Search Results (593)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has posed substantial health threats and triggered widespread global economic disruption. The nucleocapsid (N) protein of SARS-CoV-2 is not only a key structural protein but also instrumental in mediating the host immune response, contributing significantly to inflammation and viral pathogenesis. Due to its immunogenic properties, SARS-CoV-2 N protein also interacts with host factors associated with various pre-existing inflammatory conditions and may possibly contribute to the long-term symptoms suffered by some COVID-19 patients after recovery—known as long COVID. This review provides a comprehensive overview of recent advances in elucidating the biological functions of the N protein. In particular, it highlights the mechanisms by which the N protein contributes to host inflammatory responses and elaborates on its association with long COVID and pre-existing inflammatory disorders. Full article

The renin–angiotensin system (RAS) plays a central role in cardiovascular regulation and has gained prominence in the pathogenesis of Coronavirus Disease 2019 (COVID-19) due to the critical function of angiotensin-converting enzyme 2 (ACE2) as the entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin IV, but not angiotensin II, has recently been reported to enhance the binding between the viral spike protein and ACE2. To investigate the virological significance of this effect, we developed a single-round infection assay using SARS-CoV-2 viral-like particles expressing the spike protein. Our results demonstrate that while angiotensin II does not affect viral infectivity across concentrations ranging from 40 nM to 400 nM, angiotensin IV enhances viral entry at a low concentration but exhibits dose-dependent inhibition at higher concentrations. These findings highlight the unique dual role of angiotensin IV in modulating SARS-CoV-2 entry. In silico molecular docking simulations indicate that angiotensin IV was predicted to associate with the S1 domain near the receptor-binding domain in the open spike conformation. Given that reported plasma concentrations of angiotensin IV range widely from 17 pM to 81 nM, these levels may be sufficient to promote, rather than inhibit, SARS-CoV-2 infection. This study identifies a novel link between RAS-derived peptides and SARS-CoV-2 infectivity, offering new insights into COVID-19 pathophysiology and informing potential therapeutic strategies. Full article

Post-acute sequelae of COVID-19 have been associated with an elevated risk of thromboembolism and adverse cardiovascular events (CVEs). We aim to evaluate whether alterations in poorly studied hemostatic and endothelial proteins are associated with CVEs in patients previously admitted to the ICU and evaluated one year post-discharge. We carried out a cross-sectional study involving 63 COVID-19 patients previously admitted to the ICU one year post-discharge. Plasma levels of factor IX (coagulation factor), protein C, protein S (natural anticoagulant), and von Willebrand factor (VWF, an endothelial marker) were measured using a Luminex 200™ analyzer. Generalized linear models (GLMs) were used to assess the association of these coagulation proteins with CVEs and N-terminal pro-B-type natriuretic peptide (NT-proBNP). We found that lower levels of factor IX (p = 0.011), protein C (p = 0.028), and protein S (p = 0.008) were associated with CVEs one year after ICU discharge. Additionally, at the one-year follow-up, we found lower levels of factor IX (p = 0.002) and higher levels of VWF (p = 0.006) associated with higher levels of NT-proBNP, underscoring the involvement of both hemostatic imbalance and persistent endothelial dysfunction. Our findings revealed a gender-specific pattern of associations with NT-proBNP levels. These findings highlight the significant role of persistent hemostatic imbalance and endothelial dysfunction in the development of cardiovascular abnormalities among COVID-19 survivors discharged from the ICU. Full article

Background: SARS-CoV-2 booster vaccination remains essential to prevent severe COVID-19, particularly in vulnerable populations such as older adults. This study evaluated the durability and dynamics of immune responses following booster vaccination(s) in >65-year-old individuals and examined their association with protection against new infections. Methods: Immune responses were evaluated at 3, 9, and 15 months post-booster, measuring SARS-CoV-2-specific IgG antibodies against spike [IgG(S)] and nucleocapsid [IgG(N)] proteins, neutralizing activity against the Omicron BA.2 variant, and cellular immunity. A subset of participants was tested before booster administration. Regression analyses examined the influence of clinical and immunological factors—including a bivalent fourth dose—on infection risk over time. Results: Booster vaccination significantly enhanced IgG(S) and neutralizing capacity, peaking at 3 months. Although a decline was observed by 9 months, responses remained above baseline. Individuals with prior SARS-CoV-2 infection exhibited higher IgG(S) levels and neutralizing titers, and significantly lower reinfection rates (15%), compared to uninfected individuals. A fourth vaccine dose further increased IgG(S) levels. While neutralizing capacity was not consistently enhanced by the fourth dose, recipients experienced a lower rate of new infections. Immune trajectory analyses revealed that breakthrough infections elicited strong humoral responses comparable to those seen in previously infected individuals, highlighting the role of hybrid immunity. Conclusions: In older adults, booster vaccination induces durable immune responses, with hybrid immunity offering enhanced protection. A fourth dose boosts antibody levels and reduces infection risk, supporting its use in this high-risk group. Continued monitoring is needed to determine the long-term effectiveness of boosters, particularly against emerging variants. Full article

Elderly individuals infected with SARS-CoV-2 are at higher risk of developing cytokine storms and severe outcomes, yet specific biomarkers remain unclear. In this study, we investigated the alteration of primary bile acid metabolism in elderly patients with severe COVID-19 using untargeted metabolomics (n = 31), followed by targeted metabolomics to compare patients with disease progression (n = 16) to those without (n = 48). Significant reductions in chenodeoxycholic acid (CDCA) and glycochenodeoxycholic acid (GCDCA) levels were identified in severe cases, with GCDCA levels at admission correlating strongly with peak inflammatory markers. In vitro, CDCA, GCDCA, and their receptors, Farnesoid X Receptor (FXR) and Takeda G-protein-coupled receptor 5 (TGR5), effectively inhibited the inflammatory response induced by SARS-CoV-2. NOD-like receptor pathway, activated by SARS-CoV-2, may modulate inflammatory cytokines under the treatment of CDCA, GCDCA, and TGR5. CDCA and GCDCA levels at admission predicted disease progression, suggesting their potential as biomarkers for severe COVID-19 in the elderly and highlighting their regulatory role in inflammation, pointing to new therapeutic avenues. Full article

The study aimed to identify the variants of SARS-CoV-2 (Severe Acute Respiratory Syndrome related coronavirus-2) virus isolates within the window of March 2021 to February 2022 in Bangladesh and investigate their comparative mutational profiles, preferences and phylogenetics. After the collection of the sample specimen and RNA extraction, the genome was sequenced using Illumina COVID Seq, and NGS data analysis was performed in DRAGEN COVID Lineage software (version 3.5.9). Among the 96 virus isolates, 24 (25%) were from Delta (clade 21A (n = 21) and 21J (n = 3)) and 72 (75%) were from Omicron (clade 20A (n = 6) and 20B (n = 66)). In Omicron and Delta, substitutions were much higher than deletions and insertions. High-frequency nucleotide change patterns were similar (for C > T, and A > G) in both of the variants, but different in some (i.e., G > T, G > A). Preferences for specific amino acids over the other amino acids in substitutions and deletions were observed to vary in different proteins of these variants. Phylogenetic analysis showed that the most ancestral variants were from clade 21A and clade 20A, and then the other variants emerged. The study demonstrates noteworthy variations of Omicron and Delta in mutational pattern and preferences for amino acids and protein, and further study on their biological functional impact might unveil the reason behind their mutational strategies and behavioral changes. Full article

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for Coronavirus Disease 2019 (COVID-19), utilizes its spike protein to infect host cells. In addition to angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1), AXL acts as a spike protein receptor and mediates infection, especially in respiratory cells with low ACE2 expression. Angiotensin II (1–8) can be cleaved into shorter peptides within the biological system. Antibody-based binding assays showed that angiotensin II causes a two-fold increase in the binding between the spike protein and AXL, but not ACE2 or NRP1. While a longer peptide, angiotensin I (1–10), did not affect the spike–AXL binding, shorter lengths of angiotensin peptides exhibited enhancing effects. The C-terminal deletions of angiotensin II to angiotensin (1–7) or angiotensin (1–6) resulted in peptides with enhanced activity toward spike–AXL binding with a similar capacity as angiotensin II. In contrast, the N-terminal deletions of angiotensin II to angiotensin III (2–8) or angiotensin IV (3–8) as well as the N-terminal deletions of angiotensin (1–7) to angiotensin (2–7) or angiotensin (5–7) produced peptides with a more potent ability to enhance spike–AXL binding (2.7-fold increase with angiotensin IV). When valine was substituted for tyrosine at position 4 in angiotensin II or when tyrosine at position 4 was phosphorylated, spike–AXL binding was increased, suggesting that modifications to tyrosine trigger enhancement. Angiotensin IV also enhances spike protein binding to ACE2 and NRP1. Thus, angiotensin peptides may contribute to COVID-19 pathogenesis by enhancing spike protein binding and thus serve as therapeutic targets. Full article

At least three betacoronaviruses have spilled over from bats to humans and caused severe diseases, highlighting the threat of zoonotic transmission. Thus, it is important to enhance surveillance capabilities by developing tools capable of detecting a broad spectrum of bat-borne betacoronaviruses. Three monoclonal antibodies (mAbs) targeting the nucleocapsid (N) protein were generated using recombinant N proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The cross-reactivities of these mAbs were evaluated against a panel of betacoronaviruses. Sandwich ELISAs (sELISAs) were subsequently developed to detect bat-borne betacoronaviruses that have high zoonotic potential. Among the mAbs, 7A7 demonstrated the broadest cross-reactivity, recognizing betacoronaviruses from the Sarbecovirus, Merbecovirus and Hibecovirus subgenera. The first sELISA, based on mAbs 7A7 and 6G10, successfully detected N protein in all clinical swab samples from COVID-19 patients with cycle threshold (Ct) values < 25, achieving 75% positivity overall (12/16). Using this as a reference, a second sELISA was established by pairing mAb 7A7 with mAb 8E2, which binds to multiple merbecoviruses. This assay detected the N protein of two merbecoviruses, namely the human MERS-CoV and bat-borne HKU5-CoV, at high sensitivity and has a limit of detection (LOD) that is comparable to the first sELISA used successfully to detect COVID-19 infection. These broadly reactive mAbs could be further developed into rapid antigen detection kits for surveillance in high-risk populations with close contact with wild bats to facilitate the early detection of potential zoonotic spillover events. Full article

Severe acute respiratory syndrome coronavirus 2 has undergone several mutations since 2020, and novel variants continue to emerge to this day. The immune escape ability of the emerging mutants is enhanced and results in robust transmissibility. The neutralizing ability of the antibodies produced in the human body during previous infections is decreased against some of these mutants, which poses a severe challenge to the preventive and therapeutic effectiveness of vaccines and antibody drugs. The nucleocapsid protein is one of the main structural proteins of the coronavirus and plays an important role in the life cycle of the novel coronavirus. This protein is one of the key targets for drug development, and the first major step in drug development is to obtain pure nucleocapsid proteins. However, since nucleocapsid proteins have a nucleic acid-binding function and automatically undergo liquid–liquid phase separation and agglomeration, the purification of full-length nucleocapsids is challenging. In this context, a set of easy-to-operate processes was developed in this study for the purification of nucleocapsid proteins. Finally, a pure full-length nucleocapsid protein without nucleic acid contamination was obtained, which exhibited significantly enhanced accessibility for structural and functional virological studies, vaccine development, and related research applications. Further, the nucleic acid-binding domain of the nucleocapsid protein was targeted, and potential severe acute respiratory syndrome coronavirus 2 inhibitors were identified using virtual screening and biolayer interferometry technology. Notably, the eukaryotically expressed nucleocapsid protein demonstrated a significantly greater binding affinity for Light Green SF Yellowish (K_D = 119.7 nM) compared to that demonstrated by its prokaryotic counterpart (K_D = 19.9 × 10³ nM). The findings of this study suggest the importance of considering both protein source and post-translational modifications of the target proteins to be used in drug screening workflows. Therefore, this compound not only represents a novel therapeutic candidate for COVID-19 but also a critical tool for elucidating antiviral mechanisms. Full article

Vaccination with ChAdOx1 nCoV-19 is an important countermeasure to fight the COVID-19 pandemic. This vaccine enhances human immunoprotection against SARS-CoV-2 by inducing an immune response against the SARS-CoV-2 S protein. However, the immune-related genes induced by vaccination remain to be identified. This study employs feature ranking algorithms, an incremental feature selection method, and classification algorithms to analyze transcriptomic data from an experimental group vaccinated with the ChAdOx1 nCoV-19 vaccine and a control group vaccinated with the MenACWY meningococcal vaccine. According to different time points, vaccination status, and SARS-CoV-2 infection status, the transcriptomic data was divided into five groups, including a pre-vaccination group, ChAdOx1-onset group, MenACWY-onset group, ChAdOx1-7D group, and MenACWY-7D group. Each group contained samples with 13,383 RNA features and 1662 small RNA features. The results identified key genes that could indicate the efficacy of the ChAdOx1 nCoV-19 vaccine, and a classifier was developed to classify samples into the above groups. Additionally, effective classification rules were established to distinguish between different vaccination statuses. It was found that subjects vaccinated with ChAdOx1 nCoV-19 vaccine and infected with SARS-CoV-2 were characterized by up-regulation of HIST1H3G expression and down-regulation of CASP10 expression. In addition, IGHG1, FOXM1, and CASP10 genes were strongly associated with ChAdOx1 nCoV-19 vaccine efficacy. Compared with previous omics-driven studies, the machine learning algorithms used in this study were able to analyze transcriptome data faster and more comprehensively to identify potential markers associated with vaccine effect and investigate ChAdOx1 nCoV-19 vaccine-induced gene expression changes. These observations contribute to an understanding of the immune protection and inflammatory responses induced by the ChAdOx1 nCoV-19 vaccine during symptomatic episodes and provide a rationale for improving vaccine efficacy. Full article

The COVID-19 pandemic highlighted the need for rapid, cost-effective tools to monitor transmission and immune response. We developed two novel paper-based colorimetric biosensors using glutaraldehyde as a protein dye—its first use in this context. Glutaraldehyde reacts with amino groups to generate a brown color, enabling detection of SARS-CoV-2 antibodies. Wathman filter paper was functionalized with (3-aminopropyl)triethoxysilane (APTES) to immobilize virus-like particles (VLPs) and nucleocapsid protein (N-protein) as biorecognition elements. Upon incubation with antibody-containing samples, glutaraldehyde enabled colorimetric detection using RGB analysis in ImageJ software. Both sensors showed a linear correlation between antibody concentration and RGB values in buffer and serum. The VLP sensor responded linearly within the range of 1.0–20 µg/mL (green coordinate) in 500-fold diluted serum and the N-protein sensor from 1.0–40 µg/mL (blue coordinate) in 250-fold diluted serum. Both sensors demonstrated good selectivity, with glucose causing up to 18% interference. These biosensors represent a paradigm shift, as they provide a sensitive, user-friendly, and cost-effective option for semi-quantitative serological analysis. Furthermore, their versatility goes beyond the detection of SARS-CoV-2 antibodies and suggests broader applicability for various molecular targets. Full article

The COVID-19 pandemic has highlighted the complex interplay between the gut microbiota and systemic immune responses, particularly through the gut–lung axis. Disruptions in gut microbial diversity and function—commonly referred to as dysbiosis—have been increasingly implicated in the pathogenesis of SARS-CoV-2 infection. In this study, we assessed the gut bacteriome and permeability in SARS-CoV-2-infected patients using 16S sequencing and ELISA assays, respectively. We also measured blood inflammatory cytokines and fecal secretory IgA to evaluate systemic and mucosal immune responses. Significant alterations in both alpha and beta diversity metrics were observed in patients with COVID-19 (n = 79) and those with post-COVID-19 condition (n = 141) compared to the controls (n = 97). Differential abundance and taxonomic analyses revealed distinct microbial profiles in the infected groups. Increased plasma levels of IL-2, IL-6, IL-17A, IFN-γ, and zonulin were detected in patient samples. Some genera were elevated during acute infection, which was positively correlated with C-reactive protein, while Enterobacteriaceae and Escherichia-Shigella were associated with increased zonulin levels, indicating compromised intestinal barrier function. These findings suggest that gut dysbiosis may contribute to bacterial translocation and systemic inflammation. Overall, our results highlight the importance of the gut–lung axis and suggest that modulating the gut microbiota could support immune regulation in SARS-CoV-2 infection. Full article

Background and Objectives: Coronavirus disease 2019 (COVID-19) triggers a dysregulated host response that may culminate in refractory hypoxaemic shock. Whether veno-venous ECMO modifies the inflammatory cascade more effectively in COVID-19 than in other septic states, and how it compares with conventional ventilatory support for COVID-19, remains uncertain. We compared three groups: COVID-19 patients supported with ECMO (COVID-ECMO, n = 25), non-COVID-19 septic shock patients on ECMO (SEPSIS-ECMO, n = 19) and critically ill COVID-19 patients managed without ECMO (COVID-CONV, n = 74). Methods: This retrospective study (January 2018–January 2025) extracted demographic, laboratory and clinical data at baseline, 48 h and 72 h. The primary end-point was the 72 h change in SOFA score (ΔSOFA). The secondary end-points included the evolution of interleukin-6 (IL-6), C-reactive protein (CRP), D-dimer and ferritin; haemodynamic variables; and 28 day mortality. A post hoc inverse-probability-of-treatment weighting (IPTW) sensitivity analysis adjusted for between-group severity imbalances. Results: Baseline APACHE II differed significantly (29.5 ± 5.8 COVID-ECMO, 27.4 ± 6.1 SEPSIS-ECMO, 18.2 ± 4.9 COVID-CONV; p < 0.001). At 48 h, IL-6 fell by 51.8% in COVID-ECMO (−1 116 ± 473 pg mL⁻¹) versus 32.4% in SEPSIS-ECMO and 18.7% in COVID-CONV (p < 0.001). The ΔSOFA values at 72 h were −4.6 ± 2.2, −3.1 ± 2.5 and −1.4 ± 1.9, respectively (p < 0.001). ECMO groups achieved larger mean arterial pressure rises (+16.8 and +14.2 mmHg) and greater norepinephrine reduction than COVID-CONV. The twenty-eight-day mortality was 36.0% (COVID-ECMO), 42.1% (SEPSIS-ECMO) and 39.2% (COVID-CONV) (p = 0.88). Across all patients, IL-6 clearance correlated with ΔSOFA (ρ = 0.48, p < 0.001) and with vasopressor-free days (ρ = 0.37, p = 0.002). Conclusions: ECMO, regardless of aetiology, accelerates inflammatory-marker decline and organ failure recovery compared with conventional COVID-19 management, but survival advantage remains elusive. COVID-19 appears to display a steeper cytokine-response curve to ECMO than bacterial sepsis, suggesting phenotype-specific benefits that merit confirmation in prospective trials. Full article

Background/Objectives: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19), has rapidly evolved, giving rise to multiple Variants of Concern—including Alpha, Beta, Gamma, Delta, and Omicron—which emerged independently across different regions. Licensed COVID-19 vaccines primarily target the highly mutable spike protein, resulting in reduced efficacy due to immune escape by emerging variants. Previously, we developed a live attenuated Francisella tularensis LVS ΔcapB single-vector platform COVID-19 vaccine, rLVS ΔcapB/MN, expressing the conserved membrane (M) and nucleocapsid (N) proteins from the early SARS-CoV-2 WA-01/2020 strain. In this study, we evaluate the efficacy of rLVS ΔcapB/MN and an enhanced version, rLVS ΔcapB::RdRp/MN, which additionally expresses the conserved RNA-dependent RNA polymerase (RdRp) protein from the same strain, in a hamster model. Methods: Both vaccine candidates were administered orally or intranasally to golden Syrian hamsters (equal numbers of males and females) and evaluated against intranasal challenge with SARS-CoV-2 Delta (B.1.617.2-AY.1) and Omicron (BA.5) variants. Results: Vaccinated animals developed robust, TH1-biased IgG responses specific to the nucleocapsid protein. Following SARS-CoV-2 challenge, immunized hamsters exhibited reduced weight loss, lower oropharyngeal and lung viral titers, and improved lung pathology scores compared with unvaccinated controls. Conclusion: These findings support the potential of this universal vaccine to provide broad protection against current and future SARS-CoV-2 variants, with minimal need for updating. Full article

In Cali, Colombia, 405,689 COVID-19 cases were reported until March 2023, with 2463 complete genome sequences available for analysis. SARS-CoV-2 genomic data from Cali were analyzed to determine the prevalence of variants as well as the mutation frequencies. This study identified Nextstrain clades, Pango lineages, and specific mutations in key viral proteins. A total of 23 Nextstrain clades and 118 Pango lineages were detected, including variants of interest (Lambda, Mu) and variants of concern (Alpha, Gamma, Delta, Omicron). Analysis identified 2424 missense mutations, with notable frequencies in NSP3 (465), S (367), NSP2 (205), N (180), ORF3a (144), NSP12b (113), and NSP13 (108). The study also observed a high prevalence of simultaneous transmission of multiple variants. The COVID-19 epidemic waves in Cali were shaped more by social and economic dynamics than by the emergence of specific SARS-CoV-2 variants. These findings highlight the importance of context-specific public health interventions to mitigate future outbreaks effectively. Full article