Severe Acute Respiratory Syndrome Coronavirus Research Articles

Convalescent COVID-19 monocytes exhibit altered steady-state gene expression and reduced TLR2, TLR4 and RIG-I induced cytokine expression.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, can induce trained immunity in monocytes. Trained immunity is the result of metabolic and epigenetic reprogramming of progenitor cells leading to an altered inflammatory response to subsequent activation. To investigate the monocyte response 3-6months post SARS-CoV-2 infection, steady-state gene expression and innate immune receptor stimulation were investigated in monocytes from unvaccinated SARS-CoV-2 naïve individuals and convalescent COVID-19 participants. The differentially expressed genes (DEGs) identified were involved in the regulation of innate immune signalling pathways associated with anti-viral defence. COVID-19 participants who had experienced severe symptoms exhibited a larger number of DEGs than participants that had mild symptoms. Interestingly, genes encoding receptors that recognise SARS-CoV-2 RNA were downregulated. DDX58, encoding retinoic-acid inducible gene I (RIG-I), was downregulated which corresponded with a reduced response to RIG-I activation. Furthermore, toll-like receptor (TLR)1/2 and TLR4 activation also exhibited reduced cytokine secretion from convalescent COVID-19 monocytes. These data suggest that following SARS-CoV-2 infection, monocytes exhibit altered steady-state gene expression and reduced responsiveness to innate immune receptor activation. As both RIG-I and TLRs recognise components of SARS-CoV-2, this may lead to a moderated inflammatory response to SARS-CoV-2 reinfection in the months following the initial infection.

Co-administration of seasonal quadrivalent influenza and COVID-19 vaccines leads to enhanced immune responses to influenza virus and reduced immune responses to SARS-CoV-2 in naive mice.

The ongoing co-circulation of influenza viruses and severe acute respiratory disease coronavirus 2 (SARS-CoV-2) presents significant public health challenges. Vaccination is a pivotal tool to tackle infections and severe disease. Administering both the influenza and coronavirus disease 2019 (COVID-19) vaccines simultaneously could simplify vaccine delivery and is already practice in several countries. In this study, we assessed the protective efficacy and humoral immune responses elicited by concomitant administration of a quadrivalent influenza vaccine (QIV) and the Pfizer-BioNTech mRNA COVID-19 vaccine (BNT162b2) in naïve BALB/c mice. We included three ways of co-administration: a) both vaccines at contralateral limbs, b) both vaccines at ipsilateral limbs and c) admixture of the two vaccines before administration. The last regimen was included since it has been shown that the lipid nanoparticles used for mRNA vaccines can also have an adjuvant effect on protein-based antigens. Notably, co-administration of QIV and COVID-19 mRNA vaccine led to significantly higher hemagglutinin inhibiting (HAI) and binding antibody titers compared to QIV only vaccination, especially in the ipsilateral and admixed groups. Conversely, ipsilateral administration and administration of an admixed vaccine had a slightly negative impact on SARS-CoV-2 binding and neutralization titers. These findings support the hypothesis that the co-administration of QIV and COVID-19 mRNA vaccines can induce robust antibody responses, which are indicative of protective immune responses against both infectious agents.

A SARS-CoV-2 vaccine on an NIR-II/SWIR emitting nanoparticle platform.

The COVID-19 pandemic caused a global health crisis that resulted in millions of deaths. Effective vaccines have played central roles in curtailing the pandemic. Here, we developed a down-converting near-infrared IIb (NIR-IIb; 1500 to 1700 nanometers) luminescent, pure NaErF4@NaYF4 rare-earth nanoparticle (pEr) as vaccine carriers. The pEr nanoparticles were coated with three layers of cross-linked biocompatible polymers (pEr-P3; ~55 nanometers) and conjugated to the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Upon subcutaneous injection of the pEr-P3-RBD nanovaccine in mice, in vivo NIR-IIb imaging revealed active vaccine trafficking and migration to lymph nodes through lymphatic vessels. Two doses of the adjuvant-free vaccine elicited long-lasting (>7 months) high titers of serum viral neutralization antibody and anti-RBD immunoglobulin G, along with robust RBD-specific germinal center B cells and T follicular helper cells. We devised in vivo NIR-II molecular imaging of RBD-specific cells in lymph nodes, opening noninvasive assessments of vaccine-elicited immune responses longitudinally.

Pemphigus vulgaris post-coronavirus disease-19 infection: A case report and review of literature

Pemphigus vulgaris is an autoimmune blistering disorder caused by autoantibodies directed against desmogleins. Severe acute respiratory syndrome coronavirus 2 is known to trigger autoimmune skin reactions. We report a case of pemphigus vulgaris developing in a patient, around 35 days after the coronavirus disease-19 infection.

Concordance of maternal and cord blood SARS-COV-2 immunoglobulin seropositivity after COVID-19 infection or vaccination in pregnancy

Objective To assess maternal antibody response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection during pregnancy and subsequent transplacental antibody transfer in cord blood. Study Design This is a prospective cohort study of Coronavirus Disease 2019 (COVID-19) polymerase chain reaction (PCR) positive pregnant women and their newborns. SARS-CoV-2 PCR (+) women were enrolled, with SARS-CoV-2 PCR (−) as control. Maternal blood was obtained at enrollment and cord blood collected at delivery. Baseline maternal and infant characteristics and neonatal outcomes were collected. Samples were analyzed using coronavirus antigen microarray containing immunologically significant antigens from SARS-CoV-2 (including nucleocapsid protein [NP], spike protein [S], S1, S2, receptor-binding domain [RBD]) which can detect SARS-CoV-2 immunoglobulin G (IgG) and immunoglobulin M (IgM). Results Thirty-seven maternal-cord blood paired samples were analyzed for SARS-CoV-2 IgG or IgM antibodies; 15 out of 20 samples from SARS-CoV-2 PCR (+) and 14 out of 17 from SARS-CoV-2 PCR (−) mothers were IgG positive. 14 out of the 17 SARS-CoV-2 PCR (−) mothers received COVID-19 vaccine during pregnancy. Difference between IgG seropositivity of naturally infected versus vaccinated mothers were significant, 75% versus 100% ( p = 0.043). IgM antibodies were detected in 10 out of 20 SARS-CoV-2 PCR (+) women but none were detected in cord blood. Conclusions Excellent concordance of SARS-CoV-2 IgG antibodies exist between maternal and cord blood. Significantly higher SARS-COV-2 cord blood IgG seropositivity was found in vaccinated versus naturally infected mothers.

Evaluation of SARS-CoV-2 Antibody Response Between Paired Fingerprick (HemaPEN®) and Venepuncture Collected Samples in Children and Adults

Serological surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies is important to monitor population COVID-19 immunity. Dried blood spots (DBS) are a valuable method for serosurveys, particularly in remote settings and in children. We compared the measurement of SARS-CoV-2 spike-specific IgG in paired blood samples collected using standard venepuncture (serum) and the hemaPEN® microsampling DBS device from children and adults. A total of 83 participants (10 months to 65 years of age), comprising COVID-positive and -negative participants, were recruited. Paired serum and DBS samples were assayed for SARS-CoV-2 receptor-binding domain (RBD) and Spike (S1) antibodies using an established in-house ELISA. RBD and S1 IgG concentrations of paired hemaPEN DBS eluates and serum samples were compared using a non-parametric Wilcoxon matched-pairs signed ranked test. A Pearson’s correlation was used for RBD and S1 IgG concentrations and the level of agreement between the hemaPEN DBS eluates and serum samples was assessed by Bland–Altman analysis. A total of N = 41 adults (36 COVID-positive and 5 COVID-negative), and N = 42 children (37 COVID-positive, and 5 COVID-negative) have paired serum and DBS assayed. We found moderate to strong correlations between paired hemaPEN DBS eluates and serum SARS-CoV-2 IgG antibodies for RBD (r = 0.9472, p < 0.0001) and S1 proteins (r = 0.6892, p < 0.0001). Similar results were observed in both adult and paediatric populations. No significant differences in S1-specific IgG levels were observed in hemaPEN DBS samples stored for up to 35 weeks at room temperature. Eluted hemaPEN samples showed high specificity and sensitivity (100% and 89.89%, respectively) compared with serum. The use of the microsampling hemaPEN device for DBS sample collection is a feasible approach for assessing SARS-CoV-2 antibodies for serosurveillance studies, particularly in remote settings and in children.

Differential protection against SARS-CoV-2 reinfection pre- and post-Omicron.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved over short timescales, leading to the emergence of more transmissible variants such as Alpha and Delta1-3. The arrival of the Omicron variant marked a major shift, introducing numerous extra mutations in the spike gene compared with earlier variants1,2. These evolutionary changes have raised concerns regarding their potential impact on immune evasion, disease severity and the effectiveness of vaccines and treatments1,3. In this epidemiological study, we identified two distinct patterns in the protective effect of natural infection against reinfection in the Omicron versus pre-Omicron eras. Before Omicron, natural infection provided strong and durable protection against reinfection, with minimal waning over time. However, during the Omicron era, protection was robust only for those recently infected, declining rapidly over time and diminishing within a year. These results demonstrate that SARS-CoV-2 immune protection is shaped by a dynamic interaction between host immunity and viral evolution, leading to contrasting reinfection patterns before and after Omicron's first wave. This shift in patterns suggests a change in evolutionary pressures, with intrinsic transmissibility driving adaptation pre-Omicron and immune escape becoming dominant post-Omicron, underscoring the need for periodic vaccine updates to sustain immunity.

Analogs of NIH Molecular Probe ML283 Are Potent SARS-CoV-2 Helicase Inhibitors.

The National Institutes of Health molecular probe ML283 was synthesized as a potent, selective inhibitor of the helicase encoded by the hepatitis C virus. Because modeling with AutoDock Vina predicted that ML283 might bind the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nonstructural protein 13 (nsp13) helicase, the effects of a collection of ML283 analogs and other hepatitis C virus (HCV) helicase inhibitors on the SARS-CoV-2 helicase were analyzed. Only modest impacts on nsp13-catalyzed ATP hydrolyses were observed with some compounds, most of which were analogs of the drug ebselen, not ML283. In contrast, a new molecular-beacon-based helicase assay revealed that ML283 and many ML283 analogs are potent SARS-CoV-2 helicase inhibitors. Analog potencies correlate with the binding energies predicted by modeling, which suggests that a pocket surrounded by the carboxy-terminal nsp13 RecA-like helicase motor domain might be exploitable for antiviral drug development.

Serology supportive of recent coxsackievirus B infection is correlated with multisystem inflammatory syndrome in children (MIS-C).

Rarely, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will lead to myocarditis associated with multisystem inflammatory syndrome in children (MIS-C). It remains unclear why MIS-C only targets specific children. To explore an association between coxsackievirus infections with MIS-C, we investigated the sero-epidemiology of CV in admitted pediatric patients in relation to the pandemic. This retrospective case-control study was performed by chart review of children (age ≤21 years) admitted to a tertiary care hospital with CV serological testing from January 2017 to August 2023. Clinical, laboratory, and imaging findings were used to classify patients as MIS-C and CV-unlikely or CV-possible for non-MIS-C patients. Out of 182 admissions (179 patients, median age, 6), CVB complement fixation (CF) assay on serotypes B1-B6 and CVA immunofluorescence assay IgG on serotypes A7, A9, A16, and A24 were positive in at least one serotype in 59.2% and 80.7% of cases, respectively. We observed a significant drop in CVB CF seropositivity during the peak of social distancing in 2020. The likelihood of elevated CVB CF titers was significantly higher in MIS-C than the CV-unlikely group (OR: 1.92, 95% CI: 1.02-3.63, P: 0.04) and showed a trend toward higher values in African Americans than Whites (OR: 1.57, 95% CI: 0.98-2.50, P: 0.057). The frequency of MIS-C was considerably higher in African Americans than Whites (18.1% versus 9%, P: 0.1). A higher likelihood of elevated CVB CF titers in patients with MIS-C compared with those unlikely to have acute CV infection along with a relatively higher frequency of MIS-C in African Americans warrants further investigation into the role of CVB infection in MIS-C development.IMPORTANCEThe emergence of multisystem inflammatory syndrome in children (MIS-C) during the SARS-CoV-2 pandemic raised major concerns in providers caring for children. This condition presents a hyper-inflammation state that can lead to severe complications, including myocarditis and cardiogenic shock. The pathogenesis of MIS-C has not been fully understood. Understanding the pathogenesis of this condition is not only important for developing effective treatments but also for applying preventive strategies. A two-hit hypothesis leading to MIS-C has been proposed. Coxsackievirus infections are prevalent during childhood and can also cause myocarditis, and coxsackievirus B specifically has been shown to cause persistent RNA presence in host cells, leading to continued inflammation. Herein, we show that elevated coxsackievirus B titers are associated with MIS-C cases, implying a role of successive infections with these viruses contributing to such a hyperinflammatory state. This study supports the need for larger investigations into this association.

Extubation of patients with COVID-19 acute respiratory failure during extracorporeal membrane oxygenation support is associated with improved survival

Aim: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19, infection resulting in acute respiratory distress syndrome (ARDS) requiring veno-venous or veno-arterial extracorporeal membrane oxygenation (VV or VA-ECMO) support is a life-threatening disease process that requires prolonged intubation and has a high risk of mortality. Methods: In this retrospective, observational, single-center cohort study, we attempt to better understand the role of extubation in the course of treatment by dichotomizing groups into those extubated early while remaining on ECMO treatment (group A), compared to patients who remained intubated for the entirety of their ECMO treatment (group B). Results: The data indicate that early extubation of patients with COVID-19-associated ARDS requiring ECMO support leads to improved survival rates for group A (93%) compared to prolonged intubation (group B) throughout the course of ECMO therapy (64%) (p = 0.13). Additionally, patients extubated earlier (19 days vs. 59 days; p = 0.012) required significantly fewer vasoactive drugs (norepinephrine dosing: 0.03 mcg/kg/min vs. 0.093 mcg/kg/min; p = 0.04), and were less likely to require a tracheostomy (0 vs. 4, p = 0.026). Conclusions: Although the utility of ECMO in severe ARDS patients remains a contentious topic, early extubation seems to increase survival rates and overall patient outcomes in patients with COVID-19-associated ARDS requiring ECMO support.

Dexamethasone in critical coronavirus disease-2019 cases: Insights from a cross-sectional study

Objective: The objective of the study is to describe the clinical and laboratory characteristics of critically ill coronavirus disease-2019 (COVID-19) patients treated with dexamethasone in an intensive care unit (ICU) to provide a support tool for clinical decision-making. Design: A survey was conducted among hospitalized patients from November 2020 to March 2021, with data collected through patient interviews, medical records, and laboratory tests. Setting: This is a large hospital serving as a reference center for COVID-19 care in Bahia, Brazil. Patients: A convenience sample of 22 patients admitted to the COVID-19 ICU who signed informed consent to participate in the study. Methods: A cross-sectional study of patients admitted to the ICU with COVID-19. Data were analyzed using statistical methods. Results: The most common comorbidities among patients were hypertension (54%), diabetes (36%), and cardiovascular disease (27%). Among the deaths recorded, 55% of patients had hypertension, 44% had diabetes and/or required insulin therapy, 33% had a history of cardiovascular disease (including atrial fibrillation and congestive heart failure), and 22% had a history of stroke. Renal dysfunction (elevated creatinine); liver function abnormalities (increased alanine aminotransferase and aspartate aminotransferase); and elevated levels of ferritin, fibrinogen, and D-dimer were identified as potential indicators of disease progression. Among these factors, only elevated creatinine demonstrated a statistically significant association with an increased mortality risk. Conclusion: These findings provide a better understanding of the clinical course of severe acute respiratory syndrome coronavirus 2 infections and suggest that laboratory medicine is crucial in supporting clinical decision-making and advancing scientific and healthcare knowledge during the early phases of the COVID-19 pandemic. Relevance for patients: Identifying key risk factors, such as renal dysfunction, can improve early intervention and personalized treatment for critically ill COVID-19 patients.

A Case of Post-Acute Severe Acute Respiratory Syndrome Coronavirus 2-Induced Focal Nonconvulsive Status Epilepticus With Impairment of Consciousness Initially Diagnosed as Anxiety.

A Case of Post-Acute Severe Acute Respiratory Syndrome Coronavirus 2-Induced Focal Nonconvulsive Status Epilepticus With Impairment of Consciousness Initially Diagnosed as Anxiety.

Transcriptomic profiles of monocyte-derived macrophages exposed to SARS-CoV-2 VOCs reveal immune-evasion escape driven by delta.

Since the breakout of COVID-19, the mutated forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have shown enhanced rates of transmission and adaptation to humans. The variants of concern (VOC), designated Alpha, Beta, Gamma, Delta, and Omicron emerged independent of one another, and in turn rapidly became dominant. The success of each VOC, as well as the virus fitness, were enabled by altered intrinsic functional properties and, reasonably, to virus antigenicity changes, conferring the ability to evade a primed immune response. We analysed the gene expression profiles of monocyte-derived macrophages (MDM) isolated from whole blood of healthy participants exposed to the 5 different SARS-CoV-2 VOC: D614G, Alpha (B.1.1.7), Gamma (P1), Delta (B.1.617.2), and Omicron BA.1 (B.1.1.529), and to the HCoV-OC43 strain, a coronavirus already present in the population before the SARS-CoV-2 pandemic. Whole transcriptome RNA-Seq, for both coding and non-coding RNAs, was then made. After exposure to the 5 VOC of MDM, we initially assessed the presence of the viral SARS-CoV-2 transcripts to confirm viral entry. We then analysed the RNA-Seq data and observed a significant deregulation of both coding and non-coding RNAs. In particular, our RNA-Seq analysis showed a significant up-regulation of several genes involved in different immunological processes, such as PARP9/PARP14 axes, in macrophages exposed to D614G, Alpha, and Gamma variants. Surprisingly, our data showed that macrophages exposed to the Delta variant exhibited a transcriptional profile more similar to the naïve control group, while macrophages exposed to the Omicron variant showed intermediate differentially expressed genes (DEGs) between the two groups. By checking the canonical markers for M1/M2 differentiation states, we did not observe any expression in macrophages exposed to the Delta variant, suggesting an M0 status, comparable to the naïve control group. Finally, we observed a significant deregulation of 3 main types of non-coding RNAs (ncRNAs): long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and small nucleolar RNAs (snoRNAs), some of which are common to coronaviruses, and some specific to SARS-CoV-2. The SARS-CoV-2-dependent alteration of the transcriptome of monocyte-derived macrophage (MDM)-infected cells can be linked to the chronological order of the variants' appearance in the human population. Our data suggest an evolution of VOC in modulating the host immune response, with a strong change in pace beginning with the advent of the Delta variant. MDMs exposed to Delta showed a failure in the activation of the adaptive immune response, and this correlates with the more severe symptoms developed by people affected with this SARS-CoV-2 variant.

Ocular neuroinflammatory response secondary to SARS-CoV-2 infection-a review

With the consistent occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the prevalence of various ocular complications has increased over time. SARS-CoV-2 infection has been shown to have neurotropism and therefore to lead to not only peripheral inflammatory responses but also neuroinflammation. Because the receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), can be found in many intraocular tissues, coronavirus disease 2019 (COVID-19) may also contribute to persistent intraocular neuroinflammation, microcirculation dysfunction and ocular symptoms. Increased awareness of neuroinflammation and future research on interventional strategies for SARS-CoV-2 infection are important for improving long-term outcomes, reducing disease burden, and improving quality of life. Therefore, the aim of this review is to focus on SARS-CoV-2 infection and intraocular neuroinflammation and to discuss current evidence and future perspectives, especially possible connections between conditions and potential treatment strategies.

Thyroid function during COVID-19 and post-COVID complications in adults: a systematic review

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has presented multifaceted health challenges. COVID-19 primarily targets the respiratory system but also affects multiple organ systems, including the endocrine system. Emerging evidence suggests interactions between thyroid function, the acute phase of COVID-19, and the prolonged symptoms known as post-COVID sequalae or long COVID. Several studies have reported that COVID-19 can induce thyroid dysfunction, leading to conditions such as thyroiditis and alterations in thyroid hormone levels. The mechanisms through which SARS-CoV-2 affects the thyroid include direct viral infection of thyroid cells, leading to viral thyroiditis, which causes inflammation and transient or sustained thyroid dysfunction, as well as an excessive systemic immune response (cytokine storm). This is associated with elevated levels of cytokines, such as IL-6, that disrupt thyroid function and lead to nonthyroidal illness syndrome (NTIS). Medications administered during the acute illness phase, such as corticosteroids and antiviral drugs, can also impact thyroid hormone actions. The involvement of the thyroid gland in long COVID, or postacute sequelae of SARS-CoV-2 infection, is an area not well defined, with potential implications for understanding and managing this condition. Persistent low-grade inflammation affecting thyroid function over time can lead to ongoing thyroiditis or exacerbate pre-existing thyroid conditions. Viral infections, including SARS-CoV-2, can trigger or worsen autoimmune thyroid diseases, such as Hashimoto’s thyroiditis and Graves’ disease. Long COVID may disrupt the hypothalamic–pituitary–adrenal (HPA) axis, which can, in turn, affect the hypothalamic-pituitary-thyroid (HPT) axis, leading to abnormal thyroid function. This review was designed to systematically capture recent literature on COVID-19-related thyroid dysfunction in the adult population, the prognostic consequences of thyroid dysfunction during COVID-19, and the effects of thyroid dysfunction on patients with long COVID. A comprehensive search of PubMed and EMBASE databases was conducted. The systematic review was performed based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Study quality was assessed using the Critical Appraisal Skills Programme (CASP). A total of 53 studies met the inclusion criteria. The review summarises recent findings and provides an update of the current understanding of thyroid dysfunction in COVID-19-related spectrum of disorders, underscoring the complex nature of SARS-CoV-2 infection and its far-reaching impacts on human health.

Tubular ER structures shaped by ER-phagy receptors engage in stress-induced Golgi bypass.

Cellular stresses, particularly endoplasmic reticulum (ER) stress induced by ER-to-Golgi transport blockade, trigger Golgi-independent secretion of cytosolic and transmembrane proteins. However, the molecular mechanisms underlying this unconventional protein secretion (UPS) remain largely elusive. Here, we report that an ER tubulovesicular structure (ER tubular body [ER-TB]), shaped by the tubular ER-phagy receptors ATL3 and RTN3L, plays an important role in stress-induced UPS of transmembrane proteins such as cystic fibrosis transmembrane conductance regulator (CFTR) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Correlative light-electron microscopy analyses demonstrate the formation of ER-TB under UPS-inducing conditions in HEK293 and HeLa cells. Individual gene knockdowns of ATL3 and RTN3 inhibit ER-TB formation and the UPS of trafficking-deficient ΔF508-CFTR. Combined supplementation of ATL3 and RTN3L induces ER-TB formation and UPS. ATL3 also participates in the SARS-CoV-2-associated convoluted membrane formation and Golgi-independent trafficking of SARS-CoV-2 spike protein. These findings suggest that ER-TB serves a common function in mediating stress-induced UPS, which participates in various physiological and pathophysiological processes.

A comparative analysis of the binary and multiclass classified chest X-ray images of pneumonia and COVID-19 with ML and DL models

Abstract Background The highly infectious coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, the seventh coronavirus. It is the longest pandemic in recorded history worldwide. Many countries are still reporting COVID-19 cases even in the fifth year of its emergence. Objective The performance of various machine learning (ML) and deep learning (DL) models was studied for image-based classification of the lungs infected with COVID-19, pneumonia (viral and bacterial), and normal cases from the chest X-rays (CXRs). Methods The K-nearest neighbour and logistics regression as the two ML models, and Visual Geometry Group-19, Vision transformer, and ConvMixer as the three DL models were included in the investigation to compare the brevity of the detection and classification of the cases. Results Among the investigated models, ConvMixer returned the best result in terms of accuracy, recall, precision, F1-score and area under the curve for both binary as well as multiclass classification. The pre-trained ConvMixer model outperformed the other four models in classifying. As per the performance observations, there was 97.1% accuracy for normal and COVID-19 + pneumonia-infected lungs, 98% accuracy for normal and COVID-19 infected lungs, 82% accuracy for normal + bacterial + viral infected lungs, and 98% accuracy for normal + pneumonia infected lungs. The DL models performed better than the ML models for binary and multiclass classification. The performance of these studied models was tried on other CXR image databases. Conclusion The suggested network effectively detected COVID-19 and different types of pneumonia by using CXR imagery. This could help medical sciences for timely and accurate diagnoses of the cases through bioimaging technology and the use of high-end bioinformatics tools.

Sociodemographic and Psychosocial Factors Influencing Coronavirus Disease 2019 Testing Uptake: Insights from Urban and Rural Communities in South Africa.

Access, demand, and acceptance of coronavirus disease 2019 (COVID-19) testing have varied globally. This study explored the sociodemographic and psychosocial risk factors that contribute to the uptake of COVID-19 testing in community settings in South Africa. This paper presents a cross-sectional secondary analysis using data from a cluster randomized controlled trial and a nested perception survey of COVID-19 antigen testing in communities located in urban (eThekwini, KwaZulu-Natal) and rural settings (Worcester, Eastern Cape) in South Africa. Individuals who were reluctant to get tested participated in the perception survey. Data were analyzed using descriptive statistics and multivariable logistic regression to assess linear associations and estimate adjusted odds ratios (ORs). The analysis was conducted on 3,074 individuals, of whom 2,509 (81.6%) provided consent for COVID-19 testing. Among those, 2,505 (81.5%) tested negative, and 4 (0.1%) tested positive for COVID-19. The mean age of participants was 38 (SD = 14.61), and 57% were male. Females (OR: 1.27; 95% CI = 1-1.6), individuals older than 56 years (OR: 1.95; 95% CI = 1.24-3.07), and those who were vaccinated (OR: 1.99; 95% CI = 1.53-2.60) were more likely to consent. Individuals who had previously tested positive for severe acute respiratory syndrome coronavirus 2 were less likely to consent to testing (OR: 0.64; 95% CI = 0.11-0.46). No link was found between depression, anxiety, substance use, and willingness to undergo COVID-19 testing. A perceptions survey involving 704 participants, which explored factors influencing testing willingness, found that older adults, and urban populations were less likely to undergo COVID-19 testing. Targeted health campaigns may improve testing rates. Larger-scale implementation research is required to explore best practices for improving testing rates and confidence in population-level detection within South Africa.

Single-cell transcriptomics reveals a compartmentalized antiviral interferon response in the nasal epithelium of mice.

Type III interferons (IFNs) primarily act on epithelial cells and protect against virus infection of the mucosa, whereas type I IFNs act more systemically. To date, it has been unknown which epithelial subtypes in the upper airways, the primary site for initial infection for most respiratory viruses, primarily rely on type III IFN or type I IFNs for antiviral protection. To address this question, we performed a single-cell transcriptomics analysis of the epithelial IFN-mediated response focusing on the upper airways of mice. This work identified nine distinct cell types derived from the olfactory epithelium and thirteen distinct cell types from the respiratory epithelium. Interestingly, type I IFNs induced a stronger antiviral transcriptional response than type III IFN in respiratory epithelial cells, whereas in olfactory epithelial cells, including sustentacular (SUS) and Bowman's gland cells (BGC), type III IFN was more dominant compared to type I IFN. SUS and BGC, which provide structural support and maintain the integrity of olfactory sensory neurons, were highly susceptible to infection with a mouse-adapted variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 MA20) but were protected against infection if the animals were prophylactically treated with type III IFN. These findings demonstrate a high degree of cell type heterogeneity in terms of interferon-mediated antiviral responses and reveal a potent role for type III IFNs in protecting the olfactory epithelium.IMPORTANCESARS-CoV-2 infects SUS and BGC in the olfactory epithelium, causing an impairment of structural support and integrity of olfactory sensory neurons that can result in severe olfactory dysfunctions. We observed an unexpected compartmentalization of the IFN-mediated transcriptional response within the airway epithelium, and we found that olfactory epithelial cells preferentially respond to type III IFN, which resulted in robust antiviral protection of SUS and BGC. Given the proximity of the olfactory epithelium to the central nervous system, we hypothesize that evolution favored a type III IFN-biased antiviral immune response in this tissue to limit inflammatory responses in the brain. Cell type-specific antiviral responses in the upper airways, triggered by the different types of IFNs, should be investigated in more detail and carefully taken into consideration during the development of IFN-based antivirals for clinical use.

Targeting pseudoknots with Cas13b inhibits porcine epidemic diarrhoea virus replication.

Clustered regularly interspaced short palindromic repeats-associated protein 13 (CRISPR-Cas13), an RNA editing technology, has shown potential in combating RNA viruses by degrading viral RNA within mammalian cells. In this study, we demonstrate the effective inhibition of porcine epidemic diarrhoea virus (PEDV) replication and spread using CRISPR-Cas13. We analysed the sequence similarity of the pseudoknot region between PEDV and severe acute respiratory syndrome coronavirus 2, both belonging to the Coronaviridae family, as well as the similarity of the RNA-dependent RNA polymerase (RdRp) gene region among three different strains of the PED virus. Based on this analysis, we synthesized three CRISPR RNAs (crRNAs) targeting the pseudoknot region and the nonpseudoknot region, each for comparison. In cells treated with crRNA #3 targeting the pseudoknot region, RdRp gene expression decreased by 95%, membrane (M) gene expression by 89% and infectious PEDV titre within the cells reduced by over 95%. Additionally, PED viral nucleocapsid (N) and M protein expression levels decreased by 83 and 98%, respectively. The optimal concentration for high antiviral efficacy without cytotoxicity was determined. Treating cells with 1.5 µg of Cas13b mRNA and 0.5 µg of crRNA resulted in no cytotoxicity while achieving over 95% inhibition of PEDV replication. The Cas13b mRNA therapeutics approach was validated as significantly more effective through a comparative study with merafloxacin, a drug targeting the pseudoknot region of the viral genome. Our results indicate that the pseudoknot region plays a crucial role in the degradation of the PEDV genome through the CRISPR-Cas13 system. Therefore, targeting Cas13b to the pseudoknot offers a promising new approach for treating coronavirus infections.