the immune function of elderly individuals gradually decreases, increasing their susceptibility to infectious diseases. Therefore, further research on common viral infections in the elderly population, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses, is crucial for scientific progress. This review delves into the genetic structure, infection mechanisms, and impact of coinfections with these two viruses and provides a detailed analysis of the reasons for the increased susceptibility of elderly individuals to dual viral infections. We evaluated the clinical manifestations in elderly individuals following coinfections, including complications in the respiratory, gastrointestinal, nervous, and cardiovascular systems. Ultimately, we have summarized the current strategies for the prevention, diagnosis, and treatment of SARS-CoV-2 and influenza coinfections in older adults. Through these studies, we aim to reduce the risk of dual infections in elderly individuals and provide a scientific basis for the prevention, diagnosis, and treatment of age-related viral diseases, thereby improving their health status.

Transcriptomic profiling of severe and critical COVID-19 patients reveals alterations in expression, splicing and polyadenylation

Coronavirus disease 2019 (COVID-19) is a multi-systemic illness that became a pandemic in March 2020. Although environmental factors and comorbidities can influence disease progression, there is a lack of prognostic markers to predict the severity of COVID-19 illness. Identifying these markers is crucial for improving patient outcomes and appropriately allocating scarce resources. Here, an RNA-sequencing study was conducted on blood samples from unvaccinated, hospitalized patients divided by disease severity; 367 moderate, 173 severe, and 199 critical. Using a bioinformatics approach, we identified differentially expressed genes (DEGs), alternative splicing (AS) and alternative polyadenylation (APA) events that were severity-dependent. In the severe group, we observed a higher expression of kappa immunoglobulins compared to the moderate group. In the critical cohort, a majority of AS events were mutually exclusive exons and APA genes mostly had longer 3'UTRs. Interestingly, multiple genes associated with cytoskeleton, TUBA4A, NRGN, BSG, and CD300A, were differentially expressed, alternatively spliced and polyadenylated in the critical group. Furthermore, several inflammation-related pathways were observed predominantly in critical vs. moderate. We demonstrate that integrating multiple downstream analyses of transcriptomics, from moderate, severe, and critical patients confers a significant advantage in identifying relevant dysregulated genes and pathways.

Wastewater Speaks: Evaluating SARS-CoV-2 Surveillance, Sampling Methods, and Seasonal Infection Trends on a University Campus

Wastewater surveillance has emerged as a cost-effective and equitable approach for tracking the spread of SARS-CoV-2. In this study, we monitored the prevalence of SARS-CoV-2 on a university campus over three years (2021-2023) using wastewater-based epidemiology (WBE). Wastewater samples were collected from 11 manholes on campus, each draining wastewater from a corresponding dormitory building, and viral RNA concentrations were measured using reverse transcription-quantitative PCR (RT-qPCR). Weekly clinical case data were also obtained from the university health center. A strong positive and significant correlation was observed between Grab and Composite sampling methods, supporting their robustness as equally effective approaches for sample collection. Specifically, a strong correlation was observed between Aggie Village 4 Grab and Aggie Village 4 Composite samples (R2 = 0.84, p = 0.00) and between Barbee Grab and Barbee Composite samples (R2 = 0.80, p = 0.00). Additionally, higher viral RNA copies of SARS-CoV-2 (N1 gene) were detected during the Spring semester compared to the Fall and Summer semesters. Notably, elevations in raw N1 concentrations were observed shortly after the return of college students to campus, suggesting that these increases were predominantly associated with students returning at the beginning of the Fall and Spring semesters (January and August). To account for variations in fecal loading, SARS-CoV-2 RNA concentrations were normalized using Pepper Mild Mottle Virus (PMMoV), a widely used viral fecal biomarker. However, normalization using PMMoV did not improve correlations between SARS-CoV-2 RNA levels and clinical case data. Despite these findings, our study did not establish WBE as a consistently reliable complement to clinical testing in a university campus setting, contrary to many retrospective studies. One key limitation was that numerous off-campus students did not contribute to the campus wastewater system corresponding to the monitored dormitories. However, some off-campus students were still subjected to clinical testing at the university health center under mandated protocols. Moreover, the university health center discontinued reporting cases per dormitory after 2021, making direct comparisons more challenging. Nevertheless, this study highlights the continued value of WBE as a surveillance tool for monitoring infectious diseases and provides critical insights into its application in campus environments.

Semi-automated diagnostic RT-PCR as a screening assay for antiviral compounds in a 96-well format against highly pathogenic RNA viruses

In response to outbreaks of (re)emerging highly pathogenic RNA viruses, simple and scalable antiviral screening methods are urgently needed. Using established and validated diagnostic methods like RT-PCR for antiviral screening offers a rapid readout of viral replication. This becomes particular important when other traditional viral replication readouts, such as TCID50 or plaque assays cannot be used due to the absence of cytopathic effects, lack of reporter gene-containing recombinant viruses or unavailability of appropriate antibodies - the latter two common challenges when so far unknown viruses emerge. This study evaluated semi-automated diagnostic RT-PCR in a 96-well approach for antiviral compound screening using Marburg virus serving as a case study. Remdesivir, a prodrug that exhibits antiviral activities against multiple RNA viruses, was used as positive control inhibiting replication of filoviruses. Applicability of the protocol to other members of the filovirus family was feasible using the same settings, while for other viruses like Middle East respiratory syndrome coronavirus (MERS-CoV) or Crimean-Congo hemorrhagic fever virus (CCHFV) adaptations to optimal infection settings were necessary. Our results demonstrate a high reproducibility and highlight the rapid adaptability of semi-automated RT-PCR assays as an accelerated antiviral screening assay with high scalability against a wide range of newly or (re)emerging RNA viruses. This is critical especially during outbreak situations where timely antiviral assessments are urgently needed.

Beyond the Pandemic Era: Recent Advances and Efficacy of SARS-CoV-2 Vaccines Against Emerging Variants of Concern

Vaccination has been instrumental in curbing the transmission of SARS-CoV-2 and mitigating the severity of clinical manifestations associated with COVID-19. Numerous COVID-19 vaccines have been developed to this effect, including BioNTech-Pfizer and Moderna's mRNA vaccines, as well as adenovirus vector-based vaccines such as Oxford-AstraZeneca. However, the emergence of new variants and subvariants of SARS-CoV-2, characterized by enhanced transmissibility and immune evasion, poses significant challenges to the efficacy of current vaccination strategies. In this review, we aim to comprehensively outline the landscape of emerging SARS-CoV-2 variants of concern (VOCs) and sub-lineages that have recently surfaced in the post-pandemic years. We assess the effectiveness of existing vaccines, including their booster doses, against these emerging variants and subvariants, such as BA.2-derived sub-lineages, XBB sub-lineages, and BA.2.86 (Pirola). Furthermore, we discuss the latest advancements in vaccine technology, including multivalent and pan-coronavirus approaches, along with the development of several next-generation coronavirus vaccines, such as exosome-based, virus-like particle (VLP), mucosal, and nanomaterial-based vaccines. Finally, we highlight the key challenges and critical areas for future research to address the evolving threat of SARS-CoV-2 subvariants and to develop strategies for combating the emergence of new viral threats, thereby improving preparedness for future pandemics.

Design, synthesis and activity evaluation of dual-target inhibitors against papain-like and main proteases of porcine epidemic diarrhea virus

INTRODUCTION

Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), threatens the global pig industry due to lack of drugs. PEDV replication relies on PLpro and Mpro, which are crucial targets for inhibitors. Additionally, PLpro plays a role in modulating the host's immune response, and the inhibition of PLpro exhibits significant anti-inflammatory properties.

OBJECTIVES

A series of dual-targeted inhibitors of Mpro and PLpro were designed and synthesized, and their antiviral and anti-inflammatory activities were subsequently evaluated in vitro and in vivo.

METHODS

Dual-targeted inhibitors of Mpro and PLpro were designed by merging two series of Mpro inhibitors and PLpro inhibitors. sixty-four compounds were synthesized and screened in vitro by FRET for inhibitory activities and by RT-qPCR for antiviral activity on Vero-E6 cells. The anti-PEDV activity of f2 on Vero-E6 cells and IPEC-J2 cells was further confirmed by immunofluorescence. The mechanism by which f2 inhibited PEDV-induced inflammation was investigated by Western blot and RT-qPCR. The anti-colitis activity of f2 was verified in vivo.

RESULTS

Among the sixty-four synthesized compounds, seventeen potent dual-targeted inhibitors of PLpro and Mpro were identified with IC50 values less than 10 μM. Six compounds demonstrated excellent antiviral activity and safety in cell-based assays. The most potent compound f2 inhibited PEDV replication in Vero-E6 and IPEC-J2 cells with EC50 values of 1.17 ± 0.73 μM and 2.02 ± 0.56 μM, respectively, without cytotoxicity (CC50 > 800 μM). Moreover, f2 was found to inhibit the inflammatory response induced by PEDV infection via suppressing TLR2/PI3K/Akt/NF-κB signaling pathway. Oral f2 attenuated colitis by decreasing p65 phosphorylation, a major PEDV mortality cause. The in vivo acute toxicity test showed that oral administration of f2 did not affect the body weight and internal organs of mice.

CONCLUSIONS

In summary, a potent dual-targeted inhibitor of PLpro and Mpro, f2, was designed, synthesized, and found to be effective in the inhibition of PEDV replication and inflammatory response in vitro and in vivo.

SARS-CoV-2 post-acute sequelae linked to inflammation via extracellular vesicles

Background

Despite the efficacy of SARS-CoV-2 vaccines in reducing mortality and severe cases of COVID-19, a proportion of survivors experience long-term symptoms, known as post-acute sequelae of SARS-CoV-2 infection (PASC). This study investigates the long-term immunological and neurodegenerative effects associated with extracellular vesicles (EVs) in COVID-19 survivors, 15 months after SARS-CoV-2 infection.

Methods

13 Controls and 20 COVID-19 survivors, 15 months after SARS-CoV-2 infection, were recruited. Pro-inflammatory cytokines were analyzed in both plasma and EVs. A deep-immunophenotyping of monocytes, T-cells and dendritic cells (DCs) was performed, along with immunostainings of SARS-CoV-2 in the colon.

Results

Higher concentrations of pro-inflammatory cytokines and neurofilaments were found in EVs but not in plasma from COVID-19 survivors. Additionally, COVID-19 participants exhibited altered monocyte activation markers and elevated cytokine production upon lipopolysaccharide stimulation. Increased activation markers in CD4+ T-cells and decreased indoleamine 2,3-dioxygenase expression in DCs were observed in COVID-19 participants. Furthermore, the amount of plasmacytoid DCs expressing β7-integrin were higher in COVID-19, potentially associated with the viral persistence observed in the colon.

Conclusions

COVID-19 survivors exhibit long-term immune dysregulation and neurodegeneration, emphasizing the need for ongoing monitoring of PASC. The cargo of EVs can be a promising tool for early detection of virus-induced neurological disorders.

Design, synthesis and activity evaluation of 4-(quinoline-2-yl)aniline derivatives as SARS-CoV‑2 main protease inhibitors

Since 2020, numerous compounds have been investigated for their potential use in treating SARS-CoV-2 infections. By identifying the molecular targets during the virus replication process, rationally designed anti-SARS-CoV-2 agents are developed. Among these targets, the main protease (Mpro) is a crucial enzyme required for virus replication, and its highly conserved characteristic make it an important drug target for the development of anti-SARS-CoV-2 drugs. Herein, we utilized warhead-based design strategy to conduct the structural optimization of M-1 developed through virtual screening, leading to a series of novel Mpro inhibitors with 4-(quinolin-2-yl)aniline scaffold. Among them, M-32 exhibited good SARS-CoV-2 Mpro inhibitory activity (IC50 = 5.2 μM) with a nearly 25-fold increase. Isothermal titration calorimetry (ITC) directly proved that M-32 binds directly to SARS-CoV-2 Mpro in an entropy-driven manner. Mass spectrometry (MS) further confirmed the covalent binding ability of M-32 to Mpro. Meanwhile, M-32 effectively inhibited the replication of SARS-CoV-2 in Vero E6 cells (EC50 = 5.29 μM).

SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals

The immune response to viral infection is shaped by past exposures to related virus strains, a phenomenon known as imprinting. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), much of the population has been imprinted by a viral spike from an early strain, either through vaccination or infection during the early stages of the COVID-19 pandemic. As a consequence of this imprinting, infection with more recent SARS-CoV-2 strains primarily boosts cross-reactive antibodies elicited by the imprinting strain. Here we compare the neutralizing antibody specificities of imprinted individuals versus infants infected with a recent strain. Specifically, we use pseudovirus-based deep mutational scanning to measure how spike mutations affect neutralization by the serum antibodies of adults and children imprinted by the original vaccine versus infants with a primary infection by an XBB* variant. While the serum neutralizing activity of the imprinted individuals primarily targets the spike receptor-binding domain (RBD), the serum neutralizing activity of infants infected with only XBB* mostly targets the spike N-terminal domain. In these infants, secondary exposure to the XBB* spike via vaccination shifts more of the neutralizing activity toward the RBD, although the specific RBD sites targeted are different from imprinted adults. The dramatic differences in neutralization specificities among individuals with different exposure histories likely impact SARS-CoV-2 evolution.IMPORTANCEWe show that a person's exposure history to different SARS-CoV-2 strains strongly affects which regions on the viral spike that their neutralizing antibodies target. In particular, infants who have just been infected once with a recent viral strain make neutralizing antibodies that target different regions of the viral spike than adults or children who have been exposed to both older and more recent strains. This person-to-person heterogeneity means that the same viral mutation can have different impacts on the antibody immunity of different people.

Abortive PDCoV infection triggers Wnt/β-catenin pathway activation, enhancing intestinal stem cell self-renewal and promoting chicken resistance

Porcine deltacoronavirus (PDCoV) is an emerging coronavirus causing economic losses to swine industries worldwide. PDCoV can infect chickens under laboratory conditions, usually with no symptoms or mild symptoms, and may cause outbreaks in backyard poultry and wildfowl, posing a potential risk of significant economic loss to the commercial poultry industry. However, the reasons for such a subdued reaction after infection are not known. Here, using chicken intestinal organoid monolayers, we found that although PDCoV infects them nearly as well as porcine intestinal organoid monolayers, infection did not result in detectable amounts of progeny virus. In ex vivo and in vivo experiments using chickens, PDCoV infection failed to initiate interferon and inflammatory responses. Additionally, infection did not result in a disrupted intestinal barrier nor a reduced number of goblet cells and mucus secretion, as in pigs. In fact, the number of goblet cells increased as did the secreted mucus, thereby providing an enhanced protective barrier. Ex vivo PDCoV infection in chicken triggered activation of the Wnt/β-catenin pathway with the upregulation of Wnt/β-catenin pathway genes (Wnt3a, Lrp5, β-catenin, and TCF4) and Wnt target genes (Lgr5, cyclin D1, and C-myc). This activation stimulates the self-renewal of intestinal stem cells (ISCs), accelerating ISC-mediated epithelial regeneration by significant up-regulation of PCNA (transiently amplifying cells), BMI1 (ISCs), and Lyz (Paneth cells). Our data demonstrate that abortive infection of PDCoV in chicken cells activates the Wnt/β-catenin pathway, which facilitates the self-renewal and proliferation of ISCs, contributing to chickens' resistance to PDCoV infection.IMPORTANCEThe intestinal epithelium is the main target of PDCoV infection and serves as a physical barrier against pathogens. Additionally, ISCs are charged with tissue repair after injury, and promoting rapid self-renewal of intestinal epithelium will help to re-establish the physical barrier and maintain intestinal health. We found that PDCoV infection in chicken intestinal organoid monolayers resulted in abortive infection and failed to produce infectious virions, disrupt the intestinal barrier, reduce the number of goblet cells and mucus secretion, and induce innate immunity, but rather increased goblet cell numbers and mucus secretion. Abortive PDCoV infection activated the Wnt/β-catenin pathway, enhancing ISC renewal and accelerating the renewal and replenishment of shed PDCoV-infected intestinal epithelial cells, thereby enhancing chicken resistance to PDCoV infection. This study provides novel insights into the mechanisms underlying the mild or asymptomatic response to PDCoV infection in chickens, which is critical for understanding the virus's potential risks to the poultry industry.

Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics

Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon usage (RSCU) of virus genomes together with other genomic properties are predictive of virus host codon fitness through tree-based machine learning. Statistical analysis on the RSCU data matrix also revealed that the wobble position of the virus codons is critically important for the host codon fitness distinction. As the trained models can well characterise the host codon fitness of the viruses, the frequency and other details stored at the leaf nodes of these models can be reliably translated into human virus codon fitness score (HVCF score) as a readout of codon fitness of any virus infecting human. Specifically, we evaluated and compared HVCF of virus genome sequences from human sources and others and evaluated HVCF of SARS-CoV-2 genome sequences from NCBI virus database, where we found no obvious shifting trend in host codon fitness towards human-non-infectious. We also developed a bioinformatics tool to simulate codon-based virus fitness shifting using codon compositions of the viruses, and we found that Tylonycteris bat coronavirus HKU4 related viruses may have close relationship with SARS-CoV-2 in terms of human codon fitness. The finding of abundant synonymous mutations in the predicted codon fitness shifting path also provides new insights for evolution research and virus monitoring in environmental surveillance.

Enhancing the understandings on SARS-CoV-2 main protease (Mpro) mutants from molecular dynamics and machine learning

While star drugs like Paxlovid have shown remarkable performance in combating SARS-CoV-2, we still face serious challenges such as viral mutants and resistance. In this study, we employ a computational framework combining molecular dynamics (MD) simulations, enhanced sampling techniques, and machine learning (ML) approaches to systematically investigate the molecular mechanisms underlying drug resistance in SARS-CoV-2 main protease (Mpro) mutants. Specifically, based on the accuracy of the analytical structures and the advantages of MD simulation, we deeply analyze the influence of mutants on drug resistance and its intrinsic function from the dynamic dimension. The relevant data for Mpro with different states are compared and analyzed to consolidate the understanding of mutant effect. Through the free energy perturbation method, the absolute binding free energy diagrams of Mpro mutants and Nirmatrelvir are provided, which is meaningful to the design, comparison and optimization of the new-generation inhibitors. The interaction pattern between Mpro mutants and substrate is unraveled with the AlphaFold3 model, effectively filling the deficiency of experiments. Moreover, ML model is used to explore the differentiated synergetic pathways with the important dual mutants. The critical sites in the protein network are provided, which emphasizes on the importance and urgency of in-depth research on similar systems.

Phenothiazine-linked glutamic acid dendrons: an easy access and a new class of SARS-CoV-2 main protease inhibitors

In this report, a structurally unique phenothiazine (PTZ) core is linked with glutamic acid-based dendrons through a solid-phase peptide synthesis approach to access a variety of PTZ-linked dendrons conveniently. Inferior cytotoxicity of anionic surface-linked second-generation glutamic acid-based dendrons would be more desirable for various applications than respective lysine-based dendrons. Solid-phase synthesis of PTZ-linked glutamic acid-based dendrons would be a novel approach to access this class of molecules. These newly synthesized dendrons were screened as an inhibitor against the main protease (Mpro) enzyme, proposed to be the best target against SARS-CoV-2. The preliminary assay studies designated a moderate response for the Mpro inhibition, specifically by tryptophan (Trp)-enriched dendron, among other analogues, which play a vital role in combating COVID-19. Further, the experimental studies realize the essential contribution of the PTZ core in interacting with the Mpro enzyme. Molecular dynamics (MD) simulations revealed that the active dendrons formed stable complexes with Mpro, and the binding affinity of the Trp-based PTZ-linked dendrons was higher than that of the decoy dendron analogue.

Evaluation of an E. coli-expressed spike protein-based in-house ELISA system for assessment of antibody responses after COVID-19 infection and vaccination

Evaluating long-term immunity after COVID-19 infection and vaccination is critical for managing potential outbreaks. The aim of this study was to develop a cost-effective in-house enzyme-linked immunosorbent assay (ELISA) based on Escherichia coli-expressed SARS-CoV-2 spike protein (E-S1) for antibody detection and to evaluate its performance. The system was validated by comparing the in-house ELISA results with those obtained using a commercial ELISA with HEK293-expressed spike protein (H-S1). Recombinant SARS-CoV-2 spike protein was produced in E. coli, purified, and validated for antigenicity via ELISA. Indirect ELISAs with both E-S1 and H-S1 antigens were performed on 386 serum samples from COVID-19 survivors, vaccinated individuals, and pre-pandemic controls collected at different time points. The E-S1 ELISA showed a statistically significant but weak correlation with H-S1 ELISA across all samples (r=0.205; p=0.0001). Stronger correlations were observed among vaccinated individuals with prior infection on day 90 (r=0.6017; p<0.001) and in naïve vaccine recipients on day 30 (r=0.5361; p=0.0003). Pre-pandemic sera from a rural population in Sumba Island exhibited high background reactivity in E-S1 ELISA, likely due to anti-E. coli antibodies, while urban pre-pandemic sera from Jakarta showed a stronger correlation with H-S1 ELISA. This suggests potential regional or immune background differences influencing assay performance. Although E-S1 retained antigenic properties, its diagnostic utility is limited by non-specific reactivity and reduced sensitivity compared to H-S1. In conclusion, E. coli expression systems may not be ideal for producing spike protein-based ELISA antigens specific to SARS-CoV-2. Alternative expression systems, such as human or baculovirus, could enhance diagnostic accuracy and specificity for COVID-19 antibody detection.

The Yin and Yang of TLR4 in COVID-19

Various pattern recognition receptors (PRRs), including toll-like receptors (TLRs), play a crucial role in recognizing invading pathogens as well as damage-associated molecular patterns (DAMPs) released in response to infection. The resulting signaling cascades initiate appropriate immune responses to eliminate these pathogens. Current evidence suggests that SARS-CoV-2-driven activation of TLR4, whether through direct recognition of the spike glycoprotein (alone or in combination with endotoxin) or by sensing various TLR4-activating DAMPs or alarmins released during viral infection, acts as a critical mediator of antiviral immunity. However, TLR4 exerts a dual role in COVID-19, demonstrating both beneficial and deleterious effects. Dysregulated TLR4 signaling is implicated in the proinflammatory consequences linked to the immunopathogenesis of COVID-19. Additionally, TLR4 polymorphisms contribute to severity of the disease. Given its significant immunoregulatory impact on COVID-19 immunopathology and host immunity, TLR4 has emerged as a key target for developing inhibitors and immunotherapeutic strategies to mitigate the adverse effects associated with SARS-CoV-2 and related infections. Furthermore, TLR4 agonists are also being explored as adjuvants to enhance immune responses to SARS-CoV-2 vaccines.

Long-term effects of SARS-CoV-2 infection on metal homeostasis

The outbreak of COVID-19 pandemic has caused substantial health loss worldwide, and the long-term sequelae of COVID, resulting from repeated coronavirus infection, have emerged as a new public health concern. We report the widespread presence of abnormal metallomic profiles in the sera of patients who have recovered from SARS-CoV-2 coronavirus infection, even after 6 months post-discharge from hospital. We measured the concentrations of Fe, Cu, Zn, Se, Cr, Mn, Ba, Ni, Pb, Ag, As, Cd, Co, and V in the sera of 25 recovered participants and 38 healthy controls in the cross-sectional study. Higher concentrations of Cu, Ag, As, Ba, Cd, Ni, Pb, Cr and V were observed in the recovered participants, whereas lower concentrations of Fe and Se were obtained in these participants. Except for Zn, Mn, and Co, all other elements showed significant differences (p < 0.05) between the two groups, with variations dependent on age and gender. Further correlation analysis between metallome and metabolome indicated that SARS-CoV-2 infection continues to disrupt metallic homeostasis and affect metabolic processes, such as lipid metabolism and cell respiration, as well as the functions of certain organs (e.g., liver, kidney, and heart), even after 6 months recovery. Our findings provide novel insights into the potential long-term effect of COVID-19 on the human body from a new perspective of metallomics.

Enrichment of G-to-U Substitution in SARS-CoV-2 Functional Regions and Its Compensation via Concurrent Mutations

We surveyed single nucleotide variant (SNV) patterns from 5 903 647 complete SARS-CoV-2 genomes. Among 10 012 SNVs, APOBEC-mediated C-to-U (C > U) deamination was the most prevalent, followed by G > U and other RNA editing-related substitutions including (A > G, U > C, G > A). However, C > U mutations were less frequent in functional regions, for example, S protein, intrinsic disordered regions, and nonsynonymous mutations, where G > U were over-represented. Notably, G-loss substitutions rarely appeared together. Instead, G-gain mutations tended to more frequently co-occur with others, with a marked preference in the S protein, suggesting a compensatory mechanism for G loss in G > U mutations. The temporal patterns revealed C > U frequency declined until late 2021 then resurged in early 2022. Conversely, G > U steadily decreased, with a pronounced drop in January 2022, coinciding with reduced COVID-19 severity. Vaccinated individuals exhibited a slightly but significantly higher C > U frequency and a notably lower G > U frequency compared to the unvaccinated group. Additionally, cancer patients had higher G > U frequency than general patients during the same period. Interestingly, none of the C > U SNVs were uniquely identified in 2724 environmental samples. These findings suggest novel functional roles of G > U in COVID-19 symptoms, potentially linked to oxidative stress and reactive oxygen species, while C > U remains the dominant substitution, likely driven by host immune-mediated RNA editing.

Myeloid-Driven Immune Suppression Subverts Neutralizing Antibodies and T Cell Immunity in Severe COVID-19

The objective of this study was to better understand immune failure mechanisms during severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 infection, which are critical for developing targeted vaccines and effective treatments. We collected 34 cases representing different disease severities and performed high-quality single-cell TCR/BCR sequencing to analyze the peripheral immune cell profiles. Additionally, we assessed antibody-neutralizing activity through in vitro experiments. Our integrated multiomics analysis uncovers a profound immune paradox in severe COVID-19: hyperinflammation coexists with immunosuppression, driven by distinct yet interconnected dysregulatory mechanisms. Severe patients develop robust humoral immunity, evidenced by clonally expanded plasma cells producing neutralizing antibodies (e.g., IGHG1-dominated responses) and antigen-specific T cell activation. However, these protective responses are counteracted by myeloid-driven immunosuppression, particularly CD14+ HMGB2+ monocytes exhibiting metabolic reprogramming and HLA-DR downregulation, coupled with progressive T cell exhaustion characterized by IFN-γ/TNF-α hyperactivation and impaired antigen presentation. Importantly, prolonged viral persistence in severe cases arises from a failure to coordinate humoral and cellular immunity-antibody-mediated neutralization cannot compensate for defective cytotoxic T cell function and monocyte-mediated immune suppression. These findings highlight the necessity for therapeutic strategies that simultaneously enhance antibody effector functions (e.g., Fc optimization), restore exhausted T cells, and reverse myeloid suppression. They also highlight the importance of vaccines designed to elicit balanced B cell memory and durable T cell responses, which are critical to preventing severe disease progression. By addressing the dual challenges of hyperinflammation and immunosuppression, such approaches could restore immune coordination and improve outcomes in severe COVID-19.

In silico evaluation of S-adenosyl-L-homocysteine analogs as inhibitors of nsp14-viral cap N7 methyltranferase and PLpro of SARS-CoV-2: synthesis, molecular docking, physicochemical data, ADMET and molecular dynamics simulations studies

A series of S-adenosyl-L-homosysteine (SAH) analogs, with modification in the base and sugar moiety, have been designed, synthesized and screened as nsp14 and PLpro inhibitors of severe acute respiratory syndrome corona virus (SARS-CoV-2). The outcomes of ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) studies demonstrated that the physicochemical properties of all analogs were permissible for development of these SAH analogs as antiviral agents. All molecules were screened against different SARS-CoV-2 targets using molecular docking. The docking results revealed that the SAH analogs interacted well in the active site of nsp14 protein having H-bond interactions with the amino acid residues Arg289, Val290, Asn388, Arg400, Phe401 and π-alkyl interactions with Arg289, Val290 and Phe426 of Nsp14-MTase site. These analogs also formed stable H-bonds with Leu163, Asp165, Arg167, Ser246, Gln270, Tyr274 and Asp303 residues of PLpro proteins and found to be quite stable complexes therefore behaved as probable nsp14 and PLpro inhibitors. Interestingly, analog 3 showed significant in silico activity against the nsp14 N7 methyltransferase of SARS-CoV-2. The molecular dynamics (MD) and post-MD results of analog 3 unambiguously established the higher stability of the nsp14 (N7 MTase):3 complex and also indicated its behavior as probable nsp14 inhibitor like the reference sinefungin. The docking and MD simulations studies also suggested that sinefungin did act as SARS-CoV-2 PLpro inhibitor as well. This study's findings not only underscore the efficacy of the designed SAH analogs as potent inhibitors against crucial SARS-CoV-2 proteins but also pinpoint analog 3 as a particularly promising candidate. All the study provides valuable insights, paving the way for potential advancements in antiviral drug development against SARS-CoV-2.

Biocatalytic enzymes in food packaging, biomedical, and biotechnological applications: A comprehensive review

The increasing environmental concerns and health risks associated with synthetic chemicals have driven the demand for sustainable and eco-friendly solutions. Biocatalysis, employing enzymes or whole cells as biocatalysts, has emerged as a powerful alternative. This review provides a comprehensive analysis of the applications of biocatalytic enzymes in food packaging, biomedical sciences, and biotechnology. We highlight the potential of enzymes like laccase, glucose oxidase, lysozyme, protease, lipase, cellulase, and asparaginase to replace traditional chemical methods, driving innovation and sustainability. The global enzyme market is also analyzed, including current trends, emerging demands, and the impact of the COVID-19 pandemic. This review aims to bridge knowledge gaps, emphasize recent technological breakthroughs, and showcase the potential of biocatalytic enzymes to address critical industrial challenges while supporting environmental sustainability and economic growth.

Molecular Basis of High-Blood-Pressure-Enhanced and High-Fever-Temperature-Weakened Receptor-Binding Domain/Peptidase Domain Binding: A Molecular Dynamics Simulation Study

The entry and infection of the Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) involve recognition and binding of the receptor-binding domain (RBD) of the virus surface spike protein to the peptidase domain (PD) of the host cellular Angiotensin-Converting Enzyme-2 (ACE2) receptor. ACE2 is also involved in normal blood pressure control. An association between hypertension and COVID-19 severity and fatality is evident, but how hypertension predisposes patients diagnosed with COVID-19 to unfavorable outcomes remains unclear. High temperature early during SARS-CoV-2 infection impairs binding to human cells and retards viral progression. Low body temperature can prelude poor prognosis. In this study, all-atom molecular dynamics simulations were performed to examine the effects of high pressure and temperature on RBD/PD binding. A high blood pressure of 940 mmHg enhanced RBD/PD binding. A high temperature above 315 K significantly weakened RBD/PD binding, while a low temperature of 305 K enhanced binding. The curvature of the PD α1-helix and proximity of the PD β3β4-hairpin tip to the RBM motif affected the compactness of the binding interface and, hence, binding affinity. These findings provide novel insights into the underlying mechanisms by which hypertension predisposes patients to unfavorable outcomes in COVID-19 and how an initial high temperature retards viral progression.

PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance

MOTIVATION

Recommendations on the use of genomics for pathogens surveillance are evidence that high-throughput genomic sequencing plays a key role to fight global health threats. Coupled with bioinformatics and other data types (e.g., epidemiological information), genomics is used to obtain knowledge on health pathogenic threats and insights on their evolution, to monitor pathogens spread, and to evaluate the effectiveness of countermeasures. From a decision-making policy perspective, it is essential to ensure the entire process's quality before relying on analysis results as evidence. Available workflows usually offer quality assessment tools that are primarily focused on the quality of raw NGS reads but often struggle to keep pace with new technologies and threats, and fail to provide a robust consensus on results, necessitating manual evaluation of multiple tool outputs.

RESULTS

We present PathoSeq-QC, a bioinformatics decision support workflow developed to improve the trustworthiness of genomic surveillance analyses and conclusions. Designed for SARS-CoV-2, it is suitable for any viral threat. In the specific case of SARS-CoV-2, PathoSeq-QC: (i) evaluates the quality of the raw data; (ii) assesses whether the analysed sample is composed by single or multiple lineages; (iii) produces robust variant calling results via multi-tool comparison; (iv) reports whether the produced data are in support of a recombinant virus, a novel or an already known lineage. The tool is modular, which will allow easy functionalities extension.

AVAILABILITY AND IMPLEMENTATION

PathoSeq-QC is a command-line tool written in Python and R. The code is available at https://code.europa.eu/dighealth/pathoseq-qc.

Leveraging innovative diagnostics as a tool to contain superbugs

The evolutionary adaptation of pathogens to biological materials has led to an upsurge in drug-resistant superbugs that significantly threaten public health. Treating most infections is an uphill task, especially those associated with multi-drug-resistant pathogens, biofilm formation, persister cells, and pathogens that have acquired robust colonization and immune evasion mechanisms. Innovative diagnostic solutions are crucial for identifying and understanding these pathogens, initiating efficient treatment regimens, and curtailing their spread. While next-generation sequencing has proven invaluable in diagnosis over the years, the most glaring drawbacks must be addressed quickly. Many promising pathogen-associated and host biomarkers hold promise, but their sensitivity and specificity remain questionable. The integration of CRISPR-Cas9 enrichment with nanopore sequencing shows promise in rapid bacterial diagnosis from blood samples. Moreover, machine learning and artificial intelligence are proving indispensable in diagnosing pathogens. However, despite renewed efforts from all quarters to improve diagnosis, accelerated bacterial diagnosis, especially in Africa, remains a mystery to this day. In this review, we discuss current and emerging diagnostic approaches, pinpointing the limitations and challenges associated with each technique and their potential to help address drug-resistant bacterial threats. We further critically delve into the need for accelerated diagnosis in low- and middle-income countries, which harbor more infectious disease threats. Overall, this review provides an up-to-date overview of the diagnostic approaches needed for a prompt response to imminent or possible bacterial infectious disease outbreaks.

COVID-19-related hospitalizations in Italy: an application of the synthetic control method to investigate the trajectory of diagnosis-related group 79 and its counterfactual during 2010-2021

BACKGROUND

With 10.95 million cases (11 March 2020-9 February 2022), Italy was massively hit by the coronavirus disease 2019 (COVID-19) pandemic. Most of the COVID-19-related inpatient discharges were codified under the Diagnosis-Related Group (DRG) 79. During 2019-2021, DRG 79 inpatient discharges increased from 20,377 to 130,580 (+540.82%).

RESEARCH DESIGN AND METHODS

To investigate the causal relationship between DRG 79 inpatient discharges and COVID-19, the synthetic control method (SCM) compared the real with the counterfactual DRG 79. The latter was a weighted combination of control units (22 DRGs unrelated to COVID-19). The SCM mimicked the trajectory of DRG 79 in the absence of COVID-19.Placebo studies and robustness test investigated the reliability of the baseline findings.

RESULTS

Six out of the 22 control units contribute to the counterfactual DRG 79. The real and the counterfactual DRG 79 cease to overlap from 2019 onward. Placebo studies and robustness test confirm the causal relationship of COVID-19 with the increased number of inpatient discharges coded under DRG 79 during 2019-2021.

CONCLUSION

The SCM identifies a causal link between COVID-19 and DRG 79 in Italy. Hopefully, future contributions will utilize SCM (and causal inference in general) in health care decision-making within the Italian National Health Service.

Comparative spatial-temporal analysis of SARS-CoV-2 lineages B.1.1.33 and BQ.1.1 Omicron variant across pandemic phases

The evolution of COVID-19 pandemic has been characterized by the rapid emergence of new SARS-CoV-2 variants, each of which poses unique challenges to public health. This study analyzes the dispersion profiles during the Pre-Omicron and Post-Omicron phases in different epidemiological contexts. The Brazilian state of Espirito Santo, despite its low population density, plays a critical role as a commercial hub due to its intense port activity, which may have contributed to COVID-19 cases and mortality rates being higher than the national average. The state recorded 34,000 confirmed cases and 377 deaths per 100,000 inhabitants. Genomic surveillance revealed that the Pre-Omicron phase was dominated by the B.1.1.33 lineage, characterized by localized intraregional circulation. In contrast, the Post-Omicron phase, dominated by the BQ.1.1 lineage, exhibited greater diversity in circulating lineages, increased international interactions, and rapid viral dissemination, highlighting distinct transmission dynamics between such periods. This study highlights the need for adaptive public health strategies that account for both viral behavior and regional socioeconomic factors, while highlighting the strategic importance of Espirito Santo in monitoring SARS-CoV-2 evolution.

Blood type susceptibility to SARS-CoV-2 at a tertiary hospital in Accra, Ghana

Pandemics from viral outbreaks, such as that caused by SARS-CoV-2, have significant impacts worldwide. The factors that underlie differential susceptibility to severe COVID-19 outcomes are not fully understood. The role of the ABO blood group in the outcome of SARS-CoV-2 infections remains to be clarified in different populations. This study described the SARS-CoV-2 seroprevalence and examined the association of the ABO blood group with COVID-19 disease among apparently healthy and COVID-19 patients at the Korle Bu Teaching Hospital, Accra. The study involved 277 participants comprising 200 healthy individuals and 77 PCR-confirmed COVID-19 patients with mild or severe symptoms. Anti-SARS-CoV-2 antibody assay (IgM/IgG) was performed, and ABO blood grouping was done on plasma samples using the reverse blood grouping method. Statistical analyses were performed in R for the association of socio-demographic parameters and ABO blood groupings of participants with SARS-CoV-2 infection status. The total SARS-CoV-2 seropositivity was 61.4% (157/277). Most of the participants (245/277, 88.4%) were unvaccinated. Of the 245 unvaccinated individuals, 127 (51.8%) were IgG reactive. A significant association was observed between ABO blood group and COVID-19 disease status. Antigen A participants had a higher probability of symptomatic infection than non-antigen A individuals. Blood group O appeared more protective than other blood types among the participants. Seropositivity was high among the participants studied-vaccinated and unvaccinated. Blood group A is associated with an increased risk of COVID-19, whereas blood group O appears protective. Further studies involving larger sample sizes are required to confirm these findings.

IMPORTANCE

The transmissibility and virulence of SARS-CoV-2 and the severity of COVID-19 disease appeared to vary across nations and among populations. However, the factors that account for the differential susceptibility and COVID-19 outcomes are not well understood. The roles of host immune defense mechanisms and genetic makeup have been implicated. This study investigated the seroprevalence of anti-SARS-CoV-2 antibodies (IgM and IgG) in apparently healthy individuals and COVID-19 patients; using a reliable but inexpensive blood group typing based on direct hemagglutination technique and rigorous statistical analyses, we determined the association of ABO blood groups with COVID-19 disease. We found appreciably high seropositivity among the participants studied-both vaccinated and unvaccinated-and showed that blood type significantly influences SARS-CoV-2 infection and COVID-19 severity, with blood group A associated with severe COVID-19 disease, whereas blood group O appears protective. Further studies involving a larger sample size are required to confirm these findings.

Rapid and accurate detection of SARS-CoV-2 spike protein by aptamer conformation change based on a reusable aptasensor

Timely and accurate detection of the virus is of great significance to prevent the virus's harm and control the epidemic. Here, an aptasensor based on the principle of promoting hybridization through aptamer conformational change was designed to quantitatively detect the spike (S) protein of SARS-CoV-2. When the S protein binds to the 3' end of the aptamer, the 5' end of the aptamer tansforms into a straight hybridization region, which will greatly facilitate the hybridization with complementary DNA (cDNA). In the absence of S protein, hybridization is less likely to occur due to the complex G-quadruplex structure of aptamer. According to this principle, cDNA is modified onto magnetic beads (MBs) or onto the optical fiber probe of an evanescent wave fluorescence aptasensor (EWFA) detection platform to capture the fluorescently labeled aptamer-S protein conjugate, two kinds of quantitative detection methods for SARS-CoV-2 S protein were established. In particular, simple, rapid and sensitive detection could be obtained based on the EWFA detection platform, in which the whole detection procedure including the measurement and regeneration takes  only 14 min, the LOD is 5.34 ng/mL, the linear response range is 141.49 to 9507.36 ng/mL, and the optical fiber probe could be reused for 19 times. The EWFA detection platform is also potentially applicable to detect other protein biomarkers only by replacing the specifically modified optical fiber probes.

Repurposing Vancomycin as a Potential Antiviral Agent Against PEDV via nsp13 Helicase Inhibition

Porcine epidemic diarrhea virus (PEDV) causes a highly contagious intestinal disease with severe economic impacts on the global swine industry. The non-structural protein 13 (nsp13), a viral helicase, is essential for viral replication, making it a promising target for antiviral drug development. In this study, through virtual screening and molecular dynamics simulations, Vancomycin, a small-molecule drug also clinically used as an antibacterial agent, was identified to exhibit a stable binding affinity for PEDV nsp13. The NTPase and ATP-dependent RNA helicase activities of PEDV nsp13 were confirmed in vitro, and the optimal biochemical reaction conditions for its dsRNA unwinding activity were established. Further experiments demonstrated that Vancomycin effectively inhibited the dual enzymatic activities of PEDV nsp13 and reduced PEDV infections in vitro. This research highlights Vancomycin as a novel inhibitor of PEDV nsp13, providing valuable mechanistic insights and serving as a model for antiviral drug discovery. While this study suggests its potential for repurposing as a therapeutic agent against PEDV, further investigations are required to evaluate its feasibility in vivo, particularly in terms of safety, efficacy, and practical applicability.

In Silico and In Vitro development of novel small interfering RNAs (siRNAs) to inhibit SARS-CoV-2

SARS-CoV-2 is causing severe to moderate respiratory tract infections, posing global health, social life, and economic threats. Our design strategy for siRNAs differs from existing studies through a step-by-step filtration process utilizing integrative bioinformatics protocols and web tools. Stage one: Multiple Sequence Alignment was employed to identify the most conserved areas. Stage two involves using various online tools, among the most reputable tools for building siRNA. The first filtration step of siRNA uses the Huesken dataset, estimating a 90 % experimental inhibition. The second filtration stage involves choosing the most suitable and targeted siRNA by utilizing thermodynamics and Target Accessibility of siRNAs. The final filtration step is off-target filtration using BLAST with specific parameters. Four of the 258 siRNAs were chosen for their potency and specificity, targeting conserved regions (NSP8, NSP12, and NSP14) with minimal human transcripts off-targets. We conducted in-vitro experiments, including cytotoxicity, TCID50, and RT-PCR assays. When tested on the SARS-CoV-2 strain hCoV-19/Egypt/NRC-03/2020 at 100 nM, none showed cellular toxicity. The TCID50 assay confirmed viral replication reduction at 12 h.p.i; the efficacy of the four siRNAs and their P value were highly significant. siRNA2 maintaining efficacy at 24, 36, and 48 h.p.i, while siRNA4 had a significant P value (≤0.0001) at 48 h.p.i. At 24 h.p.i, siRNA2 and siRNA4 showed statistical significance in viral knockdown of the virus's S gene and ORF1b gene by 95 %, 89 %, and 96 %, 97 %, respectively. Our computational method and experimental assessment of specific siRNAs have led us to conclude that siRNA2 and siRNA4 could be promising new therapies for SARS-CoV-2 that need further development.

Study on Gender-specific Population at Risk of Developing Dementia, Anxiety and Depression Following Exposure to COVID-19

Background

The identification of COVID-19 first occurred in January 2020. The rapid transmission of this virus across human populations has led to the emergence of a global pandemic known as COVID-19. Dementia, anxiety and depression are neurological disorders that impact several higher cognitive functions, such as memory, cognition, orientation, understanding, computation, learning ability, language and decision-making.

Purpose

This study aims to examine the impact of demographic factors on the occurrence of dementia, anxiety and depression in individuals who have recovered from a COVID-19 infection.

Methods

This study aims to investigate individuals who are at risk of developing dementia, anxiety and depression following exposure to COVID-19. Ethics Committee approval was obtained from hospital (Ethics Committee-Unique Hospital, Surat, India) and University Research Ethics Committee approval was obtained from Dehradun Institute of Technology University, Dehradun, India (DITU/UREC/2022/04/6). Patients willingly participated in the study and signed the ICF as per their preferred language. Patient data was obtained from the hospital with the assistance of medical staff. The study included patients who met the specific criteria for participation, as determined by the inclusion and exclusion criteria. Patients who satisfy the eligibility conditions were obligated to complete the questionnaire. The data was examined based on the subject's responses.

Results

Exposure to COVID-19 has been linked to a heightened susceptibility to developing mental health issues, such as anxiety, depression and even dementia. Studies have demonstrated that persons who have acquired COVID-19 are more prone to developing various psychiatric disorders in comparison to those who have not been infected. Individuals with dementia encountered a decline in cognitive function and a rise in neuropsychiatric symptoms, including restlessness, confusion, irritability and lack of motivation, amidst the epidemic. Research has indicated that persons experiencing mild cognitive impairment or dementia exhibited elevated levels of despair and anxiety amongst the epidemic.

Conclusion

In this research study on the gender-specific effects of COVID-19 exposure on high-risk persons, development of dementia, anxiety and depression offers important new insights into the complex ways that the pandemic has affected mental health in different genders.

The relationship between ferroptosis and respiratory infectious diseases: a novel landscape for therapeutic approach

Respiratory infectious diseases, particularly those caused by respiratory viruses, have the potential to lead to global pandemics, thereby posing significant threats to public and human health. Historically, the primary treatment for respiratory bacterial infections has been antibiotic therapy, while severe cases of respiratory viral infections have predominantly been managed by controlling inflammatory cytokine storms. Ferroptosis is a novel form of programmed cell death that is distinct from apoptosis and autophagy. In recent years, Recent studies have demonstrated that ferroptosis plays a significant regulatory role in various respiratory infectious diseases, indicating that targeting ferroptosis may represent a novel approach for the treatment of these conditions. This article summarized the toxic mechanisms underlying ferroptosis, its relationship with respiratory infectious diseases, the mechanisms of action, and current treatment strategies. Particular attentions were given to the interplay between ferroptosis and Mycobacterium tuberculosis, Epstein-Barr virus, severe acute respiratory syndrome coronavirus-2, Pseudomonas aeruginosa, dengue virus, influenza virus and herpes simplex virus type1infection. A deeper understanding of the regulatory mechanisms of ferroptosis in respiratory infections will not only advance our knowledge of infection-related pathophysiology but also provide a theoretical foundation for the development of novel therapeutic strategies. Targeting ferroptosis pathways represents a promising therapeutic approach for respiratory infections, with significant clinical and translational implications.

Ethical challenges in conducting research in low and middle income setting during public health emergencies: a qualitative evidence of a COVID-19 pandemic: the experience of Iran

BACKGROUND

Every minute during an epidemic is important and research in such conditions is for the benefit of the society. Considering that identifying experiences is a way to prevent repeated mistakes and prepare people to face crisis situations, this study aimed to explain participants' experiences of ethical challenges encountered in conducting research related to Covid-19 in Iran.

METHOD

This qualitative study was carried out using conventional content analysis for 2 years from March 2020 to March 2022 in Tehran, Iran. A number of 30 people were selected in a purposeful method and information was obtained through semi-structured interviews. The participants in the study were people with positions including members of institutional and national research ethics committees, researchers, clinicians, university hospitals managers during the COVID-19 pandemic. The method of data analysis in this study was conventional content analysis using the Graneheim and Lundman method.

RESULTS

Participants' experiences on ethical challenges were explained through three themes: "substantive ethical values principles", "the Research Environment", "Research Governance and Management".

CONCLUSION

This study examines ethical challenges in COVID-19 research across three domains: values, environment, and research governance. The results suggest the need to develop crisis-specific ethical frameworks, strengthen research ethics infrastructure and training, and establish more transparent standards and oversight systems. These findings could be useful in refining ethical policies and managing future crises.

Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus

Prompt determination of the etiological agent is important in an outbreak of pathogens with pandemic potential, particularly for dangerous infectious diseases. Molecular genetic methods allow for arriving at an accurate diagnosis, employing timely preventive measures, and controlling the spread of the disease-causing agent. In this study, whole-genome sequencing of three SARS-CoV-2 strains was performed using the Sanger method, which provides high accuracy in determining nucleotide sequences and avoids errors associated with multiple DNA amplification. Complete nucleotide sequences of samples, KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 were obtained, with sizes of 29.751 bp, 29.815 bp, and 29.840 bp, respectively. According to the COVID-19 Genome Annotator, 127 mutations were detected in the studied samples compared to the reference strain. The strain KAZ/Britain/2021 contained 3 deletions, 7 synonymous mutations, and 27 non-synonymous mutations, the second strain KAZ/B1.1/2021 contained 1 deletion, 5 synonymous mutations, and 31 non-synonymous mutations, and the third strain KAZ/Delta020/2021 contained 1 deletion, 5 synonymous mutations, and 37 non-synonymous mutations, respectively. The variations C241T, F106F, P314L, and D614G found in the 5' UTR, ORF1ab, and S regions were common to all three studied samples, respectively. According to PROVEAN data, the loss-of-function mutations identified in strains KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 include 5 mutations (P218L, T716I, W149L, R52I, and Y73C), 2 mutations (S813I and Q992H), and 8 mutations (P77L, L452R, I82T, P45L, V82A, F120L, F120L, and R203M), respectively. Phylogenetic analysis showed that the strains studied (KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021) belong to different SARS-CoV-2 lineages, which are closely related to samples from Germany (OU141323.1 and OU365922.1), Mexico (OK432605.1), and again Germany (OV375251.1 and OU375174.1), respectively. The nucleotide sequences of the studied SARS-CoV-2 virus strains were registered in the Genbank database with the accession numbers: ON692539.1, OP684305, and OQ561548.1.

Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr

Targeting the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 with small molecules is a promising therapeutic strategy against COVID-19, but potent and safe inhibitors are lacking. HeE1-2Tyr, a nonnucleoside inhibitor of Dengue virus RdRp, was also shown to inhibit SARS-CoV-2 RdRp in vitro and to have antiviral activity in cells, but the underlying mechanism remains unclear. Here, we elucidate the molecular mechanism of HeE1-2Tyr-mediated SARS-CoV-2 RdRp inhibition. Biochemical assays confirm that HeE1-2Tyr inhibits RdRp with an IC50 of 5 µM and show that it competes with RNA binding to RdRp in vitro. Structural analysis using cryo-EM reveals that a stack of three HeE1-2Tyr molecules binds to the RNA binding site of RdRp. The identification of the conserved HeE1-2Tyr binding site and its intriguing inhibition mechanism of three stacked molecules that outcompete RNA may facilitate further development of pan-corona nonnucleoside inhibitors.

Comprehensive Analysis of Potential Common Pathogenic Mechanisms for COVID-19 Infection and Gastric Cancer

A growing body of data suggests that the prevalence of COVID-19 pneumonia in patients with stomach cancer is much higher than in the general population. However, these mechanisms are still not fully understood. After a thorough examination of shared differentially expressed genes (DEGs) for gastric cancer (GC) and COVID-19 pneumonia, we performed functional annotation, protein-protein interaction (PPI) networks, module design, and pivot gene identification. qPCR was used to verify the expression of hub genes in GC. Finally, a pivotal gene transcription factor-gene regulatory network was created and validated. According to functional enrichment analysis, common genes are mainly enriched in biological processes such as extracellular matrix tissue and extracellular structural tissue. Finally, five genes were found to be pivotal genes in the pathogenesis of GC and COVID-19 pneumonia: BGN (biglycan), UBE2C (ubiquitin-conjugating enzymes 2C), SPP1 (secreted phosphoprotein 1), THBS2 (thrombospondin 2), and COL1A1 (type I collagen alpha 1). These shared pathways and pivotal genes could provide new insights for more mechanistic studies.

A rapid ecologic analysis, confirmed by a case-control study, identifies class I HLA alleles correlated to the risk of COVID-19

BACKGROUND

Several studies suggest that the heterogeneous spread of SARS-CoV-2 pandemics started on December 2019 could be partially upheld by the prevalence of permissive class I HLA alleles in specific populations. Such HLA alleles are in fact unable to shape an efficient anti-viral immune-response in the hosts or sustain an exaggerated inflammatory T cell mediated response responsible for the COVID-19 disease. We previously reported an ecologic correlation between the risk of COVID-19 spreading across Italy and the germinal expression of permissive HLA-C*01 and -B*44 alleles in specific inter and intraregional populations along the first spreading wave.

METHODS

Considering that SARS-CoV-2 has undergone multiple adaptative mutations since the beginning of pandemics related to a natural immunization and to the worldwide campaign of anti-SARS-CoV-2 vaccination, we have carried out further analyses to evaluate whether the predictive value of class I HLA-allele gene prevalence and COVID-19 incidence has changed with time along the first four pandemics spreading waves in Italy. To this purpose we carried out an ecologic study followed by a case-control study.

RESULTS

| Our data revealed that the direct correlation of HLA-C*01, and HLA-B*44 gene expression and COVID-19 risk was completely lost just after the first pandemics wave in Italy. On the contrary, the expression of HLA-B*49 allele in specific populations emerged as inversely correlated to the risk of COVID-19 and could be considered as a protective factor. The statistical significance of this correlation was progressively enforced in each subsequent spreading wave until February 2022. The following case-control study in the two Regions of Campania and Calabria in Italy confirmed the protective value of HLA-B*49 allele gene expression (OR = 0.289; p = 0.041), although statistical significance is lost after adjustment by logistic regression model. The analysis also detected multiple class I HLA-alleles whose expression was strongly correlated with COVID-19 risk: HLA-B*08 (ORadj = 3.193; p = 0.015); -B*14:01 (ORadj = 3.596; p = 0.018); -B*15:01 (ORadj = 5.124; p = 0.001); -B*35 (ORadj = 2.972; p = 0.002).

CONCLUSIONS

Our study not only identifies specific HLA alleles related to COVID-19 risk but also exemplifies a rapid and inexpensive approach that can be used to identify individuals needing prioritization during vaccination campaigns.

Diabetes exacerbates SARS-CoV-2 replication through ineffective pulmonary interferon responses, delayed cell-mediated immunity, and disruption of leptin signaling

Comorbidities, including obesity and type 2 diabetes mellitus (T2DM), are associated with increased disease severity and mortality following SARS-CoV-2 infection. Here, we investigated virus-host interactions under the effects of these comorbidities in diet-induced obesity (DIO) and leptin receptor-deficient (T2DM) mice following infection with SARS-CoV-2. DIO mice, as well as their lean counterparts, showed limited susceptibility to SARS-CoV-2 infection. In contrast, T2DM mice showed exacerbated pulmonary SARS-CoV-2 replication and delayed viral clearance associated with down-regulation of innate and adaptative immune gene signatures, ineffective type I interferon response, and delayed SARS-CoV-2-specific cell-mediated immune responses. While T2DM mice showed higher and prolonged SARS-CoV-2-specific immunoglobulin isotype responses compared to their lean counterparts, neutralizing antibody levels were equivalent. By silencing the leptin receptor in vitro using a human alveolar epithelial cell line, we observed an increase in SARS-CoV-2 replication and type I interferons. Altogether, our data provides for the first time evidence that disruption of leptin receptor signaling leading to obesity and T2DM induces altered type I interferon and cell-mediated responses against SARS-CoV-2, mediating increased viral replication and delayed clearance. These data shed light on the alteration of the innate immune pathway in the lung using in-depth transcriptomic analysis and on adaptive immune responses to SARS-CoV-2 under T2DM conditions. Finally, this study provides further insight into this risk factor aggravating SARS-CoV-2 infection and understanding the underlying cellular mechanisms that could help identify potential intervention points for this at-risk population.

Hybrid Capture-Based Sequencing Enables Highly Sensitive Zoonotic Virus Detection Within the One Health Framework

Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized probe set consisting of 149,990 probes, targeting 663 viruses associated with humans and animals. The detection performance was initially assessed using viral reference materials in a background of human nucleic acids. Compared to standard metagenomic next-generation sequencing (mNGS), our method achieved substantial read enrichment, with increases ranging from 143- to 1126-fold, and enhanced detection sensitivity by lowering the limit of detection (LoD) from 103-104 copies to as few as 10 copies based on whole genomes. This method was further validated using infectious samples from both animals and humans, including bovine rectal swabs and throat swabs from SARS-CoV-2 patients across various concentration gradients. In both sample types, our hybrid capture-based sequencing method exhibited heightened sensitivity, increased viral genome coverage, and more comprehensive viral identification and characterization. Our method bridges a critical divide between diagnostic detection and genomic surveillance. These findings illustrate that our hybrid capture-based sequencing method can effectively enhance sensitivity to as few as 10 viral copies and genome coverage to >99% in medium-to-high viral loads. This dual capability is particularly impactful for emerging pathogens like SARS-CoV-2, where early detection and genomic characterization are equally vital, thereby addressing the limitations of metagenomics in the surveillance of emerging infectious diseases in complex samples.

Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target

Coronavirus fusion with and entry into the host cell depends on viral spike, which acts as a crucial component of viral infection. However, the lack of receptor-activated spike intermediate conformation has hindered a comprehensive understanding of spike-induced membrane fusion. Here, we captured an angiotensin-converting enzyme 2 (ACE2)-induced early fusion intermediate conformation (E-FIC) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike in which heptad repeat 1 (HR1) in S2 has ejected while S1 remains attached. This E-FIC can transition to the late FIC after S2' cleavage. Leveraging this discovery, we designed an E-FIC-targeted dual-functional antiviral protein, AL5E. AL5E effectively inactivated ACE2-using coronaviruses and inhibited their infection, outperforming a mono-functional antiviral in protecting animals against these coronaviruses. This study has identified the E-FIC and used it as a target for the development of a dual-functional antiviral for the prevention and treatment of ACE2-using coronavirus infection.

Neutrophils and COVID-19

Neutrophils are the first line of defense against pathogens, most effectively by forming Neutrophil Extracellular Traps (NETs). Neutrophiles are further classified into several subpopulations during their development, eliminating pathogens through various mechanisms. However, due to the chaotic and uncontrolled immune response, NETs are often severely resulting in tissue damage and lung infections. The uncontrolled and poorly acknowledged host response regarding the cytokine storm is one of the major causes of severe COVID-19 conditions. Specifically, the increased formation of low-density neutrophils (LDNs), together with neutrophil extracellular traps (NETs) is closely linked with the severity and poor prognosis in patients with COVID-19. In this review, we discuss in detail the ontogeny of neutrophils at different stages and their recruitment and activation after infections, focusing on SARS-CoV-2. In addition, this chapter summarized the research progress on potential targeted drugs (NETs and Cytokine inhibitors) for neutrophil medical therapy and hoped to provide reference for the development of related therapeutic drugs for critically ill COVID-19 patients.

VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog

Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.

GM-CBAM-ResNet: A Lightweight Deep Learning Network for Diagnosis of COVID-19

COVID-19 can cause acute infectious diseases of the respiratory system, and may probably lead to heart damage, which will seriously threaten human health. Electrocardiograms (ECGs) have the advantages of being low cost, non-invasive, and radiation free, and is widely used for evaluating heart health status. In this work, a lightweight deep learning network named GM-CBAM-ResNet is proposed for diagnosing COVID-19 based on ECG images. GM-CBAM-ResNet is constructed by replacing the convolution module with the Ghost module (GM) and adding the convolutional block attention module (CBAM) in the residual module of ResNet. To reveal the superiority of GM-CBAM-ResNet, the other three methods (ResNet, GM-ResNet, and CBAM-ResNet) are also analyzed from the following aspects: model performance, complexity, and interpretability. The model performance is evaluated by using the open 'ECG Images dataset of Cardiac and COVID-19 Patients'. The complexity is reflected by comparing the number of model parameters. The interpretability is analyzed by utilizing Gradient-weighted Class Activation Mapping (Grad-CAM). Parameter statistics indicate that, on the basis of ResNet19, the number of model parameters of GM-CBAM-ResNet19 is reduced by 45.4%. Experimental results show that, under less model complexity, GM-CBAM-ResNet19 improves the diagnostic accuracy by approximately 5% in comparison with ResNet19. Additionally, the interpretability analysis shows that CBAM can suppress the interference of grid backgrounds and ensure higher diagnostic accuracy under lower model complexity. This work provides a lightweight solution for the rapid and accurate diagnosing of COVD-19 based on ECG images, which holds significant practical deployment value.

Determining the best mathematical model for implementation of non-pharmaceutical interventions

At the onset of the SARS-CoV-2 pandemic in early 2020, only non-pharmaceutical interventions (NPIs) were available to stem the spread of the infection. Much of the early interventions in the US were applied at a state level, with varying levels of strictness and compliance. While NPIs clearly slowed the rate of transmission, it is not clear how these changes are best incorporated into epidemiological models. In order to characterize the effects of early preventative measures, we use a Susceptible-Exposed-Infected-Recovered (SEIR) model and cumulative case counts from US states to analyze the effect of lockdown measures. We test four transition models to simulate the change in transmission rate: instantaneous, linear, exponential, and logarithmic. We find that of the four models examined here, the exponential transition best represents the change in the transmission rate due to implementation of NPIs in the most states, followed by the logistic transition model. The instantaneous and linear models generally lead to poor fits and are the best transition models for the fewest states.

Decoding the SARS-CoV-2 infection process: Insights into origin, spread, and therapeutic approaches

Globally, over 768 million confirmed cases and 6.9 million deaths had been documented as of July 17, 2023. Coronaviruses have a relatively large RNA genome. As with other viruses, SARS-CoV-2 does have an envelope film produced from host cells that are assisted by virally encoded glycoproteins that are required for infectivity, immunological assault, and viral particle production. Although the intermediate source of origin and transmission to humans is unexplained, rapid transmission from human to human has been established. This review focuses on the mechanistic framework for understanding the SARS-CoV-2 viral infection. Additionally, it discusses the origins and implications of COVID-19 using direct quotations from the published scientific literature to avoid misinterpretation of this catastrophic event that resulted in a massive loss of human life and impact on the global economy. The current available information unfolds large number of topics related with COVID-19 and/or the coronavirus (SARS-CoV-2) responsible of the disease. This review article also delves into the multifaceted aspects of COVID-19 and SARS-CoV-2, with a specific focus on a controversial yet essential issue: the possible association between SARS-CoV-2's origin and aldose reductase, an enzyme known for its role in diabetic retinopathy. Exploring this connection holds utmost significance, offering valuable insights into COVID-19's pathogenesis and unlocking new avenues for therapeutic interventions. It is important to trace back the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19).

Torsional twist of the SARS-CoV and SARS-CoV-2 SUD-N and SUD-M domains

Coronavirus non-structural protein 3 (nsp3) forms hexameric crowns of pores in the double membrane vesicle that houses the replication-transcription complex. Nsp3 in SARS-like viruses has three unique domains absent in other coronavirus nsp3 proteins. Two of these, SUD-N (Macrodomain 2) and SUD-M (Macrodomain 3), form two lobes connected by a peptide linker and an interdomain disulfide bridge. We resolve the first complete x-ray structure of SARS-CoV SUD-N/M as well as a mutant variant of SARS-CoV-2 SUD-N/M modified to restore cysteines for interdomain disulfide bond naturally lost by evolution. Comparative analysis of all structures revealed SUD-N and SUD-M are not rigidly associated but rather have significant rotational flexibility. Phylogenetic analysis supports that the potential to form the disulfide bond is common across betacoronavirus isolates from many bat species and civets, but also one or both of the cysteines that form the disulfide bond are absent across isolates from bats and pangolins. The absence of these cysteines does not impact viral replication or protein translation.