N-protein vaccine Convacell(R) is effective against COVID-19: phase 3, randomized, double-blind, placebo-controlled clinical trial (preprint)

We have developed a Convacell(R), a COVID-19 vaccine based on the conservative viral nucleocapsid (N) protein. The N protein is evolutionary conservative and is abundantly expressed on the surface of infected cells, allowing anti-N immune response generated by Convacell(R) to rapidly clear infected cells and provide long-lasting protection against COVID-19. Convacell(R) has been demonstrated to be safe and highly immunogenic, creating immune responses lasting over a year, in phase I/II and IIb clinical trials. Phase IIb clinical trial has also demonstrated that a single dose vaccination regimen with Convacell(R) is sufficient to provide an immune response. Here we report the finding of the phase III clinical trial of Convacell(R). Two groups of volunteers from Russia have been either vaccinated with a single dose of Convacell(R) or injected with placebo, and then monitored for incidence of COVID-19 and adverse effects. Anti-N antibody titers at admission were also analyzed, to take into account for potential effects of previous virus encounters. Disease incidence over 6 months results indicate an overall vaccine efficacy of 85.2% (95% confidence interval: 67.4-93.3%). Additionally, Convacell(R) has shown a good safety profile. Overall, Convacell(R) demonstrated highly desirable qualities and good performance as a vaccine and can be considered as valuable COVID-19 preventative measure.

Dispersal history of SARS-CoV-2 in Galicia, Spain (preprint)

The dynamics of SARS-CoV-2 transmission are influenced by a variety of factors, including social restrictions and the emergence of distinct variants. In this study, we delve into the origins and dissemination of the Alpha, Delta, and Omicron variants of concern in Galicia, northwest Spain. For this, we leveraged genomic data collected by the EPICOVIGAL Consortium and from the GISAID database, along with mobility information from other Spanish regions and foreign countries. Our analysis indicates that initial introductions during the Alpha phase were predominantly from other Spanish regions and France. However, as the pandemic progressed, introductions from Portugal and the USA became increasingly significant. Notably, Galicia's major coastal cities emerged as critical hubs for viral transmission, highlighting their role in sustaining and spreading the virus. This research emphasizes the critical role of regional connectivity in the spread of SARS-CoV-2 and offers essential insights for enhancing public health strategies and surveillance measures.

COVID-19 and its impact on biodiversity in coffee farms in the Andean landscape (preprint)

In Buesaco (BUE) and The Tablón of Gómez (TTG), farms in the Nariño Department fauna likely benefited from reduced human activities by COVID-19. However, this phenomenon has not been documented, and perhaps this article is the first on this topic. A survey was conducted on 431 farmers to identify fauna sightings and plant species. The non-parametric Kruskal Wallis test and multiple regression explored variables influencing species composition. Additionally, BUE and TTG’s fauna composition reports were utilized in a multi-temporal analysis before and after the COVID-19 lockdown. Analyzing data resulted in a compilation of lists containing the names of existing plant and fauna species. Sixty-four species of fauna were mentioned in BUE and TTG; birds accounted for 50%, and mammals accounted for 25%. Sciurus pucheranii had the highest mention frequency (MF), with 165 times by the producers in BUE and 188 times in TTG. This is the first record for the Nariño Department. According to the dominance index, four shade species within coffee plantations are considered the most dominant. Besides, five forest species around coffee are considered dominants. The Kruskal Wallis test (p = 0,013) and the regression analyses (R2 = 0,14) indicate that the null hypothesis should be rejected (p > 0.05). Species interaction between forest and fauna probably did not influence the increased biodiversity. The COVID-19 lockdown impacted how other fauna species appeared in BUE and TTG. Moreover, from 2021 to 2023, it can be determined that more species are mentioned than those recorded in years before COVID-19.

Multiple layers of innate immune response antagonism of SARS-CoV-2 (preprint)

Several SARS-CoV-2 proteins have been shown to counteract the host innate immune response, mostly using in vitro protein expression, which may not fully reflect their role in the context of viral infection. In addition, while each viral protein was characterized in a different experimental system, their relative contribution in immunosuppression remains unclear. Here we used a SARS-CoV-2 bacterial artificial chromosome with en passant mutagenesis to recover a panel of twelve infectious recombinant SARS-CoV-2 viruses, each with mutations in either NSP1, NSP2, NSP3, NSP6, NSP12, NSP13, NSP14, NSP15, NSP16, ORF3a, ORF6 or ORF8. We used the interferon-stimulated response element (ISRE)-driven luciferase assay in 293T-ACE2/TMPRSS2 cells to test the panel, demonstrating that mutations in many proteins, especially in NSP1 and NSP15, increased the type I interferon response relative to the parental wild-type virus. RNA-seq analysis of mutant-virus infected Calu-3 cells showed that the mutations in NSP1 or NSP15 lead to higher expression of multiple genes involved in innate immune response, cytokine-mediated signaling and regulation of lymphocyte proliferation. Furthermore, mutations in either NSP1 or NSP15 resulted in a greater maturation of human monocyte-derived dendritic cells in vitro. Infection of K18 hACE2 transgenic mice with either NSP1 or NSP15 mutated viruses demonstrated attentuated respiratory tract replication. Analysis of lung immune cells from infected mice by single-cell RNA-seq identified 15 populations of major myeloid and lymphoid cells with changes in the pattern of their activation associated with viral infection. The effects of mutations in NSP1 or NSP15 on these responses are consistent with differences in the immunosuppressive mechanisms utilized by the two proteins. Overall, these data demonstrate different and redundant mechanisms of innate immune antagonism by SARS-CoV-2 and suppression of activation of antigen presenting cells and T and B lymphocytes mediated by multiple viral proteins.

Adverse Events Following SARS-CoV-2 mRNA Vaccination in Adolescents: A Norwegian Nationwide Register-Based Study (preprint)

BackgroundVaccination of older adolescents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) started in the spring of 2021 and continued with younger adolescents throughout the summer and fall. We assessed risks of adverse events following immunization (AEFI) in adolescents aged 12-19 years following SARS-CoV-2 vaccination with a messenger RNA (mRNA) vaccine in Norway. Materials and MethodsThe study sample included 496,432 adolescents born in 2002-2009, residing in Norway, and unvaccinated against SARS-CoV-2 at the beginning of the age-specific waves of vaccination in 2021. The exposures under study were first- and second-dose SARS-CoV-2 mRNA vaccinations vs. no dose. We applied Poisson regression and self-controlled case series (SCCS) analysis to estimate incidence rate ratios (IRRs) of 17 preselected outcomes, with associated 95% confidence intervals (CIs), between vaccinated and unvaccinated subjects using predefined post-vaccination risk windows. ResultsMost outcome-specific numbers of cases were low. There were no statistically significant associations between first-dose vaccination and any of the outcomes. In the main Poisson regression, second-dose vaccination was associated with increased risks of anaphylactic reaction (adjusted IRR [aIRR]: 10.05; 95% CI: 1.22-82.74), lymphadenopathy (aIRR: 2.33; 95% CI: 1.46-3.72), and myocarditis and pericarditis (aIRR: 5.27; 95% CI: 1.98-14.05). We also observed increased incidence of acute appendicitis outside the 14-day risk window. When expanding the risk window to 42 days in a post-hoc analysis, there was increased incidence of acute appendicitis following both first-dose vaccination (aIRR: 1.39; 95% CI: 1.09-1.78) and second-dose vaccination (aIRR: 1.43; 95% CI: 1.07-1.91). Results of the SCCS analysis were similar to the Poisson regression. ConclusionsIn general, potential AEFI were rare among adolescents. We found increased risks of anaphylactic reaction, lymphadenopathy, and myocarditis and pericarditis following second-dose vaccination. There were also indications of increased acute appendicitis risk when applying longer risk windows.

Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures (preprint)

Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.

Air Pollutants and Their Impact on Chronic Diseases—A Retrospective Study in Bucharest, Romania

Air pollution is a serious problem in Romania, with the country ranking 13th among the most polluted countries in Europe in the 2021 World Air Quality Report. Despite the recognized impact of pollutants on health, there has been a lack of large-scale studies conducted in Romania. This study investigated the impact of air pollutants on patients with chronic respiratory, cardiovascular, cerebrovascular, or metabolic diseases in Bucharest and its metropolitan area from 20 August 2018 to 1 June 2022. The daily limit values for particulate matter PM10 and PM2.5 were exceeded every month, especially during the cold season, with a decrease during the COVID-19 pandemic restrictions. A significant statistical correlation was found between the monthly average values of PM2.5 and PM10 and hospitalizations for respiratory and cardiovascular diseases. A 10 µg/m3 increase in monthly average values resulted in a 40–60% increase in admissions for each type of pathology, translating to more than 2000 admissions for each pathology for the study period. This study highlights the urgent need for national and local measures to ensure a cleaner environment and enhance public health in Romania according to international regulations. © 2023 by the authors.

Pandemia de la COVID-19 y las Políticas de Salud Pública en el Perú: marzo-mayo 2020/COVID-19 pandemic and Public Health Policies in Peru: March-May 2020

Objetivo El trabajo tiene como objetivo analizar la dinámica del comportamiento de la COVID-19 en el Perú, estimar y evaluar el impacto de la política pública de supresión (cuarentena). Métodos El modelo epidemiológico SIR y la estimación con el método de Mínimos Cuadrados Ordinarios (MCO). Resultados Se encontró que el número básico de propagación (Ro) cayó de 6,0 a 3,2 habiéndose reducido en 54% por efecto de la estrategia de supresión, y dos meses después cayó a 1,7. Sin embargo, sigue siendo alto y evidencia que aún continúa en expansión el nivel de infectados, con los efectos sociales y económicos adversos que esta medida implica. Conclusión La COVID-19 es una enfermedad que crece exponencialmente, por lo cual, la política de salud basada en la estrategia de supresión ha permitido aplanar la curva de contagio, evitando el colapso del Sistema de Salud. Objective The objective of the study is to analyze the behavior dynamics of COVID-19 in Peru, estimate and evaluate the impact of the suppression public policy (quarantine). Methods The SIR epidemiological model and the estimation with the ordinary Least Squares (OLS) method. Results It was found that the basic number of propagation (Ro) fell from 6,0 to 3,2 having been reduced by 54% due to the suppression strategy;and two months later it falls to 1,7. However, it remains high and evidence that the level of those infected continues to expand with its adverse social and economic effects. Conclusion COVID-19 is a disease that grows exponentially, and that the health policy based on the suppression strategy has allowed to flatten the contagion curve, thus avoiding the collapse of the Health System.

Safety, efficacy, and immunogenicity of the NVX-CoV2373 vaccine.

INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in significant morbidity and mortality worldwide. As SARS-CoV-2 moves into endemic status, vaccination remains a key element in protecting the health of individuals, societies, and economies worldwide. AREAS COVERED: NVX-CoV2373 (Novavax, Gaithersburg, MD) is a recombinant protein vaccine composed of SARS-CoV-2 spike trimer nanoparticles formulated with saponin-based Matrix-M™ adjuvant (Novavax, Gaithersburg, MD). NVX-CoV2373 is authorized for emergency use in adults and adolescents aged ≥12 years in the United States and numerous other countries. EXPERT OPINION: In clinical trials, NVX-CoV2373 showed tolerable reactogenicity and favorable safety profiles characterized by mostly mild-to-moderate adverse events of short duration and by low rates of severe and serious adverse events comparable to those seen with placebo. The two-dose primary vaccination series resulted in robust increases in anti-spike protein immunoglobulin G, neutralizing antibody titers, and cellular immune responses. NVX-CoV2373 vaccination was associated with complete protection against severe disease and a high (90%) rate of protection against symptomatic disease in adults, including symptomatic disease caused by SARS-CoV-2 variants. Additionally, the NVX-CoV2373 adjuvanted recombinant protein platform offers a means to address issues of COVID-19 vaccination hesitancy and global vaccine equity.

Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain.

Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8-36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.

Disseminated tuberculosis and diagnosis delay during the COVID-19 era in a Western European country: a case series analysis.

Background: Disseminated tuberculosis is frequently associated with delayed diagnosis and a poorer prognosis. Objectives: To describe case series of disseminated TB and diagnosis delay in a low TB burden country during the COVID-19 period. Methodology: We consecutively included all patients with of disseminated TB reported from 2019 to 2021 in the reference hospital of the Northern Crown of the Metropolitan Area of Barcelona. We collected socio-demographic information, clinical, laboratory and radiological findings. Results: We included all 30 patients reported during the study period-5, 9, and 16 in 2019, 2020, and 2021 respectively-20 (66.7%) of whom were male and whose mean age was 41 years. Twenty-five (83.3%) were of non-EU origin. The most frequent system involvement was central nervous system (N = 8; 26.7%) followed by visceral (N = 7; 23.3%), gastro-intestinal (N = 6, 20.0%), musculoskeletal (N = 5; 16.7%), and pulmonary (N = 4; 13.3%). Hypoalbuminemia and anemia were highly prevalent (72 and 77%). The median of diagnostic delay was 6.5 months (IQR 1.8-30), which was higher among women (36.0 vs. 3.5 months; p = 0.002). Central nervous system involvement and pulmonary involvement were associated with diagnostic delay among women. We recorded 24 cured patients, two deaths, three patients with post-treatment sequelae, and one lost-to-follow up. We observed a clustering effect of patients in low-income neighborhoods (p < 0.001). Conclusion: There was a substantial delay in the diagnosis of disseminated TB in our study region, which might impacted the prognosis with women affected more negatively. Our results suggest that an increase in the occurrence of disseminated TB set in motion by diagnosis delay may have been a secondary effect of the COVID-19 pandemic.

Mobile Health Requirements for the Occupational Health Assessment of Health Care Professionals: Delphi Study.

BACKGROUND: In recent years, owing to the COVID-19 pandemic, awareness of the high level of stress among health care professionals has increased, and research in this area has intensified. Hospital staff members have historically been known to work in an environment involving high emotional demands, time pressure, and workload. Furthermore, the pandemic has increased the strain experienced by health care professionals owing to the high number of people they need to manage and, on many occasions, the limited available resources with which they must carry out their functions. These psychosocial risks are not always well dealt with by the organization or the professionals themselves. Therefore, it is necessary to have tools to assess these psychosocial risks and to optimize the management of this demand from health care professionals. Digital health, and more specifically, mobile health (mHealth), is presented as a health care modality that can contribute greatly to respond to these unmet needs. OBJECTIVE: We aimed to analyze whether mHealth tools can provide value for the study and management of psychosocial risks in health care professionals, and assess the requirements of these tools. METHODS: A Delphi study was carried out to determine the opinions of experts on the relevance of using mHealth tools to evaluate physiological indicators and psychosocial factors in order to assess occupational health, and specifically, stress and burnout, in health care professionals. The study included 58 experts with knowledge and experience in occupational risk prevention, psychosocial work, and health-related technology, as well as health professionals from private and public sectors. RESULTS: Our data suggested that there is still controversy about the roles that organizations play in occupational risk prevention in general and psychosocial risks in particular. An adequate assessment of the stress levels and psychosocial factors can help improve employees' well-being. Moreover, making occupational health evaluations available to the team would positively affect employees by increasing their feelings of being taken into account by the organization. This assessment can be improved with mHealth tools that identify and quickly highlight the difficulties or problems that occur among staff and work teams. However, to achieve good adherence and participation in occupational health and safety evaluations, experts consider that it is essential to ensure the privacy of professionals and to develop feelings of being supported by their supervisors. CONCLUSIONS: For years, mHealth has been used mainly to propose intervention programs to improve occupational health. Our research highlights the usefulness of these tools for evaluating psychosocial risks in a preliminary and essential phase of approaches to improve the health and well-being of professionals in health care settings. The most urgent requirements these tools must meet are those aimed at protecting the confidentiality and privacy of measurements.

Clinical Profile and Determinants of Mortality in Patients with Interstitial Lung Disease Admitted for COVID-19.

BACKGROUND: Concern has risen about the effects of COVID-19 in interstitial lung disease (ILD) patients. The aim of our study was to determine clinical characteristics and prognostic factors of ILD patients admitted for COVID-19. METHODS: Ancillary analysis of an international, multicenter COVID-19 registry (HOPE: Health Outcome Predictive Evaluation) was performed. The subgroup of ILD patients was selected and compared with the rest of the cohort. RESULTS: A total of 114 patients with ILDs were evaluated. Mean ± SD age was 72.4 ± 13.6 years, and 65.8% were men. ILD patients were older, had more comorbidities, received more home oxygen therapy and more frequently had respiratory failure upon admission than non-ILD patients (all p < 0.05). In laboratory findings, ILD patients more frequently had elevated LDH, C-reactive protein, and D-dimer levels (all p < 0.05). A multivariate analysis showed that chronic kidney disease and respiratory insufficiency on admission were predictors of ventilatory support, and that older age, kidney disease and elevated LDH were predictors of death. CONCLUSIONS: Our data show that ILD patients admitted for COVID-19 are older, have more comorbidities, more frequently require ventilatory support and have higher mortality than those without ILDs. Older age, kidney disease and LDH were independent predictors of mortality in this population.

Treatment of Long-Haul COVID Patients With Off-Label Acyclovir.

The SARS-CoV-2 virus (COVID-19) became a global pandemic in March 2020. This novel, highly infectious virus caused millions of infections and deaths around the world. Currently, there are few medications that are available for the treatment of COVID-19. Those affected are most commonly given supportive care, with some experiencing symptoms for months. We report a series of four cases depicting the successful use of acyclovir in the treatment of the virus SARS-CoV-2 in patients with long-haul symptoms, especially those in the realm of encephalopathy and neurological problems. Treatment with acyclovir in these patients resolved their symptoms and lowered their IgG and IgM titers, supporting the use of acyclovir as a safe and effective treatment for COVID-19 neurologic symptoms. We suggest the use of the antiviral medication, acyclovir, as a treatment for patients with long-term symptoms and unusual presentations of the virus, such as encephalopathy or coagulopathy.

Clinical Characteristics of Sars-Cov-2 Infection in Patients with Systemic Lupus Erythematosus in Argentina: Data from the Sar-Covid National Registry

Objectives: Patients with systemic lupus erythematosus (SLE) present greater severity of SARS-CoV-2 infection compared to the general population, particularly those with glomerulonephritis and who are treated with glucocorticoids. Likewise, high disease activity and some immunosuppressants have been associated with worse outcomes. The aim of this study was to describe the characteristics of SARS-CoV-2 infection in patients with SLE in Argentina from the SAR-COVID registry and to establish factors associated with a worse outcome. Method(s): Observational study. Patients diagnosed with SLE with confirmed SARS-CoV-2 infection (RT-PCR and/or positive serology) from the SAR-COVID registry were included. Data were collected from August 2020 to March 2022. The outcome of the infection was measured using the World Health Organization-ordinal scale (WHO-OS). Severe COVID-19 was defined as an WHO-OS value >=5. Descriptive analysis, Student's t , Mann Whitney U, ANOVA, Chi2 and Fisher's tests. Multivariable logistic regression. Result(s): A total of 399 patients were included, 93%female, with a mean age of 40.9 years (SD 12.2), 39.6% had at least one comorbidity. At the time of infection, 54.9% were receiving glucocorticoids, 30.8% immunosuppressants, and 3.3% biological agents. SARS-CoV-2 infection was mild in most cases, while 4.6% had a severe course and/or died. The latter had comorbidities, used glucocorticoids, and had antiphospholipid syndrome (APS) more frequently and higher disease activity at the time of infection. In the multivariate analysis, high blood pressure (OR 5.1, 95% CI 1.8-15.0), the diagnosis of APS (4.7, 95% CI 1.2-15.8), and the use of glucocorticoids (10 mg/day or more: OR 5.5, 95% CI 1.6-20.5) were associated with severe hospitalization and/or death from COVID-19 (WHO-EO >= 5). Conclusion(s): In this cohort of SLE patients with confirmed SARS-CoV-2 infection, most had a symptomatic course, 22.1% were hospitalized, and 5% required mechanical ventilation. Mortality was close to 3%. The diagnosis of APS, having high blood pressure, and the use of glucocorticoids were significantly associated with severe COVID-19.

Application of new indicators to assess the quality of antimicrobial use in intensive care units.

This study explored the feasibility of a bundle of indicators aimed at assessing the quality of antimicrobial use in intensive care units (ICUs) through an observational prospective study spanning 12 quarters (January 2019-December 2021) in a 1290-bed teaching hospital in Spain. Members of the antimicrobial stewardship programme team selected the indicators to analyse the quality of antimicrobial use based on consumption data from a list proposed in a previous study. Antimicrobial use in the ICU was measured as defined daily dose (DDD) per 100 occupied bed-days. Trends and points of change were analysed with segmented regression. The intravenous macrolides/intravenous respiratory fluoroquinolones ratio in the ICU increased progressively, although not significantly, by 11.14% per quarter, likely related to prioritization of the use of macrolides in serious community-acquired pneumonia and the coronavirus disease 2019 pandemic. A remarkable upward trend of 2.5% per quarter was detected in the anti-methicillin-susceptible Staphylococcus aureus/anti-methicillin-resistant S. aureus agents ratio in the ICU, which could be explained by the low prevalence of methicillin-resistant S. aureus at the study centre. Patterns of amoxicillin-clavulanic acid/piperacillin-tazobactam ratio and diversification of anti-pseudomonal beta-lactams showed an increment in use over the study. The use of these novel indicators provides additional information for the current analysis of DDD. Implementation is feasible, and led to the detection of patterns that agree with local guidelines and cumulative antibiogram reports, and foster targeted improvement actions within antimicrobial stewardship programmes.