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We developed a 4-parameter clinical assay using Electric Field Induced Release and Measurement (EFIRM) technology to simultaneously assess SARS-CoV-2 RNA (vRNA), nucleocapsid antigen, host binding (BAb) and neutralizing antibody (NAb) levels from a drop of saliva with performance that equals or surpasses current EUA-approved tests. The vRNA and antigen assays achieved lower limit of detection (LOD) of 100 copies/reaction and 3.5 TCID₅₀/mL, respectively. The vRNA assay differentiated between acutely infected (n = 10) and infection-naïve patients (n = 33) with an AUC of 0.9818, sensitivity of 90%, and specificity of 100%. The antigen assay similarly differentiated these patient populations with an AUC of 1.000. The BAb assay detected BAbs with an LOD of 39 pg/mL and distinguished acutely infected (n = 35), vaccinated with prior infection (n = 13), and vaccinated infection-naïve patients (n = 13) from pre-pandemic (n = 81) with AUC of 0.9481, 1.000, and 0.9962, respectively. The NAb assay detected NAbs with a LOD of 31.6 Unit/mL and differentiated between COVID-19 recovered or vaccinated patients (n = 31) and pre-pandemic controls (n = 60) with an AUC 0.923, sensitivity of 87.10%, and specificity of 86.67%. Our combo assay represents a significant technological advancement to simultaneously address SARS-CoV-2 infection and immunity, and it lays the foundation for tackling potential future pandemics.

The COVID-19 pandemic and ensuing lockdowns led to sweeping changes in the everyday lives of children and families, including school closures, remote work and learning, and social distancing. To date no study has examined whether these profound changes in young childrens day to day social interactions impacted the development of social cognition skills in early childhood. To address this question, we compared the performance of two cohorts of 3.5- to 5.5-year-old children tested before and after the COVID-19 lockdowns on several measures of false-belief understanding, a critical social cognition skill that undergoes important developments in this age range. Controlling for age and language skills, children tested after the pandemic demonstrated significantly worse false-belief understanding than those tested before the pandemic, and this difference was larger for children from lower socioeconomic status (SES) backgrounds. These results suggest that the pandemic negatively impacted the development of social cognition skills in early childhood, especially for lower SES children.

The effects of the COVID-19 pandemic on comprehensive maternal deaths in Brazil have not been fully explored. Using publicly available data from the Brazilian Mortality Information (SIM) and Information System on Live Births (SINASC) databases, we used two complementary forecasting models to predict estimates of maternal mortality ratios using maternal deaths (MMR) and comprehensive maternal deaths (MMRc) in the years 2020 and 2021 based on data from 2008 to 2019. We calculated national and regional standardized mortality ratio estimates for maternal deaths (SMR) and comprehensive maternal deaths (SMRc) for 2020 and 2021. The observed MMRc in 2021 was more than double the predicted MMRc based on the Holt-Winters and autoregressive integrated moving average models (127.12 versus 60.89 and 59.12 per 100,000 live births, respectively). We found persisting sub-national variation in comprehensive maternal mortality: SMRc ranged from 1.74 (95% confidence interval [CI] 1.64, 1.86) in the Northeast to 2.70 (95% CI 2.45, 2.96) in the South in 2021. The observed national estimates for comprehensive maternal deaths in 2021 were the highest in Brazil in the past three decades. Increased resources for prenatal care, maternal health, and postpartum care may be needed to reverse the national trend in comprehensive maternal deaths.

COVID-19 is associated with increased risk for cognitive decline but very little is known regarding the neural mechanisms of this risk. We enrolled 49 adults (55% female, mean age = 30.7 ± 8.7), 25 with and 24 without a history of COVID-19 infection. We administered standardized tests of cognitive function and acquired brain connectivity data using MRI. The COVID-19 group demonstrated significantly lower cognitive function (W = 475, p

With over 16 million submitted genomic sequences, the SARS-CoV-2 (SC2) virus, the cause of the most recent worldwide COVID-19 pandemic, has become the most sequenced genome of all known viruses, revealing, for example, a vast number of expanding viral lineages. Since the pandemic phase appears to be over, we performed a retrospective re-examination of the demographic grouping pattern and their genomic characteristics during the entire pandemic period up to the peak of the last pandemic wave. For our study, we extracted from the NCBI only unique viral sequences and converted each sequence data to a relational vector, indicating the presence/absence of each variational event compared to a reference sequence. Our study revealed several genomic features that are unexpected or different from those of previous studies. For example, approximately 44,000 variants with unique sequences emerged during the pandemic period; they group into only four major viral-genomic groups and each has a set of mostly unique highly-conserved variant-genotypes (HCVGs); and a small set from the first (ancestral) group was inherited by the three (descendant) groups, suggesting that HCVGs in the next group may be predictable from the current group(s). Such a concept may be potentially important in designing panvalent vaccines against the current and future waves of viral infections.

COVID-19 infection is associated with a variety of vascular occlusive morbidities. However, a comprehensive understanding of how this virus can induce vascular complications remains lacking. Here, we show that a peptide fragment of SARS-CoV-2 spike protein, S192 (sequence 192-211), is capable of forming amyloid-like aggregates that can induce agglutination of red blood cells, which was not observed with low- and non-aggregated S192 peptide. We subsequently screened eight amyloid-binding molecules and identified BAM1-EG6, a benzothiazole amphiphile, as a promising candidate capable of binding to aggregated S192 and partially inhibiting its agglutination activity. These results provide new insight into a potential molecular mechanism for the capability of spike protein metabolites to contribute to COVID-19-related blood complications and suggest a new therapeutic approach for combating microvascular morbidities in COVID-19 patients.

Across the world, the officially reported number of COVID-19 deaths is likely an undercount. Establishing true mortality is key to improving data transparency and strengthening public health systems to tackle future disease outbreaks. In this study, we estimated excess deaths during the COVID-19 pandemic in the Pune region of India. Excess deaths are defined as the number of additional deaths relative to those expected from pre-COVID-19-pandemic trends. We integrated data from: (a) epidemiological modeling using pre-pandemic all-cause mortality data, (b) discrepancies between media-reported death compensation claims and official reported mortality, and (c) the wisdom of crowds public surveying. Our results point to an estimated 14,770 excess deaths [95% CI 9820-22,790] in Pune from March 2020 to December 2021, of which 9093 were officially counted as COVID-19 deaths. We further calculated the undercount factor-the ratio of excess deaths to officially reported COVID-19 deaths. Our results point to an estimated undercount factor of 1.6 [95% CI 1.1-2.5]. Besides providing similar conclusions about excess deaths estimates across different methods, our study demonstrates the utility of frugal methods such as the analysis of death compensation claims and the wisdom of crowds in estimating excess mortality.

A clear understanding of real-world uptake of nirmatrelvir-ritonavir for treatment of SARS-CoV-2 can inform treatment allocation strategies and improve interpretation of effectiveness studies. We used data from a large US healthcare system to describe nirmatrelvir-ritonavir dispenses among all SARS-CoV-2 positive patients aged ≥ 12 years meeting recommended National Institutes of Health treatment eligibility criteria for the study period between 1 January and 31 December, 2022. Overall, 10.9% (N = 34,791/319,900) of treatment eligible patients with SARS-CoV-2 infections received nirmatrelvir-ritonavir over the study period. Although uptake of nirmatrelvir-ritonavir increased over time, by the end of 2022, less than a quarter of treatment eligible patients with SARS-CoV-2 infections had received nirmatrelvir-ritonavir. Across patient demographics, treatment was generally consistent with tiered treatment guidelines, with dispenses concentrated among patients aged ≥ 65 years (14,706/63,921; 23.0%), and with multiple comorbidities (10,989/54,431; 20.1%). However, neighborhoods of lower socioeconomic status (upper third of neighborhood deprivation index [NDI]) had between 12% (95% CI: 7-18%) and 28% (25-32%) lower odds of treatment dispense over the time periods studied compared to the lower third of NDI distribution, even after accounting for demographic and clinical characteristics. A limited chart review (N = 40) confirmed that in some cases a decision not to treat was appropriate and aligned with national guidelines to use clinical judgement on a case-by-case basis. There is a need to enhance patient and provider awareness on the availability and benefits of nirmatrelvir-ritonavir for the treatment of COVID-19 illness.

The COVID-19 pandemic has burdened healthcare systems globally. To curb high hospital admission rates, only patients with genuine medical needs are admitted. However, machine learning (ML) models to predict COVID-19 hospitalization in Asian children are lacking. This study aimed to develop and validate ML models to predict pediatric COVID-19 hospitalization. We collected secondary data with 2200 patients and 65 variables from Malaysian aged 0 to 12 with COVID-19 between 1st February 2020 and 31st March 2022. The sample was partitioned into training, internal, and external validation groups. Recursive Feature Elimination (RFE) was employed for feature selection, and we trained seven supervised classifiers. Grid Search was used to optimize the hyperparameters of each algorithm. The study analyzed 1988 children and 30 study variables after data were processed. The RFE algorithm selected 12 highly predicted variables for COVID-19 hospitalization, including age, male sex, fever, cough, rhinorrhea, shortness of breath, vomiting, diarrhea, seizures, body temperature, chest indrawing, and abnormal breath sounds. With external validation, Adaptive Boosting was the highest-performing classifier (AUROC = 0.95) to predict COVID-19 hospital admission in children. We validated AdaBoost as the best to predict COVID-19 hospitalization among children. This model may assist front-line clinicians in making medical disposition decisions. [ABSTRACT FROM AUTHOR]

A substantial proportion of patients suffer from Post-COVID Syndrome (PCS) with fatigue and impairment of memory and concentration being the most important symptoms. We here set out to perform in-depth neuropsychological assessment of PCS patients referred to the Neurologic PCS clinic compared to patients without sequelae after COVID-19 (non-PCS) and healthy controls (HC) to decipher the most prevalent cognitive deficits. We included n = 60 PCS patients with neurologic symptoms, n = 15 non-PCS patients and n = 15 healthy controls. Basic socioeconomic data and subjective complaints were recorded. This was followed by a detailed neuropsychological test battery, including assessments of general orientation, motor and cognitive fatigue, screening of depressive and anxiety symptoms, information processing speed, concentration, visuomotor processing speed, attention, verbal short-term and working memory, cognitive flexibility, semantic and phonematic word fluency, as well as verbal and visual memory functions. Neurologic PCS patients had more complaints with significantly higher fatigue scores as well as higher levels of depressive and anxiety symptoms compared to Non-PCS and HC. Deep neuropsychological assessment showed that neurologic PCS patients performed worse in a general screening of cognitive deficits compared to HC. Neurologic PCS patients showed impaired mental flexibility as an executive subfunction, verbal short-term memory, working memory and general reactivity (prolonged reaction time). Multiple regression showed fatigue affected processing speed; depression did not. Self-reported cognitive deficits of patients with neurologic PCS including fatigue, concentration, and memory deficits, are well mirrored in impaired performance of cognitive domains of concentration and working memory. The present results should be considered to optimize treatment algorithms for therapy and rehabilitation programs of PCS patients with neurologic symptoms. [ABSTRACT FROM AUTHOR]

During the COVID-19 pandemic, heterologous vaccination strategies were employed to alleviate the strain on vaccine supplies. The Thailand Ministry of Health adopted these strategies using vector, inactivated, and mRNA vaccines. However, this approach has introduced challenges for SARS-CoV-2 sero-epidemiology studies. Our study analysed 647 samples from healthcare workers who received CoronaVac, ChAdOx1 nCoV-19, and BNT162b2 vaccines. The serological profile encompassed responses to various SARS-CoV-2 variants and vectors, measuring IgG, IgM, and IgA isotypes, alongside IgG avidity assays. The results demonstrated that heterologous CoronaVac/ChAdOx1 nCoV-19 schedules elicited significantly stronger antibody responses compared to homologous schedules (IgG: 1.2-fold, IgM: 10.9-fold, IgA: 3.1-fold increase). Additionally, a heterologous BNT162b2 boost at 4-weeks post-initial vaccination showed greater antibody levels than a ChAdOx1 nCoV-19 boost (IgG: 1.1-fold, IgM: slight decrease, IgA: 1.5-fold increase). Using a combination of three analytes, IgG against wild-type Spike trimer, nucleoprotein and Omicron receptor binding domains, enabled the clustering of responses within a statistical Gaussian mixture model that successfully discriminates between breakthrough infections and vaccination types (F-score = 0.82). The development of statistical models to predict breakthrough infections can improve serological surveillance. Overall, our study underscores the necessity for vaccine (re-)development and the creation of serological tools to monitor vaccine performance. [ABSTRACT FROM AUTHOR]

The ongoing emergence of SARS-CoV-2 variants, combined with antigen exposures from different waves and vaccinations, poses challenges in updating COVID-19 vaccine antigens. We collected 206 sera from individuals with vaccination-only, hybrid immunity, and single or repeated omicron post-vaccination infections (PVIs), including non-JN.1 and JN.1, and evaluated neutralization against omicron BA.5, BA.2.75, BQ.1.1, XBB.1.16, XBB.1.5, and JN.1. Neutralizing antibodies exhibited a narrow breadth against BA.5 and BA.2.75 and failed to neutralize BQ.1.1 and XBB lineages after three to five doses of the ancestral monovalent vaccine. Hybrid immunity elicited higher neutralizing titers than vaccination alone, but titers remained relatively low. A single omicron PVI elicited lower neutralization titers to all variants compared to wild-type (WT), indicating immunological imprinting. Repeated omicron PVIs, particularly JN.1, slightly mitigated these effects by increasing broad neutralization responses to all variants, though not significantly. Antigenic mapping demonstrated that XBB lineages and JN.1 are antigenically distant from WT and also evaded antibodies induced by earlier omicron variants (BA.1–5) PVIs. However, repeated JN.1 PVIs shortened this antigenic distance, indicating broader neutralization across omicron variants. These findings highlight SARS-CoV-2 immunity following various antigen boosts and the impact of repeated omicron JN.1 exposure on broad immunity, informing future COVID-19 vaccination strategies. [ABSTRACT FROM AUTHOR]

It has been hypothesized that the biopsychosocial stress associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, in combination with the immunological effects of SARS-CoV-2 and pancreatic β-cell dysfunction, may contribute to the onset of type 1 diabetes (T1D) in children. In this study, we documented the incidences of T1D in Yamanashi Prefecture, Japan, from 1986 to 2018, and expanded the analysis to include cases from 2019 to 2022 to evaluate the potential influence of coronavirus disease 2019 (COVID-19) on T1D incidence. The COVID-19 pandemic period was defined as 2020 to 2022. Data spanning from 1986 to 2022 were analyzed in annual increments, while data from 1987 to 2022 were analyzed in 3-year interval increments using Joinpoint regression analysis. Across all analyses, no joinpoints were identified, and a consistent linear increase was observed. These findings suggest that there was no statistically significant change in the incidence of T1D attributable to the COVID-19 pandemic in Yamanashi Prefecture. The annual increase in the incidence was calculated to be 3.384% per year, while the increase in the 3-year interval incidence was calculated to be 2.395% per year. Although the incidence of pediatric T1D among children aged 0–14 years in Yamanashi Prefecture increased during the COVID-19 pandemic (2020–2022), this trend appeared to be a continuation of the pre-2019 increase. The direct or indirect impact of COVID-19 on this trend could not be conclusively determined due to the limited number of cases included in this study. [ABSTRACT FROM AUTHOR]

The ongoing global pandemic caused by the SARS-CoV-2 virus has demanded the urgent search for effective therapeutic interventions. In response, our research aimed at identifying natural products (NPs) with potential inhibitory effects on the entry of the SARS-CoV-2 spike (S) protein into host cells. Utilizing the Protein Data Bank Japan (PDBJ) and BindingDB databases, we isolated 204 S-glycoprotein sequences and conducted a clustering analysis to identify similarities and differences among them. We subsequently identified 33,722 binding molecules (BMs) by matching them with the sequences of 204 S-glycoproteins and compared them with 52,107 secondary metabolites (SMs) from the KNApSAcK database to identify potential inhibitors. We conducted docking and drug-likeness property analyses to identify several SMs with potential as drug candidates based on binding energy (BE), no Lipinski's rule violation (LV), psychochemical properties within the pink area of the bioavailability radar, and a bioavailability score (BAS) not less than 0.55. Fourteen SMs were predicted through computational analysis as potential candidates for inhibiting the three major types of S proteins. Our study provides a foundation for further experimental validation of these compounds as potential therapeutic agents against SARS-CoV-2. [ABSTRACT FROM AUTHOR]

The heparan sulfate (HS)-rich extracellular matrix (ECM) serves as an initial interaction site for the homotrimeric spike (S) protein of SARS-CoV-2 to facilitate subsequent docking to angiotensin-converting enzyme 2 (ACE2) receptors and cellular infection. More recent variants, notably Omicron, have evolved by swapping several amino acids to positively charged residues to enhance the interaction of the S-protein trimer with the negatively charged HS. However, these enhanced interactions may reduce Omicron's ability to move through the HS-rich ECM to effectively find ACE2 receptors and infect cells, raising the question of how to mechanistically explain HS-associated viral movement. In this work, we show that Omicron S proteins have evolved to balance HS interaction stability and dynamics, resulting in enhanced mobility on an HS-functionalized artificial matrix. This property is achieved by the ability of Omicron S-proteins to cross-link at least two HS chains, allowing direct S-protein switching between chains as a prerequisite for cell surface mobility. Optimized HS interactions can be targeted pharmaceutically, as an HS mimetic significantly suppressed surface binding and cellular infection specifically of the Omicron variant. These findings suggest a robust way to interfere with SARS-CoV-2 Omicron infection and potentially future variants. [ABSTRACT FROM AUTHOR]

This manuscript details the application of Isothermal Titration Calorimetry (ITC) to characterize the kinetics of 3CLpro, the main protease from the Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2), and its inhibition by Ensitrelvir, a known non-covalent inhibitor. 3CLpro is essential for producing the proteins necessary for viral infection, which led to the COVID-19 pandemic. The ITC-based assay provided rapid and reliable measurements of 3CLpro activity, allowing for the direct derivation of the kinetic enzymatic constants KM and kcat by monitoring the thermal power required to maintain a constant temperature as the substrate is consumed. The manuscript highlights several advantages of the proposed ITC-based assay over traditional methods used to study 3CLpro, such as Förster Resonance Energy Transfer (FRET) and Liquid Chromatography-Mass Spectrometry (LC–MS) and overcomes the need for non-biological substrates or discontinuous post-reaction steps. The ease of application of the ITC method allowed for the determination of the temperature dependence of the catalytic constants, enabling the estimation of the reaction activation energy. Additionally, the assay was used to determine the inhibition mode and kinetic parameters for 3CLpro inhibition by Ensitrelvir. This molecule was revealed to act as a slow- and tight-binding inhibitor that forms an initial E•I complex (KI = 9.9 ± 0.7 nM) quickly transitioning to a tighter E•I* assembly (KI* = 1.1 ± 0.2 nM). This versatile calorimetric method is proposed for general use in the discovery and development of drugs targeting 3CLpro. [ABSTRACT FROM AUTHOR]

One of the most common post-COVID-19 condition is persistent fatigue, while post-COVID fatigue among Parkinson's disease (PD) patients is less known. This study was aimed to investigate the prevalence and risk factors of post-COVID fatigue in PD patients at 1 month and 12 months after symptom onset. PD patients attending clinic from December 2022 to January 2023 were enrolled consecutively in the study. All participants were assessed demographics, details of COVID-19 infection, clinical characteristics as well as fatigue status with Fatigue Severity Scale (FSS) (cutoff ≥ 36) at 1-month and 12-month after symptom onset. Univariate and multivariate Logistic regression analysis were used to evaluate the risk factors of post-COVID fatigue. Fatigue symptoms were reported by 75.89% of PD patients and associated with decreased physical activity and number of initial symptoms of COVID-19 at 1 month. Meanwhile, 32.99% of PD patients at 12 months reported persistent fatigue. Using of antiviral drugs, decreased physical activity, anxiety status and delayed ON were associated with persistent fatigue at 12 months. Clinically persistent fatigue was pervasive in our study at 12-month after COVID infection. These findings implicate using of antiviral drugs, decreased physical activity, anxiety status and delayed ON were possible predictors of post-COVID persistent fatigue. [ABSTRACT FROM AUTHOR]

This study examined the incidence, characteristics, and risk factors of new gastrointestinal disorders (GID) associated with SARS-CoV-2 infection up to 3.5 years post-infection. This retrospective study included 35,102 COVID-19 patients and 682,594 contemporary non-COVID-19 patients without past medical history of GID (controls) from the Montefiore Health System in the Bronx (3/1/2020 to 7/31/2023). Comparisons were made with unmatched and propensity-matched (1:2) controls. The primary outcome was new GID which included peptic ulcer, inflammatory bowel disease, irritable bowel syndrome, diverticulosis, diverticulitis, and biliary disease. Multivariate Cox proportional hazards model analysis was performed with adjustment for covariates. There were 2,228 (6.34%) COVID-19 positive patients who developed new GID compared to 38,928 (5.70%) controls. COVID-19 patients had an elevated risk of developing new GID (adjusted HR = 1.18 (95% CI 1.12–1.25) compared to propensity-matched controls, after adjusting for confounders that included smoking, obesity, diabetes, hypertension. These findings underscore the need for additional research and follow-up of at-risk individuals for developing GID post infection. [ABSTRACT FROM AUTHOR]

The Paneth cell, a secretory cell of the small intestine, expresses numerous host defense proteins, and is hypothesized to play an important role in host defense against infection. However, studying gene expression in this cell requires invasive procedures. To test the hypothesis that we could observe Paneth cell-specific gene regulation from exfoliated cells in infectious conditions, we obtained stool samples from patients with COVID-19 and uninfected controls. Total mRNA was isolated, and Paneth cell-specific and non-specific gene expression was quantified by RT-PCR. Results revealed a significant decrease in mRNA levels from Paneth cell-specific genes, including DEFA5, DEFA6, PLA2G2A, PRSS2 and ITLN2 in SARS-CoV-2 positive patients compared with controls. Other gut markers, not specific to Paneth cells were unchanged. To validate this experimentally, we infected mice with SARS-CoV-2 and collected fecal pellets over the course of 7 days. We observed a similar time-dependent reduction in Paneth cell-specific transcripts, which correlates with histological changes in the gut. This is the first demonstration of quantification of Paneth cell-specific transcripts without invasive sampling. It also shows the coordinate regulation of these genes as a response to infection with SARS-CoV-2, possibly through viral pathogenesis, to increase infectivity in the gut. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, the cause of COVID-19, primarily targets lung tissue, leading to pneumonia and lung injury. The spike protein of this virus binds to the common receptor on susceptible tissues and cells called the angiotensin-converting enzyme-2 (ACE2) of the angiotensin (ANG) system. In this study, we produced chimeric Macrobrachium rosenbergii nodavirus virus-like particles, presenting a short peptide ligand (ACE2tp), based on angiotensin-II (ANG II), on their outer surfaces to allow them to specifically bind to ACE2-overexpressing cells called ACE2tp-MrNV-VLPs. Replacing the ACE2tp at the protruding domains (P-domain) of the MrNV capsid proteins did not affect their normal assembly into icosahedral VLPs. The presentation of the ACE2tp on the P-domains significantly improved the binding and internalization of ACE2tp-MrNV-VLPs to hACE2-overexpressing HEK293T cells in a concentration-dependent manner. Furthermore, ACE2tp-MrNV-VLPs exhibited the ability to block the binding and infection of SARS-CoV-2 pseudovirus variants, including Wuhan, BA.2 Omicron, and Delta subtypes. Our results suggest that chimeric ACE2tp-MrNV-VLPs can serve as a blocking agent against various SARS-CoV-2 mutated variants and could also potentially serve as target-specific nano-containers to carry therapeutic agents to combat SARS-CoV-2 infections in the future. [ABSTRACT FROM AUTHOR]

High SARS-CoV-2-specific antibody levels can protect against SARS-CoV-2 reinfection. The gut microbiome can affect a host's immune response. However, its role in the antibody response to SARS-CoV-2 in people living with HIV (PLWH) remains poorly understood. Here, we categorised PLWH and healthy individuals into high- and low-antibody-response groups. Shotgun metagenomic sequencing and targeted metabolomic assays were used to investigate the differences in the gut microbiome and metabolic functions between the high- and low-antibody-response groups. PLWH demonstrated a higher abundance of short-chain fatty acid (SCFA)-producing species, accompanied by high serum levels of several SCFAs, in the high-antibody-response group than in the low-antibody-response group. In contrast, healthy individuals demonstrated higher enrichment of pilus-bearing bacterial species, with flagella-expressing genes, in the high-antibody-response group than in the low-antibody-response group. Therefore, gut-microbiota-derived SCFAs play a key role in antibody responses in PLWH but not in healthy individuals. Our results afford a novel understanding of how the gut microbiome and its metabolites are associated with host immunity. Moreover, they may facilitate the exploration of modalities to prevent SARS-CoV-2 reinfection through various gut-microbiota-targeted interventions tailored to different populations. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 virus that resulted in the COVID-19 pandemic has been implicated in a range of neurological issues, such as encephalopathy, stroke, and cognitive decline. Although the precise mechanism causing these issues is unknown, mounting evidence shows that blood–brain barrier (BBB) disruption is probable2 a major factor. The integrity of the blood–brain barrier (BBB), a highly selective barrier that divides the brain from the systemic circulation, is crucial for preserving normal brain function. By analysing the multi-transcriptome data, this work explores the neurological impacts of the SARS-CoV-2 virus and provides insight into the molecular mechanisms behind BBB breakdown and neurological symptoms in COVID-19 patients. The endothelial cells of BBB expresses inflammatory genes in response to the systemic inflammation induced due to SARS-CoV-2 remnants in the body. This raises the possibility that systemic inflammation brought on by SARS-CoV-2 and BBB integrity are correlated. Furthermore, the study highlights the pathways involved in oxidative stress and endothelial cell activation, revealing their role in COVID-19 passage through BBB and induction of systemic inflammation and advancement toward neurological disorders. The article showcases the evidence that mitochondrial dysfunction is a major aftermath associated with SARS-CoV-2 infection as the impaired Mitochondria leads to an accumulation of reactive oxygen species (ROS), triggering endothelial dysfunction, and leading to the passage of harmful molecules across the BBB. This study offers insightful information that may open up the possibilities for new treatment plans by targeting biomarkers specifically associated with inflammation and BBB dysfunctioning conditions. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of antibody responses following vaccination and SARS-CoV-2 infection is important for informing effective vaccination strategies and other public health interventions. This study investigates SARS-CoV-2 antibody dynamics in a Puerto Rican cohort, analyzing how IgG levels vary by vaccination status and previous infection. We assess waning immunity and the distribution of hybrid immunity with the aim to inform public health strategies and vaccination programs in Puerto Rico and similar settings. We conducted a prospective, longitudinal cohort study to identify SARS-CoV-2 infections and related outcomes in Ponce, Puerto Rico, from June 2020–August 2022. Participants provided self-collected nasal swabs every week and serum every six months for RT-PCR and IgG testing, respectively. IgG reactivity against nucleocapsid (N) antigens, which generally indicate previous infection, and spike (S1) and receptor-binding domain (RBD) antigens, which indicate history of either infection or vaccination, was assessed using the Luminex Corporation xMAP® SARS-CoV-2 Multi-Antigen IgG Assay. Prior infection was defined by positive RT-PCRs, categorized by the predominant circulating SARS-CoV-2 variant at the event time. Demographic information, medical history, and COVID-19 vaccination history were collected through standardized questionnaires. Of 882 participants included in our analysis, 34.0% experienced at least one SARS-CoV-2 infection, with most (78.7%) occurring during the Omicron wave (December 2021 onwards). SARS-CoV-2 antibody prevalence increased over time, reaching 98.4% by the final serum collection, 67.0% attributable to vaccination alone, 1.6% from infection alone, and 31.4% from both. Regardless of prior infection status, RBD and S1 IgG levels gradually declined following two vaccine doses. A third dose boosted these antibody levels and showed a slower decline over time. N-antibody levels peaked during the Omicron surge and waned over time. Vaccination in individuals with prior SARS-CoV-2 infection elicited the highest and most durable antibody responses. N or S1 seropositivity was associated with lower odds of a subsequent positive PCR test during the Omicron period, with N antibodies showing a stronger association. By elucidating the differential decay of RBD and S1 antibodies following vaccination and the complexities of N-antibody response following infection, this study in a Puerto Rican cohort strengthens the foundation for developing targeted interventions and public health strategies. [ABSTRACT FROM AUTHOR]

To combat the SARS-CoV-2 pandemic, innovative prevention strategies are needed, including reducing ACE2 expression on respiratory cells. This study screened approved drugs in China for their ability to downregulate ACE2. Daphnetin (DAP) was found to significantly reduce ACE2 mRNA and protein levels in PC9 cells. DAP exerts its inhibitory effects on ACE2 expression by targeting HIF-1α and JAK2, thereby impeding the transcription of the ACE2 gene. The SARS-CoV-2 pseudovirus infection assay confirmed that DAP-treated PC9 cells exhibited decreased susceptibility to viral infection. At therapeutic doses, DAP effectively lowers ACE2 expression in the respiratory systems of mice and humans. This suggests that DAP, already approved for other conditions, could be a new preventive measure against SARS-CoV-2, offering a cost-effective and accessible way to reduce SARS-CoV-2 spread. [ABSTRACT FROM AUTHOR]

When infected with SARS-CoV-2, Syrian hamsters (Mesocricetus auratus) develop moderate disease severity presenting key features of human COVID-19. We here develop a biomathematical model of the disease course by translating known biological mechanisms of virus-host interactions and immune responses into ordinary differential equations. We explicitly describe the dynamics of virus population, affected alveolar epithelial cells, and involved relevant immune cells comprising for example CD4+ T cells, CD8+ T cells, macrophages, natural killer cells and B cells. We also describe the humoral response dynamics of neutralising antibodies and major regulatory cytokines including CCL8 and CXCL10. The model is developed and parametrized based on experimental data collected at days 2, 3, 5, and 14 post infection. Pulmonary cell composition and their transcriptional profiles were obtained by lung single-cell RNA (scRNA) sequencing analysis. Parametrization of the model resulted in a good agreement of model and data. The model can be used to predict, for example, the time course of the virus population, immune cell dynamics, antibody production and regeneration of alveolar cells for different therapy scenarios or after multiple-infection events. We aim to translate this model to the human situation in the future. [ABSTRACT FROM AUTHOR]

Fatigue is the most prevalent symptom within the post-COVID condition (PCC). Furthermore, many patients suffer from decreased physical performance capacity and post-exertional malaise. Although exercise has been proposed as an effective therapeutic strategy for PCC, there is limited evidence on individualised and symptom-titrated exercise interventions in patients with fatigue and PEM. Therefore, we conducted a multi-centre randomised controlled trial to investigate the effectiveness of an individualised and symptom-titrated exercise program. We measured fatigue, health-related quality of life, hand-grip strength, endurance capacity and PEM before and after the 10-week intervention. A total of 118 individuals with PCC were included in the final intention-to-treat analysis. All tests and training sessions took place in commercial fitness and health facilities. We found significant effects on fatigue severity, health-related quality of life and physical performance capacity. Adjusting the individual exercise load to daily fatigue has proven to be an effective and safe strategy in PCC patients with fatigue. Under the guidance of qualified professionals and by utilising symptom-titrated training recommendations, commercial fitness and health facilities present an appropriate setting for outpatient exercise rehabilitation in PCC. [ABSTRACT FROM AUTHOR]

Abstract The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a major challenge to global health. Targeting the main protease of the virus (Mpro), which is essential for viral replication and transcription, offers a promising approach for therapeutic intervention. In this study, advanced computational techniques such as molecular docking and molecular dynamics simulations were used to screen a series of antiviral compounds for their potential inhibitory effect on the SARS-CoV-2 Mpro. A comprehensive analysis of compounds from the ChemDiv and PubChem databases was performed. The physicochemical properties, pharmacokinetics, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles were evaluated to determine drug similarity and safety. Compound 4896 − 4038 proved to be the most promising candidate. It exhibited a favorable balance between molecular weight (491.06) and lipophilicity (logP 3.957), high intestinal absorption (92.119%), and broad tissue distribution (VDss of 0.529), indicating good oral bioavailability and therapeutic potential. Molecular docking studies showed that 4896 − 4038 has a strong binding affinity to the active site of Mpro and forms key interactions, such as hydrogen bonds, carbon-hydrogen bonds, pi-sulfur, and multiple van der Waals and pi-pi stacked bonds. The binding energy was comparable to that of the reference drug X77, indicating potential efficacy. Molecular dynamics simulations over 300 ns confirmed the stability of the Mpro/4896 − 4038 complex of protein-ligand. Free energy landscape mapping and MM/PBSA calculations further substantiated the favorable binding and stability of the complex. Importantly, 4896 − 4038 exhibited a comparatively favorable safety profile. In summary, compound 4896 − 4038 shows significant potential as a potent SARS-CoV-2 Mpro inhibitor, combining potent inhibitory activity with favorable pharmacokinetic and safety profiles. These results support the further development of 4896 − 4038 as a promising therapeutic agent in the fight against COVID-19 that warrants experimental validation and clinical investigation.

Abstract During the omicron wave of the COVID-19 pandemic and with SARS-CoV-2 vaccines becoming available, seroprevalence rates rose in children and adolescents. This study investigated the impact of both SARS-CoV-2 infections and vaccinations on the incidence of acute and prolonged symptoms in real-world conditions during the transition from the pandemic to the endemic phase. Participants from a pediatric population based seroprevalence study (CorKID study) were followed up at least two and for almost four years by survey of health status features and symptoms suggestive of post-COVID syndrome (PCS). In a subgroup (n = 259) SARS-CoV-2 antibody serology was further investigated. 789 participants of the original CorKID study cohort (n = 2.121; 37.2%) were included. 67.9% reported at least one SARS-CoV2 infection. 46.6% had received one or more SARS-CoV-2 vaccinations. In the vast majority of serologically tested participants antibodies again SARS-CoV-2 spike (98.9%) or nucleocapsid (93.3%) antigen were detected following infection and/or vaccination. At least 30% experienced one unrecognized SARS-CoV-2 infection. The overall health status was comparable between children, irrespective of SARS-CoV-2 infections and similar to pre-pandemic assessment. However, a subset of young adolescents exhibited a decline in physical performance compared to pre-pandemic conditions. After infection, PCS-like symptoms persisted in 7% of the respondents for more than three months and up to four years. SARS-CoV-2 vaccinated participants (47%) reported 12% less acute flu-like infections other than SARS-CoV-2. Nearly all participants developed SARS-CoV-2 antibodies in this longitudinal study through either vaccination or infection during the Omicron wave. About 7% of participants suffered from PCS symptoms, predominately fatigue and exhaustion. Furthermore, participants who received vaccinations against SARS-CoV-2 reported a lower frequency of acute infections during follow-up.

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has imposed substantial challenges on our society due to the COVID-19 pandemic. This virus relies heavily on its surface glycoprotein (S-glycoprotein) to facilitate attachment, fusion, and entry into host cells. While the nucleoprotein (N) in the ribonucleoprotein core binds to the viral RNA genome. Therefore, our objective is to develop a novel vaccine candidate targeting the dominant T-cell and B-cell epitopes of the immune system. On the S-glycoprotein and nucleoprotein. Employing an immunoinformatic approach, we constructed a vaccine candidate with 13 highly antigenic B-cell epitopes, 19 HTL antigenic epitopes, and 18 CTL epitopes following a rigorous assessment. The multi-epitope construct successfully passed three-fold toxicity, allergenicity, and antigenicity tests, affirming its non-toxic, non-allergenic, and antigenic nature. This demonstrates the potentiality of the vaccine design to trigger an immunological response. Furthermore, the vaccine-ACE-2 receptor complex was tested, confirming its ability to interact with ACE-2’s core pocket and induce an immunological response. Additionally, the vaccine’s binding prowess for human toll-like receptors (TLR) (1, 3, 4, and 8) was investigated. According to the Ramachandran plot, 77.46% of the construct’s amino acid residues fall within a favorable zone, establishing it as a viable vaccine candidate.

Abstract SARS-CoV-2 is the viral pathogen responsible for COVID-19. Although morbidity and mortality frequently occur as a result of lung disease, the gastrointestinal (GI) tract is recognized as a primary location for SARS-CoV-2. Connections and interactions between the microbiome of the gut and respiratory system have been linked with viral infections via what has been referred to as the ‘gut-lung axis’ with potential aerodigestive communication in health and disease. This research explored the relationship between the microbiomes of the upper respiratory and GI tracts in patients with COVID-19 and examined Extraesophageal reflux (EOR), a mechanism which could contribute to dysregulated communication between the GI and respiratory tract (as identified in COVID-19). 97 patients with a laboratory diagnosis of COVID-19 infection, and 50 age-matched controls were recruited and stool, saliva and sputum were obtained from each participant. ELISA Pepsin tests and Reflux Symptom Index scores (RSI) were conducted for EOR assessment. DNA sequencing of the V4 region of the 16 S rRNA gene was performed for microbiome analysis. No differences were observed between the fecal microbiome’s alpha and Shannon diversity indices; however, a distinct microbial composition was observed in COVID-19 patients (when compared to the controls). The respiratory microbiota from individuals with COVID-19 demonstrated a statistically significant reduction in Shannon diversity and bacterial richness alongside an overall reduction in the prevalence of organisms from a typical healthy respiratory microbiome. Furthermore, the bacterial richness of the stool and sputum samples was significantly lower among COVID-19 patients admitted to ICU. A significantly higher RSI score and salivary pepsin level were detected among those with COVID-19. The data indicates that COVID-19 is associated with a dysregulation of both the gut and lung microbiome with a more marked perturbation in the lung, particularly among COVID-19 patients who had been admitted to the ICU. The presence of increased RSI scores, combined with elevated levels of Pepsin, suggests that increased micro-aspiration may occur, which is consistent with of under-recognized interactions between the GI and lung microbiomes in COVID-19 patients and requires additional study. Such studies would benefit from the insights provided by biological samples which reflect the continuum of the aerodigestive tract.

Abstract Healthcare Workers (HCWs) are at ongoing risk of SARS-CoV-2 infection, potentially contributing to its transmission. This study assessed full vaccination and vaccination timeliness impact on SARS-CoV-2 infections among HCWs in Italy’s Marche Region, using Healthcare Utilization Databases. We evaluated vaccination coverage and its associated factors. The cohort comprised 21,118 HCWs aged 18–70 from the region’s five Local Health Authorities (LHA), enrolled between February 2020 - May 2021. Factors associated with full vaccination were assessed using multiple logistic regression. The impact of vaccination status, time to vaccination, occupational role, age, gender, and health status on infection risk was analysed with a multiple Cox regression model, adjusting for vaccination coverage velocity, swabbing probability, and monthly intensive care unit admissions rate in each LHA. Of the cohort, 81.2% were fully vaccinated. Factors associated with full vaccination included age, role, LHA, prior infection, and health status. Vaccination reduced infection risk by 77% (95% CI: 70–82). Infection risk was higher among healthcare assistants, nurses/physiotherapists/technicians compared to physicians, among male HCWs, and it decreased as vaccination timeliness increased. Vaccination timeliness is crucial for reducing SARS-CoV-2 infection risk among HCWs, regardless of their characteristics. This underscores the importance of efficiently organizing vaccination administration across different territories and for all HCW categories.

Abstract The global spread of the novel coronavirus disease 2019, caused by SARS-CoV-2 virus, impacts individuals of all age groups, including lactating women and children. Concerns have been raised regarding the potential transmission of SARS-CoV-2 from mother to child, following the discovery of SARS-CoV-2 RNA in human milk. Therefore, this study aims to investigate whether the Omicron novel coronavirus variants are transmitted through human milk. This study was conducted between March and May 2022 at Children’s Medical Center, the First Hospital of Jilin University, Lequn Branch. Fourteen lactating mothers and their breastfed children hospitalized with COVID-19 (Omicron variant) formed mother–child pairs, which constituted the test group. Additional 11 non-breastfed children of the same age hospitalized with COVID-19 (Omicron variant) participated in the study as the control group. Their clinical manifestations were observed, and the milk of lactating mothers with COVID-19 was collected for SARS-CoV-2 RNA detection. Milk samples from each lactating mother were collected consecutively for 2–18 days and subjected to polymerase chain reaction (PCR) testing forSARS-CoV-2 RNA detection. The time span for sample collection ranged from admission to discharged. The symptoms observed in mothers and children infected with the Omicron variant of COVID-19 were primary upper respiratory tract infection, with fever and cough being the main clinical manifestations. In total, 104 breast milk samples were collected from 14 lactating mothers with COVID-19, and all samples were negative for SARS-CoV-2 RNA. This study found no evidence of Omicron variants transmission through breast milk and accepts the safety of breastfeeding for novel coronavirus-positive mothers when contact precautions are taken. Our findings provide additional support for recommendations that lactating women with COVID-19 continue to breastfeed while taking precautions.

Abstract We investigated and compared mortality rates and risk factors for pre-pandemic and pandemic all-cause mortality in a population-based cohort of men and women in Arkhangelsk, Russia. A prospective cohort study enrolled 2,324 participants aged 35 to 69 years between 2015 and 2017. All participants were followed up for all-cause deaths using the mortality registry. Mortality rates per 1000 person-years were calculated for men and women in the pre-pandemic and pandemic periods. Cox regression models were used to investigate demographic, lifestyle, and health characteristics associated with increased risk of death in both periods. During the pandemic, age-standardized all-cause mortality increased in women, but minor change was observed in men. Older age, smoking, and diabetes were associated with a higher risk of all-cause death in both periods and for both sexes. In women, higher risk during the pandemic was associated with obesity, angina, elevated cystatin C levels, and a history of COVID-19. In men, asthma and elevated hs-Troponin T levels increased the risk of death during the pandemic, while elevated hs-CRP and NT-proBNP levels were associated with higher risk in both periods. Targeted preventive interventions for men and women with specific risk factors can be implemented during potential future infectious disease outbreaks.

As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that recapitulate the cell-intrinsic response to arising viral variants are needed. Here we describe an adult stem cell-derived human airway organoid model overexpressing the ACE2 receptor (ACE2-OE) that supports robust viral replication while maintaining 3D architecture and cellular diversity of the airway epithelium. ACE2-OE organoids were infected with SARS-CoV-2 variants and subjected to single-cell RNA-sequencing. Interferon-lambda was upregulated in cells with low-level infection while the NF-kB inhibitor alpha gene (encoding IkBa) was consistently upregulated in infected cells, and its expression positively correlated with infection levels. Confocal microscopy showed more IkBa expression in infected than bystander cells, but found concurrent nuclear translocation of NF-kB that IkBa usually prevents. Overexpressing a nondegradable IkBa mutant reduced NF-kB translocation and increased viral infection. These data demonstrate the functionality of ACE2-OE organoids in SARS-CoV-2 research and underscore that the strength of the NF-kB feedback loop in infected cells controls viral replication.

All-cause COVID-19 hospitalization ≤ 30 days of infection is a common outcome for severe illness in observational/surveillance studies. Milder COVID-19 disease and COVID-19-specific measurements calls for an evaluation of this endpoint. This was a descriptive, retrospective cohort study of adults ≥ 18 who were established in primary care at Veteran Health Administration (VHA) facilities. The outcome was hospitalization within 30 days of a laboratory-confirmed, symptomatic SARS-CoV-2 infection. Between December 15, 2021 and May 1, 2022, a simple random sample of all VA facilities, excluding Puerto Rico or Philippines, was drawn to identify these hospitalized cases and determine whether hospitalization was due to COVID-19-specific causes. A chart review was conducted to record the inpatient clinical team's diagnosis and whether the inpatient team classified the diagnosis as COVID-19 related or not. These data were used to classify hospitalizations as either due to COVID-19-specific causes (direct manifestations of SARS-CoV-2 infection) or non-COVID-19-specific hospitalizations (incidental SARS-CoV-2 infection), A simple random sample of 9966 (12.3%) all-cause hospitalizations (95% CI: 12.1%, 12.5%) was used to select 300 representative patients. Of these, 226/300 (75.3%) were determined to be COVID-19-specific. COVID-19 pneumonia was most common (147/226, 65.0%). The highest proportion of COVID-19-specific hospitalizations occurred among unvaccinated (85.0%), followed by vaccinated but not boosted (73.7%) and boosted (59.4%) (p

It is unclear if SARS CoV-2 infection during pregnancy is associated with adverse neurodevelopmental repercussions to infants. We assessed pediatric neurodevelopmental outcomes in children born to mothers with laboratory-confirmed SARS CoV-2 infection during pregnancy. Neurodevelopmental outcomes of in-utero exposed children were compared to that of pre-pandemic control children in Los Angeles (LA), CA, USA and Rio de Janeiro, Brazil. Bayley Scales of Infant and Toddler Development, 3rd edition (Bayley-III), the gold standard tool for evaluating neurodevelopment until 36 months of age and Ages and Stages Questionnaires (ASQ-3), a frequently used screening instrument for evaluating neurodevelopment in this same age group were the assessment tools used. Developmental delay (DD) was defined as having a score

SARS-CoV-2 often causes viral pneumonitis, hyperferritinemia, elevations in D-dimer, lactate dehydrogenase (LDH), transaminases, troponin, CRP, and other inflammatory markers. Lung ultrasound is increasingly used to diagnose and stratify viral pneumonitis severity. We retrospectively reviewed 427 visits in patients aged 14 days to 21 years who had had a point-of-care lung ultrasound in our pediatric emergency department from 30/November/2019 to 14/August/2021. Lung ultrasounds were categorized using a 6-point ordinal scale. Lung ultrasound abnormalities predicted increased hospitalization with a threshold effect. Increasingly abnormal laboratory values were associated with decreased discharge from the ED and increased admission to the ward and ICU. Among patients SARS-CoV-2 positive patients ferritin, LDH, and transaminases, but not CRP or troponin were significantly associated with abnormalities on lung ultrasound and also with threshold effects. This effect was not demonstrated in SARS-CoV-2 negative patients. D-Dimer, CRP, and troponin were sometimes elevated even when the lung ultrasound was normal.

Abstract Clinical data indicate that COVID-19 causes cardiovascular complications, regardless of the severity of the disease. In this work, we have shown that SARS-CoV-2 infection causes vascular dysfunction due to the modification of endothelial cell elasticity. We used human pulmonary endothelial cells (HPAECs) expressing the ACE2 receptor as a model of the endothelium. This system mimics in vivo conditions, as it allows virus entry but not replication. As a reference, we used A549 epithelial cells, a well-described model that supports productive replication of SARS-CoV-2. We show that the infection of HPAECs results in loss of cell elasticity, which correlates with increased polymerization of actin filaments and induction of the inflammatory response. On the contrary, A549 epithelial cells supporting viral replication showed increased elasticity. We also showed that the endothelial cell elasticity were impaired after infection with Alpha, Beta and Delta variants. Consequently, we believe that nonproductive SARS-CoV-2 infection associated with loss of the endothelium elasticity may be clinically relevant and result in dysfunction and damage to this tissue.

Abstract Various public health measures have contained outbreaks of SARS-CoV-2, but concerns remain over the possibility of future surges. Improvements in broadening the vaccine response can stifle new and nascent infections. In this study, we tested the effects of different adjuvant combinations on the immunization of mice with the receptor-binding domain (RBD)-containing the S1-subunit of the spike protein (S1 protein) from SARS-CoV-2 to induce a robust humoral and cellular immune response. We showed that subcutaneous immunization of S1 protein co-delivered with IL-15 and TLR-ligands (MALP-2, poly I: C, and CpG) or with IL-12 and GM-CSF in DOTAP, or Alum induced significantly high titers of durable antibodies, predominantly IgG1, IgG2a, and IgG2b, that could bind to RBD, S1-subunit, and the full-length ectodomain of SARS-CoV-2 spike protein in sera compared to the immunization with S1 protein alone in both B6 wild-type (WT) and the K18-hACE2 transgenic mice. In addition, immunization with S1 protein co-delivered with IL-15 and TLR-ligands induced antibody responses against S1 protein in aged mice, and sera from younger mice reduced plaque formation of live SARS-CoV-2, and had effective binding to S1 protein from ten different variants of SARS-CoV-2, including Omicron (B.1.1.529), and greater neutralization activity as early as day 21 post-immunization measured by inhibition of RBD binding to hACE2 than sera from mice immunized with S1 protein alone or co-delivered with Alum. We also identified antibody-binding epitopes using 18-mer peptides with 9-residue overlaps from the S1 protein. CD8+ T-cell responses specific to RBD and S1 protein peptide pools were observed up to day 200 post-immunization by tetramer staining. These data show the efficacy of specific immunologically targeted adjuvants for increasing S1 protein immunogenicity in mice and can contribute to more effective vaccines.

Abstract Trace elements, specifically magnesium (Mg), zinc (Zn), and selenium (Se) have been linked with immunomodulatory properties. This research delves into identifying the potential impression of serum levels Mg, Zn, and Se on the protective immunity arisen through Sinopharm COVID-19 vaccine in the vaccinated subjects. Levels of Mg, Zn, and Se, cytokine and antibody production as well as virus neutralization potency were investigated in 75 males and 75 females before and 2 weeks after first and second dose of vaccination. Level of Mg, Zn, and Se did not change significantly before and 2 weeks after first and second dose of vaccine administration. Concentrations of Interleukin (IL)-2, IL-6, and Interferon (IFN)-γ were significantly higher in the supernatant of peripheral blood mononuclear cells (PBMCs) obtained from subjects 2 weeks after both first and second dose of vaccination compared to before vaccination. Serum level IgG was significantly higher 2 weeks after first and second dose of vaccination compared to before vaccination. Serum level IgM was only higher after first dose of vaccination compared with before vaccine. Also, 2 weeks after both first and second dose of vaccination compared to before vaccination, FRNT50 titer was significantly higher. Levels of Mg, Zn, and Se did not significantly correlate with levels of IL-2, IL-6, IFN-γ, IgM and IgG, and FRNT50 after first and second dose of vaccination. No severe unwanted clinical symptoms were detected after vaccination. Mg, Zn, and Se do not play a role in modulating protective immunity during Sinopharm COVID-19 vaccine.

Abstract We study the prevalence of SARS-CoV-2 antibodies in a diverse population in Milwaukee County, Wisconsin from May 2021 to June 2022. We find that 99.4% (523/526) of the participants had positive results for antibodies to the SARS CoV2 spike protein over April-June 2022, soon after the early-2022 Omicron surge. Positive tests for spike protein antibodies were very high (86%; 19/22) even among unvaccinated persons who reported no knowledge of prior infection. Thus, by mid-2022, almost all persons were no longer COVID-naïve, defined as vaccination, infection (often without symptoms), or both. Nucleocapsid antibody tests, especially the Abbott test, were far less sensitive than spike protein tests, and Abbott test sensitivity faded with time since infection. Thus, studies which rely on nucleocapsid tests will understate prior infection rates. We also report large sample evidence on the performance of the Abbott and Roche spike and nucleocapsid protein tests in capturing prior vaccination, infection, or both. The Roche spike protein test outperforms the Abbott spike test, and the Roche nucleocapsid test greatly outperforms the Abbott nucleocapsid test.

Abstract Coronavirus disease-2019 (COVID-19), attributed to the severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2), has posed global health challenges since it first emerged in 2019, and its impact continues to persist. The neurotropic nature of SARS-CoV-2 remains undisclosed, though researchers are proposing hypotheses on how the virus is transmitted to the central nervous system. One of the prevailing hypotheses is that SARS-CoV-2 travels through the olfactory nerve system via the olfactory epithelium (OE). Using a K18-human angiotensin converting-enzyme 2 (hACE2) transgenic mouse model with impaired olfactory sensory neurons (OSNs) induced by zinc sulfate, we examined the role of the olfactory nerve in the brain invasion by SARS-CoV-2. Mice lacking OSNs exhibited reduced levels of viral transmission to the brain, leading to significantly improved outcomes following SARS-CoV-2 infection. Moreover, a positive correlation was observed between viral persistence in the OE and brain infection. These results indicate that early inhibition of the olfactory nerve pathway effectively prevents viral invasion of the brain in K18-hACE2 mice. Our study underscores the significance of the olfactory nerve pathway in the transmission of SARS-CoV-2 to the brain.

Abstract With the continuous spread of the SARS-CoV-2 globally, viral mutations have accumulated. As a result, SARS-CoV-2 became more contagious, and has a higher risk of immune escape and reinfection. To identify variants and have an awareness of the prevalence of these variants, this study selected four segments containing mutations on the S gene of the SARS-CoV-2. Then a rapid and convenient variants detection method was established using high-resolution melting(HRM) analysis combined with nested polymerase chain reaction(PCR). The total detection process takes about 5 h. Through comprehensive analysis of the results from the four reaction systems, the identification of seven important Omicron variants(BA.2, BA.2.75, BA.5.2, BF.7, BQ.1, XBB.1 and XBB.2) can be achieved, with significant differentiation in the melting curves of each variant group. The method established in this study was used to genotype positive specimens in COVID-19 nucleic acid testing, the overall concordance rate compared to whole genome sequencing results was 88.9%, and the positive concordance rate of each sublineage was greater than 80% and the negative concordance rate was greater than 94.4%. The detection of clinical specimens has demonstrated that the HRM analysis established in this study is an effective, rapid and convenient variant identification method, which can be used for monitoring SARS-CoV-2 variants and has important value in addressing public health issues caused by the ongoing mutations of the SARS-CoV-2.

Abstract To investigate the characteristics of acute visual dysfunction and fundus lesions in patients with COVID-19 pneumonia. A retrospective case series study was conducted. Data from 48 patients (96 eyes) with COVID-19 infection who presented to our ophthalmology department with acute onset visual disturbance between December 5, 2022, and February 28, 2023 were collected. Asymptomatic patients and those who had already recovered were excluded. Data collected included patient demographics, ophthalmic examinations, multicolor imaging (MCI), infrared autofluorescence (IR), spectral-domain optical coherence tomography (OCT), fundus fluorescein angiography (FFA). Of the 48 patients, 15 were male and 33 were female, with a mean age of 32 years. All patients had bilateral involvement. OCT showed hyperreflective signals in the outer plexiform layer and outer nuclear layer of the macular region in all 96 eyes of 48 patients (100%). Additionally, 66 eyes of 33 patients (68.8%) of eyes demonstrated abnormal reflectivity in the ellipsoid and interdigitation zones. MCI revealed petaloid or wedge-shaped hyperreflective areas in the macula in 46 (47.9%) of eyes, corresponding to hyporeflective areas on IR. Cotton-wool spots were observed in the peripapillary or posterior pole area in 54 (56.3%) of eyes. COVID-19 infection can lead to acute, bilateral, symmetric, and widespread retinal damage. Characteristic findings can be observed in ophthalmological examinations such as OCT, MCI, and IR.

Abstract The COVID-19 pandemic highlighted the need for the rapid development of antiviral therapies. Viral RNA-dependent RNA polymerases (RdRp) are promising targets, and numerous virtual screenings for potential inhibitors were conducted without validation of the identified hits. Here we have tested a set of presumed RdRp inhibitors in biochemical assays based on fluorometric detection of RdRp activity or on the electrophoretic separation or RdRp products. We find that fluorometric detection of RdRp activity is unreliable as a screening method because many small compounds interfere with fluorophore binding to dsRNA, and this effect is enhanced by the Mg2+ metal ions used by nucleic acid polymerases. The fact that fluorimetric detection of RdRp activity leads to false-positive hits underscores the requirement for independent validation methods. We also show that suramin, one of the proposed RdRp inhibitors that could be validated biochemically, is a multi-polymerase inhibitor. While this does not hinder its potential as an antiviral agent, it cannot be considered an specific inhibitor of SARS-CoV-2 RdRp.

Abstract Humans get SARS-CoV-2 infection mainly through inhalation; thus, vaccine that induces protective immunity at the virus entry site is important for early control of the infection. In this study, two anionic liposome (L)-adjuvanted VLP vaccines against SARS-CoV-2 were formulated. Baculovirus-Sf21 insect cell system was used for production of VLPs made of full-length S, M and E proteins. S protein of one vaccine (L-SME-VLPs) contained furin cleavage site at the S1/S2 junction, while that of another vaccine (L-S′ME-VLPs) did not. Both vaccines were innocuous and immunogenic when administered IP and IN to mice. Mice immunized IP with L-SME-VLPs/L-S′ME-VLPs (three doses, two-weeks intervals) had serum virus neutralizing (VN) antibodies (in falling order of isotype frequency): IgG3, IgA and IgG2a/IgG3, IgA and IgM, respectively. The L-S′ME VLPs vaccine induced significantly higher serum VN antibody titers than the L-SME-VLPs vaccine. All mice immunized IN with both vaccines had significant rise of VN antibodies in their bronchoalveolar lavage fluids (BALF). The VN antibodies in 67% of immunized mice were Th1- isotypes (IgG2a and/or IgG2b); the immunized mice had also other antibody isotypes in BALF. The intranasal L-S′ME-VLPs should be tested further step-by-step towards the clinical use as effective and safe vaccine against SARS-CoV-2.

Abstract Despite all the efforts acquired in four years of the COVID-19 pandemic, the path to a full understanding of the biological mechanisms involved in this disease remains complex. This is partly due to a combination of factors, including the inherent characteristics of the infection, socio-environmental elements, and the variations observed within both the viral and the human genomes. Thus, this study aimed to investigate the correlation between genetic host factors and the severity of COVID-19. We conducted whole exome sequencing (WES) of 124 patients, categorized into severe and non-severe groups. From the whole exome sequencing (WES) association analysis, four variants (rs1770731 in CRYBG1, rs7221209 in DNAH17, rs3826295 in DGKE, and rs7913626 in CFAP46) were identified as potentially linked to a protective effect against the clinical severity of COVID-19, which may explain the less severe impact of COVID-19 on the Northern Region. Our findings underscore the importance of carrying out more genomic studies in populations living in the Amazon, one of the most diverse from the point of view of the presence of rare and specific alleles. To our knowledge, this is the first WES study of admixed individuals from the Brazilian Amazon to investigate genomic variants associated with the clinical severity of COVID-19.

Abstract Despite the end of the global Coronavirus Disease 2019 (COVID-19) pandemic, the risk factors for COVID-19 severity continue to be a pivotal area of research. Specifically, studying the impact of the genomic diversity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on COVID-19 severity is crucial for predicting severe outcomes. Therefore, this study aimed to investigate the impact of the SARS-CoV-2 genome sequence, genotype, patient age, gender, and vaccination status on the severity of COVID-19, and to develop accurate and robust prediction models. The training set (n = 12,038), primary testing set (n = 4,006), and secondary testing set (n = 2,845) consist of SARS-CoV-2 genome sequences with patient information, which were obtained from Global Initiative on Sharing all Individual Data (GISAID) spanning over four years. Four machine learning methods were employed to construct prediction models. By extracting SARS-CoV-2 genomic features, optimizing model parameters, and integrating models, this study improved the prediction accuracy. Furthermore, Shapley Additive exPlanes (SHAP) was applied to analyze the interpretability of the model and to identify risk factors, providing insights for the management of severe cases. The proposed ensemble model achieved an F-score of 88.842% and an Area Under the Curve (AUC) of 0.956 on the global testing dataset. In addition to factors such as patient age, gender, and vaccination status, over 40 amino acid site mutation characteristics were identified to have a significant impact on the severity of COVID-19. This work has the potential to facilitate the early identification of COVID-19 patients with high risks of severe illness, thus effectively reducing the rates of severe cases and mortality.

Abstract Wastewater-based epidemiological surveillance has proven to be a useful and cost-effective tool for detecting COVID-19 outbreaks. Here, our objective was to evaluate its potential as an early warning system in Venezuela by detecting SARS-CoV-2 RNA in wastewater and its correlation with reported cases of COVID-19. Viral RNA was concentrated from wastewater collected at various sites in Caracas (northern Venezuela), from September 2021 to July 2023, using the polyethylene glycol (PEG) precipitation method. Viral quantification was performed by RT-qPCR targeting the N1 and ORF1ab genes. A significant association (p

Abstract The long-term effects of SARS-CoV-2 infection, and their determinants, are still unknown. This study aimed to assess symptoms one year after admission for COVID-19, according to the organ/system involved, and to identify factors. Cross-sectional study with retrospective data collection from March 2020 to February 2021. Inclusion criteria: aged ≥ 18 years and admitted for COVID-19. Exclusion criteria: death, not localized, refusal to participate, cognitive impairment or language barrier. A telephone survey was conducted on long COVID-related symptoms one year after hospital discharge. n = 486. The most frequent symptom groups were neurological (n = 225; 46.3%) and respiratory (n = 201; 41.4%). Multivariable analysis showed that a history of anxiety was significantly associated with psychiatric symptoms (ORa = 2.04, 95%CI = 1.02–4.06), fibromyalgia/chronic fatigue with general symptoms (ORa = 11.59, 95%CI = 1.47–9.34) and obesity with respiratory (ORa 1.90, 95%CI = 1.27–2.83) and musculoskeletal symptoms (ORa 1.96, 95%CI = 1.30–2.96). Male sex was associated with a significantly lower risk of neurological (ORa 0.64, 95%CI = 0.44–0.93), respiratory (ORa 0.45, 95%CI = 0.31–0.67), general (ORa 0.43, 95%CI = 0.29–0.63), psychiatric (ORa 0.34, 95%CI = 0.22–0.51), musculoskeletal (ORa 0.47, 95%CI = 0.32–0.70), dermatological (ORa 0.24, 95%CI = 0.14–0.42) and digestive (ORa 0.38, 95%CI = 0.20–0.73) symptoms. Advanced age (≥ 71 years) also had a protective effect against general (ORa 0.60, 95%CI = 0.39–0.95), psychiatric (ORa 0.39, 95%CI = 0.23–0.64), and dermatological (ORa 0.47, 95%CI = 0.24–0.92) symptoms. Patients admitted for SARS-CoV-2 infection frequently experience symptoms at one year, especially neurological and respiratory symptoms. Female sex, obesity, a history of anxiety and fibromyalgia/chronic fatigue were independent risk factors for presenting symptoms. Advanced age acted as a protective factor.