Aging shapes infection profiles of influenza A virus and SARS-CoV-2 in human lung slices (preprint)

The recent coronavirus disease 2019 (COVID-19) outbreak revealed the susceptibility of elderly patients to respiratory virus infections, showing cell senescence or subclinical persistent inflammatory profiles and favouring the development of severe pneumonia. In our study, we evaluated the potential influence of lung aging on the efficiency of replication of influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2), as well as determined the pro-inflammatory and antiviral responses of the distal lung tissue. Using precision-cut lung slices (PCLS) from donors of different ages, we found that pandemic H1N1 and avian H5N1 IAV replicated in the lung parenchyma with high efficacy. In contrast to these IAV strains, SARS-CoV-2 early isolate and Delta variant of concern (VOC) replicated less efficiently in PCLS. Interestingly, both viruses showed reduced replication in PCLS from older compared to younger donors, suggesting that aged lung tissue represents a sub optimal environment for viral replication. Regardless of the age-dependent viral loads, PCLS responded to infection with both viruses by an induction of IL-6 and IP-10/CXCL10 mRNAs, being highest for H5N1. Finally, while SARS-CoV-2 infection was not causing detectable cell death, IAV infection caused significant cytotoxicity and induced significant early interferon responses. In summary, our findings suggest that aged lung tissue might not favour viral dissemination, pointing to a determinant role of dysregulated immune mechanisms in the development of severe disease.

Managing Patients with Immune-Mediated Inflammatory Diseases on Disease-Modifying Antirheumatic Drug Therapy in a COVID-19 Endemic World: A Narrative Review and Expert Insights (preprint)

During the coronavirus disease 2019 (COVID-19) pandemic, individuals with immune-mediated inflammatory diseases (IMIDs), such as systemic lupus erythematosus and rheumatoid arthritis, face a heightened risk of infection and severe outcomes due to immunological alterations resulting from their underlying conditions and immunosuppressive treatments. Even as the pandemic has transitioned to an endemic state, it remains crucial to recognize that these patients continue to be at risk. In this narrative review, we analyzed existing literature to explore the impact of IMIDs, clinical risk factors, and the influence of immunosuppressive therapies on COVID-19-related risks and outcomes. Notably, certain disease-modifying antirheumatic drugs (DMARDs), like rituximab, are associated with worse COVID-19 outcomes, and rituximab-treated patients show impaired immune responses to COVID-19 vaccination. Additionally, we outline the diverse effects of glucocorticoids on COVID-19 outcomes and management. To highlight real-life challenges faced by clinicians caring for patients with IMIDs, we present an illustrative scenario that underscores the importance of effective vaccination, timely boosting, and additional mitigation strategies against COVID-19. Given the clinical heterogeneity and diverse disease states within IMIDs, it is crucial to understand the ongoing implications and risks associated with COVID-19 in these patients, to guide the implementation of appropriate measures and optimize care and outcomes in the current endemic era.

Perceptions of COVID-19 Vaccination among Organ Transplant Recipients (preprint)

Understanding vaccine hesitancy in organ transplant recipients (OTR) is critical, given clear, alt-hough attenuated, benefits from vaccination. Adult OTR were surveyed regarding vaccine-related values and a novel outcome variable called Vaccine Acceptance Composite Score (VACS) was built as the average Likert score of 7 domains of vaccination confidence. Of 46 OTR included (93.5% kidney transplant recipients), 32.6% were female, 13.3% Black, 6.77% Hispan-ic/Latino/a/x; median age was 58 years. Patients were most concerned about COVID-19 vac-cine-associated risks (46.3%), its potential effect on allograft (47.6%) and motives of government officials involved with vaccine policy (55.6%). Politically conservative patients were likely to have a significantly lower VACS, while those who lived with someone ≥65 had a higher VACS. The VACS was not significantly associated with race, income, religious beliefs, comorbidities, COVID-19 history, or influenza vaccination status. Higher VACS was significantly associated with ≥3 and ≥4 COVID-19 immunizations. This study highlighted political beliefs and elderly household members as correlates of vaccine acceptance among OTR. The VACS may be a useful tool to help standardize multifaceted analyses in vaccination-focused behavioral research, as well as identify individuals and groups at risk for vaccine hesitancy, who may benefit from tai-lored outreach and educational interventions.

Post-COVID-19: Time to Change Our Way of Life for a Better Future (preprint)

Rationale - From the year 1 anno Domini until 1855 with the third Plague, major pandemics occurred on average every 348 years. Since then, they have occurred on average every 33 years, with Coronavirus disease 2019 (COVID-19) now underway.Even though current technologies have greatly improved the way of life of human beings, COVID-19, with more than 700 000 000 cases and 6 950 000 deaths worldwide by the end of 2023, reminds us that much remains to be done. Objective - Given the frequency and duration of recent pandemics, it might be wise to start thinking about preventative methods to minimize the impact of future pandemics. This report looks back at 18 months of COVID-19, from March 2020 to August 2021, with the aim of highlighting potential solutions that could prove practical, or even essential, for the future. Material - COVID-19 data, including case and death reports, were extracted daily from the Worldometer platform to build a database for macroscopic analysis of the spread of the virus around the world. Demographic data were integrated into the COVID-19 database for a better understanding of the spatial spread of the SARS-CoV-2 virus in cities/municipalities. Method - Without loss of generality, we only analyzed data from the top 30 (out of 200 and above) countries ranked by total number of COVID-19 cases. Statistics (regression, t-test (p < 0.05), correlation, mean ± std, etc.) were carried out with Excel software. Spectral analysis, using Matlab software, was also used to try to better understand the temporal spread of COVID-19. Results - A good linear correlation was observed between the number of cases and the respective number of deaths depending on the country, i.e. y = 0.0121x + 19559 with R² = 0.8042. The analysis then focused mainly on the number of cases.This study showed that COVID-19 mainly affects G20 countries. The most interesting result is that cities/municipalities with high population density are a powerful activator of the spread of the virus. The current demographic context seems to be becoming a societal problem that must be addressed adequately.Spectral analysis highlighted that the very first months of spread of COVID-19 were the most notable with a strong expansion of the SARS-CoV-2 virus. On the other hand, the following six months showed a certain stability due mainly to multiple preventive measures such as confinement, closure of non-essential services, wearing of masks, distancing of 2 meters, etc. Discussion - Analysis of case and death data showed that COVID-19 mainly affects G20 countries. Nevertheless, the most interesting result of this study is that cities and municipal areas with population densities of several thousand inhabitants per square kilometer largely favored the spread of the SARS-CoV-2 virus. It is believed that such a demographic context is becoming a societal problem that developed countries around the world will sooner or later face and therefore needs to be adequately addressed. Conclusion - COVID-19 has made us understand that it is time to act both preventatively and curatively. Phenomenological insights suggest that the next pandemic could occur in less than 50 years. It may be time to launch new societal projects aimed at relieving congestion in densely populated regions.

Burnout in Medical Specialists Redeployed to Emergency Care During the COVID-19 Pandemic (preprint)

Burnout represents a concern for all healthcare providers, particularly those specializing in emergency medical care for whom burnout outcomes have been well-documented. What remains unknown is the effect of burnout on redeployed medical specialists during the COVID-19 pandemic from an appointment-centered practice to emergency care directed by public health considerations. This research aims to identify and assess the burnout responses of fourteen medical specialties noted in searched returns of the four most cited articles published since 2020 about non-emergency physicians regarding their burnout brought on by the unanticipated need for them to provide emergency care during the recent pandemic. The hypothesis is that medical specialists accustomed to planning for emergency possibilities in their appointment-centered practice would demonstrate the least burnout regarding COVID-19-related emergencies. Considering coping as a process based on Lazarus's research, comparing and ranking the COVID-19 emergency responses across the various normally appointment-centered medical specialties in their employed coping strategies determines the outcome. With the hypothesis supported, suggested interventions for future pandemics—when these specialists are, again, redeployed to emergency care directed by public health considerations—are those coping strategies identified as most effective in reducing burnout while maintaining the viability of the medical specialty and excellent patient care.

Uncovering Latent Arguments in Social Media Messaging by Employing LLMs-in-the-Loop Strategy (preprint)

The widespread use of social media has led to a surge in popularity for automated methods of analyzing public opinion. Supervised methods are adept at text categorization, yet the dynamic nature of social media discussions poses a continual challenge for these techniques due to the constant shifting of the focus. On the other hand, traditional unsupervised methods for extracting themes from public discourse, such as topic modeling, often reveal overarching patterns that might not capture specific nuances. Consequently, a significant portion of research into social media discourse still depends on labor-intensive manual coding techniques and a human-in-the-loop approach, which are both time-consuming and costly. In this work, we study the problem of discovering arguments associated with a specific theme. We propose a generic LLMs-in-the-Loop strategy that leverages the advanced capabilities of Large Language Models (LLMs) to extract latent arguments from social media messaging. To demonstrate our approach, we apply our framework to contentious topics. We use two publicly available datasets: (1) the climate campaigns dataset of 14k Facebook ads with 25 themes and (2) the COVID-19 vaccine campaigns dataset of 9k Facebook ads with 14 themes. Furthermore, we analyze demographic targeting and the adaptation of messaging based on real-world events.

The Psychological Ability to Cope Reduced Infections During the Pandemic: A Two-Year Population-Based Study of The Determinants of 123 Million COVID-19 Test Results in Denmark (preprint)

During the COVID-19 pandemic, a key concern for authorities was to identify and activate the psychological states most likely to motivate the public to engage in protective behavior such as physical distancing and hygienic protection. While feelings of fear and threat were rampant during the pandemic, theories of health psychology have highlighted appraisals related to the ability to cope (e.g., the feeling of being able to cost-effectively adhere to government advice) and argued that coping appraisals are superior predictors of motivations to protect the self against risks. In this study, we provide a massive population-based comparison of the association between, on the one hand, threat appraisals, and coping appraisals and, on the other hand, protection against actual infection during the COVID-19 pandemic. To this end, we utilize a unique data infrastructure from Denmark that couple surveys of 8 % of the adult Danish population (N= 386.633) with the individual results of all 123 million COVID-19 tests performed in Denmark during 23 months of the COVID-19 pandemic. Overall, controlling for a comprehensive range of sociodemographic measures and employing panel data to bolster internal validity, we observe that stronger coping appraisals are consistently associated with lower individual probability of COVID-19 infection risk. We find no con-sistent evidence for a similar association for threat appraisals. Threat appraisals rather seem to index – to some extent, accurately – individual feelings of infection exposure. As appeals to fear also have unintended negative consequences (includ-ing anxiety, fatigue, and stigmatization), the findings provide strong empirical support for relying on coping-oriented public health communication in future societal crises in the domain of health and beyond.

Retrospective Analysis of Clostridioides difficile Infection Rates in Hospitalized Patients during COVID-19 Pandemic. A Unicenter Study in Reus, Spain (preprint)

.Background: Clostridioides difficile infections (CDI) vary in severity from mild diarrhea to life-threatening conditions like pseudomembranous colitis or toxic megacolon, often leading to sepsis and death. The COVID-19 pandemic prompted changes in healthcare practices, potentially affecting CDI incidence, though reported data are inconclusive. We studied factors influencing CDI incidence and outcomes at a university hospital throughout the COVID-19 pandemic years. Methods: We conducted a retrospective study on all adult hospitalized CDI cases from January 1, 2020, to December 31, 2022. We collected demographic information, comorbid conditions, and concurrent infections. Results: While overall CDI and COVID-19 rates decreased in 2022, a nota-ble increase in CDI infections was observed among oncological patients and those undergoing some aggressive treatments, such as colon or gastroscopies. The prevalence of comorbidities remained unmodified, and there were declines in prior gastrointestinal surgeries and proton pump inhibitor prescriptions. Factors associated with patient fatality or prolonged hospitaliza-tion included older age, cancer, chronic kidney disease, higher Charlson and McCabe indices, elevated C-reactive protein, and low albumin concentrations. Conclusion: Our study shows the evolving landscape of CDI during the COVID-19 pandemic and emphasizes the impact of de-layed diagnoses and treatments exacerbated by telemedicine adoption. Identified risk factors for CDI-related mortality or prolonged hospital stays underscore the importance of targeted inter-ventions in high-risk populations.

Saving High-Risk Patients from COVID-19 Severity and Death Mainly with Plant-Based Diets and Supplements (preprint)

Our report presents the findings from a treatment program that involved plant-based diets (PBDs) and supplements for 1,750 elderly cardiology patients diagnosed with COVID-19 between April 2020 and June 2023. At the start of the program, there was no published data supporting the use of PBDs for COVID-19 patients. However, after 18 months, studies were released that indicated the effectiveness of PBDs in decreasing the incidence and severity of COVID-19. Our treatment protocol differed from these studies in several ways. We carefully controlled the quality, quantity, and processing method of the foods we provided, opting for raw instead of cooked vegetables. Additionally, we incorporated supplementation that complemented the nutrients lacking in a PBD and enhanced the anti-viral, anti-inflammatory, antioxidant, antithrombotic, and immunomodulatory properties of a PBD. Our patients recovered faster (12±1.4 days vs. 20.9±4.3 days), with lower severity (2% vs. 10-20%), hospitalizations (0 vs. 5-10%), and deaths (0 vs. 15-17%) compared to the general population. These favorable outcomes are particularly noteworthy given Indonesia's high COVID-19 morbidity and mortality rates, among the highest in Asia. The findings of this report provide valuable insights for practitioners in managing high-risk elderly COVID-19 patients, particularly in avoiding severity and mortality.

SARS-CoV-2 spike S2 subunit inhibits p53 activation of p21(WAF1), TRAIL Death Receptor DR5 and MDM2 proteins in cancer cells (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and COVID-19 infection has led to worsened outcomes for patients with cancer. SARS-CoV-2 spike protein mediates host cell infection and cell-cell fusion that causes stabilization of tumor suppressor p53 protein. In-silico analysis previously suggested that SARS-CoV-2 spike interacts with p53 directly but this putative interaction has not been demonstrated in cells. We examined the interaction between SARS-CoV-2 spike, p53 and MDM2 (E3 ligase, which mediates p53 degradation) in cancer cells using an immunoprecipitation assay. We observed that SARS-CoV-2 spike protein interrupts p53-MDM2 protein interaction but did not detect SARS-CoV-2 spike bound with p53 protein in the cancer cells. We further observed that SARS-CoV-2 spike suppresses p53 transcriptional activity in cancer cells including after nutlin exposure of wild-type p53-, spike S2-expressing tumor cells and inhibits chemotherapy-induced p53 gene activation of p21(WAF1), TRAIL Death Receptor DR5 and MDM2. The suppressive effect of SARS-CoV-2 spike on p53-dependent gene activation provides a potential molecular mechanism by which SARS-CoV-2 infection may impact tumorigenesis, tumor progression and chemotherapy sensitivity. In fact, cisplatin-treated tumor cells expressing spike S2 were found to have increased cell viability as compared to control cells. Further observations on gamma-H2AX expression in spike S2-expressing cells treated with cisplatin may indicate altered DNA damage sensing in the DNA damage response pathway. The preliminary observations reported here warrant further studies to unravel the impact of SARS-CoV-2 and its various encoded proteins including spike on pathways of tumorigenesis and response to cancer therapeutics.

Characterization of spike processing and entry mechanisms of seasonal human coronaviruses NL63, 229E and HKU1 (preprint)

Although much has been learned about the entry mechanism of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the details of entry mechanisms of seasonal human coronaviruses (HCoVs) remain less well understood. In the present study, we established that 293T cell lines that stably express angiotensin converting enzyme (ACE2), aminopeptidase N (APN), or transmembrane serine protease 2 (TMPRSS2) support high level transduction of lentiviral pseudoviruses bearing spike proteins of seasonal HCoVs, HCoV-NL63, -229E, or -HKU1, respectively. Our results showed that entry of HCoV-NL63, -229E and -HKU1 pseudoviruses is sensitive to endosomal acidification inhibitors (chloroquine and NH4Cl), indicating virus entry via the endocytosis route. Although HCoV-HKU1 pseudovirus infection requires TMPRSS2 expression on cell surface, endocytosis-mediated HCoV-HKU1 entry requires the serine protease domain but not the serine protease activity of TMPRSS2. We also show that amino acids in the predicted S1/S2 junctions of spike proteins of HCoV-NL63, and -229E are essential for optimal entry but non-essential for spike-mediated entry of HCoV-HKU1. Our findings provide insights into entry mechanism of seasonal HCoVs that may support the development of novel treatment strategies.

Associations between SARS-CoV-2 Infection or COVID-19 Vaccination and Human Milk Composition: A Multi-Omics Approach (preprint)

The risk of contracting SARS-CoV-2 via human milk-feeding is virtually non-existent. Adverse effects of COVID-19 vaccination for lactating individuals are not different from the general population, and no evidence has been found that their infants exhibit adverse effects. Yet, there remains substantial hesitation among this population globally regarding the safety of these vaccines. Herein we aimed to determine if compositional changes in milk occur following infection or vaccination, including any evidence of vaccine components. Using an extensive multi-omics approach, we found that compared to unvaccinated individuals SARS-CoV-2 infection was associated with significant compositional differences in 67 proteins, 385 lipids, and 13 metabolites. In contrast, COVID-19 vaccination was not associated with any changes in lipids or metabolites, although it was associated with changes in 13 or fewer proteins. Compositional changes in milk differed by vaccine. Changes following vaccination were greatest after 1-6 hours for the mRNA-based Moderna vaccine (8 changed proteins), 3 days for the mRNA-based Pfizer (4 changed proteins), and adenovirus-based Johnson and Johnson (13 changed proteins) vaccines. Proteins that changed after both natural infection and Johnson and Johnson vaccine were associated mainly with systemic inflammatory responses. In addition, no vaccine components were detected in any milk sample. Together, our data provide evidence of only minimal changes in milk composition due to COVID-19 vaccination, with much greater changes after natural SARS-CoV-2 infection.

Machine Learning for Affordable Diagnosis of SARS-COV-2 from Hematological and Biochemical Tests (preprint)

COVID-19, caused by the SARS-CoV-2 virus, has spread around the world and killed around 6.9 million people. Rapid and accurate diagnosis is essential for preventing and controlling the disease, reducing transmission and consequently saving lives. RT-PCR is the gold standard test used to detect the disease. However, the test is expensive and the result is time-consuming, which makes mass testing difficult, especially in countries with limited resources. In addition, the test has high analytical specificity and low diagnostic sensitivity, which leads to false-negative results. Several studies in the literature report the presence of hematological and biochemical alterations in infected patients and use these alterations with machine learning algorithms to help diagnose the disease. Therefore, this article presents the results obtained by different neural network architectures based on Adaptive Resonance Theory (ART) for the diagnosis of COVID-19. The study was conducted in two distinct stages: the first consisted of selecting the best ART network among several, using three open-access datasets and comparing the results with the literature. In the second stage, the chosen model was tested on a dataset containing patients from various hospitals in four countries. In addition, the model was subjected to external validation, including data from a country not present during the training and adjustment of the model, in order to validate the robustness and generalization capacity of the model. The results obtained by the ART networks in this study are promising, outperforming not only classical models, but also the deep learning models often used in the literature. Validation on data from different countries strengthens the model’s reliability and effectiveness.

Precision medicine for pandemics: stratification of COVID-19 molecular phenotypes defined by topological analysis of global blood gene expression. (preprint)

Precision medicine offers a promising avenue for better therapeutic responses to pandemics such as COVID-19. This study leverages independent patient cohorts in Florence and Liege gathered under the umbrella of the DRAGON consortium for the stratification of molecular phenotypes associated with COVID-19 using topological analysis of global blood gene expression. Whole blood from 173 patients was collected and RNA was sequenced on the Novaseq platform. Molecular phenotypes were defined through topological analysis of gene expression relative to the biological network using the TopMD algorithm. The two cohorts from Florence and Liege allowed for independent validation of the findings in this study. Clustering of the topological maps of differential pathway activation revealed three distinct molecular phenotypes of COVID-19 in the Florence patient cohort, which were also observed in the Liege cohort. Cluster 1, was characterised by high activation of pathways associated with ESC pluripotency, NRF2, and TGF-B; receptor signalling. Cluster 2 displayed high activation of pathways including focal adhesion-PI3K-Akt-mTOR signalling and type I interferon induction and signalling, while Cluster 3 exhibited low IRF7-related pathway activation. TopMD was also used with the Drug-Gene Interaction Database (DGIdb), revealing pharmaceutical interventions targeting mechanisms across multiple phenotypes and individuals. The data illustrates the utility of molecular phenotyping from topological analysis of blood gene expression, and holds promise for informing personalised therapeutic strategies not only for COVID-19 but also for Disease X. Its potential transferability across multiple diseases highlights the value in pandemic response efforts, offering insights before large-scale clinical studies are initiated.

Exploring the Spatial Distribution of Persistent SARS-CoV-2 Mutations - Leveraging mobility data for targeted sampling (preprint)

Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking lineage spread, we investigated the potential of combining mobile service data and fine-granular metadata (such as postal codes and genomic data) to advance integrated genomic surveillance of the pandemic in the federal state of Thuringia, Germany. We sequenced over 6,500 SARS-CoV-2 Alpha genomes (B.1.1.7) across seven months within Thuringia while collecting patients' isolation dates and postal codes. Our dataset is complemented by over 66,000 publicly available German Alpha genomes and mobile service data for Thuringia. We identified the existence and spread of nine persistent mutation variants within the Alpha lineage, seven of which formed separate phylogenetic clusters with different spreading patterns in Thuringia. The remaining two are sub-clusters. Mobile service data can indicate these clusters' spread and highlight a potential sampling bias, especially of low-prevalence variants. Thereby, mobile service data can be used either retrospectively to assess surveillance coverage and efficiency from already collected data or to actively guide part of a surveillance sampling process to districts where these variants are expected to emerge. The latter concept proved successful as we introduced a mobility-guided sampling strategy for the surveillance of Omicron sublineage BQ.1.1. The combination of mobile service data and SARS-CoV-2 surveillance by genome sequencing is a valuable tool for more targeted and responsive surveillance.

A Critical Analysis of UK Media Characterisations of Long Covid in Children and Young People (preprint)

Long Covid is the continuation or development of symptoms related to a SARSCoV2 infection. Those with Long Covid may face epistemic injustice, where they are unjustifiably viewed as unreliable evaluators of their own illness experiences. Media articles both reflect and influence perception and subsequently how people regard children and young people (CYP) with Long Covid, and may contribute to epistemic injustice.? We aimed to explore how the UK media characterises Long Covid in CYP through examining three key actor groups: parents, healthcare professionals, and CYP with Long Covid, through the lens of epistemic injustice. A systematic search strategy resulted in the inclusion of 103 UK media articles. We used an adapted corpus-assisted Critical Discourse Analysis in tandem with thematic analysis. Specifically, we utilised search terms to locate concordances of key actor groups. In the corpus, parents highlighted minimisation of Long Covid, barriers to care, and experiences of personal attacks. Mothers were presented as also having Long Covid. Fathers were not mentioned once. Healthcare professionals emphasised the rarity of Long Covid in CYP, avoided pathologizing Long Covid, and overemphasised psychological components. CYP rarely were consulted in media articles but were presented as formerly very able. Manifestations of Long Covid in CYP were validated or invalidated in relation to adults. Media characterisations contributed to epistemic injustice. The disempowering portrayal of parents promote stigma and barriers to care. Healthcare professionals' narratives often contributed to negative healthcare experiences and enacted testimonial injustice, where CYP and parents credibility was diminished due to unfair identity prejudice, in their invalidation of Long Covid. Media characterisations reveal and maintain a lack of societal framework for understanding Long Covid in CYP. The findings of this study illustrate the discursive practices employed by journalists that contribute to experiences of epistemic injustice. Based on our findings, we propose recommendations for journalists.

The asymptomatic proportion of SARS-CoV-2 Omicron-variant infections in households: A systematic review (preprint)

Background Understanding the clinical spectrum of SARS-CoV-2 infection, including the asymptomatic fraction, is important as asymptomatic individuals are still able to infect other individuals and contribute to ongoing transmission. The WHO Unity Household transmission investigation (HHTI) protocol provides a platform for the prospective and systematic collection of high-quality clinical, epidemiological, serological, and virological data from SARS-CoV-2 confirmed cases and their household contacts. These data can be used to understand key severity and transmissibility parameters - including the asymptomatic proportion - in relation to local epidemic context and help inform public health response. Methods We aimed to estimate the asymptomatic proportion of SARS-CoV-2 Omicron-variant infections in Unity-aligned HHTIs. We conducted a systematic review and meta-analysis in alignment with the PRISMA 2020 guidelines and registered our systematic review on PROSPERO (CRD42022378648). We searched EMBASE, Web of Science, MEDLINE, and bioRxiv and medRxiv from 1 November 2021 to 22 August 2023. Results We identified 8,368 records, of which 98 underwent full text review. We identified only three studies for data extraction, with substantial variation in study design and corresponding estimates of the asymptomatic proportion. As a result, we did not generate a pooled estimate or I2 metric. Conclusions The limited number of quality studies that we identified highlights the need for improved preparedness and response capabilities to facilitate robust HHTI implementation, analysis and reporting, to better inform national, regional and global risk assessments and policy making.

Physical activity, low-grade inflammation, and psychological responses to the COVID-19 pandemic among older adults in England (preprint)

Mental health responses to the COVID-19 pandemic have been widely studied, but less is known about the potentially protective role of physical activity (PA) and the impact of low-grade inflammation. Using a sample of older adults from England, this study tested (1) if pre-pandemic PA and its changes during the pandemic were associated with mental health responses; (2) if older adults with low-grade inflammation experienced greater increases in depression and anxiety, compared to pre-pandemic levels; (3) if PA attenuated the association between inflammation and depression/anxiety. The study used data from the English Longitudinal Study of Ageing, a cohort study following a national sample aged 50+. Information on mental health and PA were collected before the pandemic (2016/17 and 2018/19) and during November and December 2020. Inflammation was ascertained using pre-pandemic C-reactive protein (CRP). Analyses were adjusted for sociodemographic and health-related factors and pre-pandemic mental health. Increasing PA from before to during the pandemic was linked to reduced odds of depression (OR = 0.955, 95%CI [0.937, 0.974]) and anxiety (OR = 0.954, 95%CI [0.927; 0.982]). Higher pre-pandemic PA was associated with reduced odds of depression (OR = 0.964, 95%CI [0.948, 0.981]) and anxiety (OR = 0.976, 95%CI [0.953, 1.000]), whereas elevated CRP was associated with 1.343 times higher odds of depression (95%CI [1.100, 1.641]). PA did not attenuate the inflammation-depression association. The findings suggest that PA may contribute to psychological resilience among older adults, independently of inflammation. Further research is needed to explore the psychobiological pathways underlying this protective mechanism.

Precision Phenotyping for Curating Research Cohorts of Patients with Post-Acute Sequelae of COVID-19 (PASC) as a Diagnosis of Exclusion (preprint)

Scalable identification of patients with the post-acute sequelae of COVID-19 (PASC) is challenging due to a lack of reproducible precision phenotyping algorithms and the suboptimal accuracy, demographic biases, and underestimation of the PASC diagnosis code (ICD-10 U09.9). In a retrospective case-control study, we developed a precision phenotyping algorithm for identifying research cohorts of PASC patients, defined as a diagnosis of exclusion. We used longitudinal electronic health records (EHR) data from over 295 thousand patients from 14 hospitals and 20 community health centers in Massachusetts. The algorithm employs an attention mechanism to exclude sequelae that prior conditions can explain. We performed independent chart reviews to tune and validate our precision phenotyping algorithm. Our PASC phenotyping algorithm improves precision and prevalence estimation and reduces bias in identifying Long COVID patients compared to the U09.9 diagnosis code. Our algorithm identified a PASC research cohort of over 24 thousand patients (compared to about 6 thousand when using the U09.9 diagnosis code), with a 79.9 percent precision (compared to 77.8 percent from the U09.9 diagnosis code). Our estimated prevalence of PASC was 22.8 percent, which is close to the national estimates for the region. We also provide an in-depth analysis outlining the clinical attributes, encompassing identified lingering effects by organ, comorbidity profiles, and temporal differences in the risk of PASC. The PASC phenotyping method presented in this study boasts superior precision, accurately gauges the prevalence of PASC without underestimating it, and exhibits less bias in pinpointing Long COVID patients. The PASC cohort derived from our algorithm will serve as a springboard for delving into Long COVID's genetic, metabolomic, and clinical intricacies, surmounting the constraints of recent PASC cohort studies, which were hampered by their limited size and available outcome data.

Effects of the Covid-19 pandemic on the continuity of sexual and reproductive health care in the maternity ward of a health and social promotion centre in Burkina Faso: a qualitative study (preprint)

The COVID-19 pandemic has significantly impacted the continuity of maternity care in Burkina Faso. This study aimed to compare the volumes of in-person visits and explore the experiences of healthcare providers and users regarding the continuity of healthcare in the maternity ward of a Health and Social Promotion Center (HSPC) before, during, and after the lockdown during the COVID-19 pandemic in Ouagadougou, Burkina Faso. Methods We conducted a multimethod, cross-sectional exploratory study with a phenomenological approach. Monthly health administrative data regarding family planning visits, antenatal visits, deliveries, and postnatal care before, during, and after COVID-19 were collected and compared. Qualitative data were collected through semi-structured interviews with family healthcare providers and users and thematically analyzed. Results The study found that the pandemic led to a decline in the demand for healthcare, as people were afraid of contracting COVID-19. This was particularly true for pregnant women who had recently given birth. The study also found that the pandemic disrupted the supply of essential medicines and medical supplies, which made it difficult for healthcare providers to provide quality care. The qualitative analysis allowed us to highlight three themes: the representation of respondents on COVID-19, their perception of the effectiveness of barrier measures and their analysis of the continuity of care in times of COVID-19: the picture of respondents on COVID-19, their perception of the efficacy of barrier measures and their analysis of the continuity of care in times of COVID-19. Despite these challenges, the study found that healthcare providers and users could find ways to maintain continuity of care. Conclusion The study concludes that the COVID-19 pandemic has significantly impacted the continuity of maternity care in Burkina Faso. However, healthcare providers and users have found ways to maintain continuity of care, and the study provides recommendations for improving continuity of care in the future.

A spatio-temporal model to detect potential outliers in disease mapping (preprint)

Spatio-temporal disease mapping models are commonly used to estimate the relative risk of a disease over time and across areas. For each area and time point, the disease count is modelled with a Poisson distribution whose mean is the product of an offset and the disease relative risk. This relative risk is commonly decomposed in the log scale as the sum of fixed and latent effects. The Rushworth model allows for spatio-temporal autocorrelation of the random effects. We build on the Rushworth model to accommodate and identify potentially outlying areas with respect to their disease relative risk evolution, after taking into account the fixed effects. An area may display outlying behaviour at some points in time but not all. At each time point, we assume the latent effects to be spatially structured and include scaling parameters in the precision matrix, to allow for heavy-tails. Two prior specifications are considered for the scaling parameters: one where they are independent across space and one with spatial autocorrelation. We investigate the performance of the different prior specifications of the proposed model through simulation studies and analyse the weekly evolution of the number of COVID-19 cases across the 33 boroughs of Montreal and the 96 French departments during the second wave. In Montreal, 6 boroughs are found to be potentially outlying. In France, the model with spatially structured scaling parameters identified 21 departments as potential outliers. We find that these departments tend to be close to each other and within common French regions.

Completeness of the COVID-19 Vaccination Schedule among Persons Experiencing Homelessness in Brazil (preprint)

Almost four years after COVID-19 was declared a global health emergency, equitable distribution of the vaccine remains a challenge, especially among homeless people, the fastest growing population in Brazil. Therefore, we sought to identify the factors associated with completion of the COVID-19 vaccination schedule among homeless people in Brazil. Materials and Methods: We carried out a cross-sectional study in the capital cities of Brazil's Federative Units, considering people living on the streets as the target population. We used a sequential inclusion approach, with individual interviews conducted by trained professionals, using a validated questionnaire. We used descriptive statistics to analyze the data and a binary logistic regression model to identify factors associated with homeless individuals who completed the COVID-19 vaccination schedule. Results: It was identified that the highest density of homeless people and indicators related to COVID-19 is located in the Northeast, Southeast and South regions of Brazil. The primary data sample consisted of 1,392 participants, predominantly male (n: 961; 69.0%), with an average age of 38.3±15.2 years, belonging to the black/brown race/color (n: 1,097; 78.8%), with an elementary school education (n: 1,060; 76.1%). The factors associated with completing the vaccination schedule were: receiving government aid (OR: 1.58; 95%CI: 1.09 - 2.30), visits from Health Agents from the Street Clinic (OR: 3.19; 95%CI: 1.95 - 5.36), history of COVID-19 (OR: 5.77; 95%CI: 3.17 - 11.15), support for mandatory vaccination against COVID-19 (OR: 3.76; 95%CI: 2.48 - 5.76), trust in the efficacy of vaccines (OR: 3.92; 95%CI: 2.63 - 5.89), seeking information from NGOs, street clinics, community leaders (OR: 1.91; 95%CI: 1.01 - 3.88) and trust in the Federal Government's statements on vaccines (OR: 1.57; 95%CI: 1.06 - 2.31).Conclusion: The study advances knowledge by highlighting the completeness of the COVID-19 vaccination schedule among the homeless population. The source of information proved to be one of the determinants of completeness, and the Unified Health System played a leading role in raising awareness among homeless people, notably through its strategy of street clinics, when available. The evidence points to the importance of affirmative and inclusive actions that guarantee access to the vaccine for homeless people.

Deaths averted by COVID-19 vaccination in select Latin American and Caribbean Countries: a modelling study (preprint)

BackgroundThe COVID-19 pandemic has had a significant impact on global health, with millions of lives lost worldwide. Vaccination has emerged as a crucial strategy in mitigating the impact of the disease. This study aims to estimate the number of deaths averted through vaccination in LAC during the first year and a half of vaccination rollout (January 2021 - May 2022). MethodsPublicly available data on COVID-19 deaths and vaccination rates were used to estimate the total number of deaths averted via vaccination in LAC. Using estimates for number of deaths, number of vaccinated, and vaccine effectiveness, a counterfactual estimated number of deaths observed without vaccination was calculated. Vaccine effectiveness estimates were obtained from published studies. The analysis focused on 17 countries in LAC and considered adults aged 18 years and above. FindingsAfter accounting for underreporting, the analysis estimated that over 1.49 million deaths were caused by COVID-19 in the selected countries during the study period. Without vaccination, the model estimated that between 2.10 and 4.11 million COVID-19 deaths would have occurred. Consequently, vaccination efforts resulted in approximately 610,000 to 2.61 million deaths averted. InterpretationThis study represents the first large-scale, multi-center estimate of population-level vaccine impact on COVID-19 mortality in LAC. The findings underscore the substantial impact of timely and widespread vaccination in averting COVID-19 deaths. These results provide crucial support for vaccination programs aimed at combating epidemic infectious diseases in the region and future pandemics. FundingThis study was funded by the Pan-American Health Organization (PAHO).

SARS-CoV-2 Antigen Rapid Detection Tests: test performance during the COVID-19 pandemic and the impact of COVID-19 vaccination (preprint)

IntroductionDuring the COVID-19 pandemic, SARS-CoV-2 antigen rapid detection tests (RDTs) emerged as point-of-care diagnostics in addition to the RT-qPCR as the gold standard for SARS-CoV-2 diagnostics. Facing the course of the COVID-19 pandemic to an endemic characterised by several SARS-CoV-2 virus variants of concern (VOC) and an increasing public COVID-19 vaccination rate the aim of the study was to investigate the long-term test performance of SARS-CoV-2 RDT in large-scale, clinical screening use during and its influencing factors, above all SARS-CoV-2 VOC and COVID-19 vaccination. MethodsIn a prospective performance assessment conducted at a single centre tertiary care hospital, RDTs from three manufacturers (NADAL(R), Panbio, MEDsan(R)) were compared to RT-qPCR among individuals aged [≥] 6 month. The evaluation involved the determination of standardised viral load from oropharyngeal swabs as well as the evaluation of their influencing factors, especially the COVID-19 vaccination, for detecting SARS-CoV-2 in a clinical point-of-care environment spanning from 12 November 2020 to 30 June 2023 among patients, staff, and visitors of the hospital. ResultsAmong the 78,798 RDT/RT-qPCR tandems analysed, 2,016 (2.6%) tandems tested positive for SARS-CoV-2, with an overall sensitivity of 34.5% (95% CI 32.4-36.6%). A logistic regression revealed that typical COVID-19 symptoms significantly declined over the course of the study and throughout the COVID-19 pandemic, and that among the vaccinated, significantly fewer presented with an infection exhibiting typical symptoms. The employed lasso regression model indicated that only higher viral load and typical COVID-19 symptoms significantly increase the likelihood of a positive RDT result in the case of a SARS-CoV-2 infection directly. ConclusionOur findings indicate that only viral load and COVID-19 symptoms directly influence RDT performance while the obtained effects of COVID-19 vaccination and Omicron VOC both reducing RDT performance were mediated by these two factors. RDTs remain an adequate diagnostic tool for detecting SARS-CoV-2 in individuals showing respiratory symptoms. RDTs show promise beyond SARS-CoV-2, proving adaptable for detecting other pathogens like Influenza and RSV, highlighting their ongoing importance in infection control and prevention efforts.

Psychosocial Predictors of Sleep Disturbances during COVID-19: differential contributions of demographic, psychological, pandemic-related factors to sleep health. (preprint)

Aim: Since the declaration of COVID-19 as a Public Health Emergency of International Concern on January 30, 2020, the disease escalated into a global pandemic forcing governments around the world to impose measures that affected all aspects of life. Among other countries, Greece adopted social restriction, lockdowns, and quarantines to reduce transmission from person to person.  Subjects and Methods: This cross-sectional study aimed to investigate the impact of those measures on sleep health in a Greek adult sample. An online questionnaire collected data during from 650 participant.  Results: 60% of responders scored below the clinical cut-off on the RU-SATED, indicating they experienced poor sleep health. Better sleep health was reported with increased age and years of education. On the other hand, higher trauma-related distress, depression, anxiety and stress symptomatology were related to poorer sleep health. No gender differences were observed, and degree of compliance to pandemic restrictions did not influence sleep health. Hierarchical regression analysis indicated difficulty in securing enough/healthy food, testing positive for COVID-19, experiencing an increase in verbal arguments/conflicts at home and an increase in responsibilities were the strongest predictors of poor sleep heath.  Conclusions: Results highlight the importance of maintaining good sleep health as a pillar of general physical and mental health.

Barriers and facilitators for strengthening physiotherapy services in Nepal: perspectives from physiotherapists and health providers (preprint)

Background: Physiotherapy provides non-invasive and non-pharmaceutical intervention for curative, rehabilitation and preventative purposes.  Physiotherapy is also a central provider of health promotion. As the global burden of non-communicable diseases and chronic health conditions is rising, the importance of physiotherapy services increases. Unfortunately, physiotherapy services in low- and middle-income countries (LMICs) are generally unsatisfactory. In Nepal, the earthquake in 2015 and the COVID pandemic have clearly illuminated the importance of physiotherapy. Objective: This qualitative study aimed to identify barriers and facilitators at different system levels for strengthening physiotherapy services in Nepal. Methods: Forty semi-structured individual interviews were performed with different health providers. Transcribed interviews were assessed with thematic analysis. A five-level socioecological framework conceptualised multilevel determinants of barriers and facilitators. Results: The study revealed various factors that were potential barriers and facilitators across five different levels, namely individual (taking the lead, need for advocacy), interpersonal (lack of recognition and autonomy, networking for referrals and coordination), community (lack of knowledge and awareness, social and family support), organisational (accessibility, workplace and clinical practice, educational opportunities, role of organisations and rehabilitation centres), and public policy level (planning and implementation of policies and programs, medical hegemony, priorities). Government officials, local leaders, and clinicians, half of whom were physiotherapists, agreed on many of the same issues, where a lack of awareness of what physiotherapy is and knowledge about what physiotherapists do was central. Conclusions: The results provide information for the development of physiotherapy by pointing out key elements that need attention, which are applicable to the situation in most LMIC countries where special focus needs to be directed towards rural and remote areas.

MAJOR METABOLITES FROM HYPERICUM PERFORATUM L., HYPERFORIN AND HYPERICIN, ARE BOTH ACTIVE AGAINST HUMAN CORONAVIRUSES (preprint)

COVID-19 pandemic has highlighted the need of antiviral molecules against coronaviruses. Plants are an endless source of active compounds. In the current study, we investigated the potential antiviral effects of Hypericum perforatum L. Its extract contained two major metabolites belonging to distinct chemical classes, hypericin (HC) and hyperforin (HF). First, we demonstrated that HC inhibited HCoV-229E at the entry step by directly targeting the viral particle in a light-dependent manner. While antiviral properties have already been described for HC, the study here showed for the first time that HF has pan-coronavirus antiviral capacity. Indeed, HF was highly active against Alphacoronavirus HCoV-229E (IC50 value of 1.10 {micro}M), and Betacoronaviruses SARS-CoV-2 (IC50 value of of 0.24 to 0.98 {micro}M), SARS-CoV (IC50 value of 1.01 {micro}M) and MERS-CoV (IC50 value of 2.55 {micro}M). Unlike HC, HF was active at a post-entry step, most likely the replication step. Antiviral activity of HF on HCoV-229E and SARS-CoV-2 was confirmed in primary human respiratory epithelial cells. Furthermore, in vitro combination assay of HF with remdesivir showed that their association was additive, which was encouraging for a potential therapeutical association. As HF was active on both Alpha- and Betacoronaviruses, a cellular target was hypothesized. Heme oxygenase 1 (HO-1) pathway, a potential target of HF, has been investigated but the results showed that HF antiviral activity against HCoV-229E was not dependent on HO-1. Collectively, HF is a promising antiviral candidate in view of our results and pharmacokinetics studies already published in animal models or in human.

The abortive SARS-CoV-2 infection of osteoclast precursors promotes their differentiation into osteoclasts (preprint)

The COVID-19 pandemic has resulted in the loss of millions of lives, although a majority of those infected have managed to survive. Consequently, a set of outcomes, identified as long COVID, is now emerging. While the primary target of SARS-CoV-2 is the respiratory system, the impact of COVID-19 extends to various body parts, including the bone. This study aims to investigate the effects of acute SARS-CoV-2 infection on osteoclastogenesis, utilizing both ancestral and Omicron viral strains. Monocyte-derived macrophages (MDM), which serve as precursors to osteoclasts, were exposed to both viral variants. However, the infection proved abortive, even though ACE2 receptor expression increased post-infection, with no significant impact on cellular viability and redox balance. Both SARS-CoV-2 strains heightened osteoclast formation in a dose-dependent manner, as well as CD51/61 expression and bone resorptive ability. Notably, SARS-CoV-2 induced early pro-inflammatory M1 macrophage polarization, shifting towards an M2-like profile. Osteoclastogenesis-related genes (RANK, NFATc1, DC-STAMP, MMP9) were upregulated, and surprisingly, SARS-CoV-2 variants promoted RANKL-independent osteoclast formation. This thorough investigation illuminates the intricate interplay between SARS-CoV-2 and osteoclast precursors, suggesting potential implications for bone homeostasis and opening new avenues for therapeutic exploration in COVID-19.

Exploring the Perspectives of Clients and Clinicians Regarding Digitally Delivered Psychotherapies Utilized for Trauma-Affected Populations. (preprint)

During the COVID-19 pandemic, many clinical sites shifted towards digital delivery of mental health services. However, there is still much to learn regarding tailoring interventions for trauma-affected populations, including military members, Veterans, and public safety personnel. This study examined perceptions of psychotherapies utilized for trauma-affected populations, as reported by Canadian military members, Veterans, and public safety personnel who completed such interventions and mental health clinicians who provided them. Specifically, we explored the shift to digital health use, what changed with this rapid shift, what needs, problems, and solutions arose, and important future considerations associated with delivering trauma-focused and adjunct treatments digitally.   Quantitative survey data were collected from 11 Canadian patients (military members, Veterans, and public safety personnel with post-traumatic stress injury) and 12 Canadian mental health clinicians. Survey questions were adapted from the Alberta Quality Matrix for Health (AQMH) and Unified Theory of Acceptance and Use of Technology (UTAUT) model. As a follow-up, participants were invited to participate in either a semi-structured qualitative interview or focus group to further explore their perspectives on digitally delivered trauma-focused and adjunct therapies. Four clients and 19 clinician participants participated in an interview or focus group.   In survey and interview/focus group results, patient and clinician participants reported that digitally delivered trauma and adjunct therapies offered similar treatment effectiveness as in-person delivery while also improving treatment access. Participants indicated unique advantages of digital delivery, including the increased accessibility of treatment, cost effectiveness, and more efficient use of resources. However, some participants struggled with using digital platforms and felt less comfortable working in a digital environment. Further research with a larger, more diverse population is required to corroborate our results and identify other avenues in which psychotherapies utilized for trauma-affected populations can be engaged with and improved upon.

Impact of COVID-19 on diabetes mellitus outcomes and care in sub-Saharan Africa: A scoping review (preprint)

Background: The COVID-19 pandemic impacted diabetes mellitus clinical outcomes and chronic care globally. However, little is known about its impact in low-resource settings such as sub-Saharan Africa. Hence, to address this, we systematically conducted a scoping review to explore the COVID-19 impact on diabetes outcomes and care in countries of sub-Saharan Africa. Methods We applied our search strategy to PubMed, Web of Science, CINAHL, African Index Medicus, Google Scholar, Cochrane Library, Scopus, Science Direct, ERIC and Embase to obtain relevant articles published from January 2020 to March 2023. Two independent reviewers were involved in the screening of retrieved articles. Data from eligible articles were extracted from quantitative, qualitative and mixed methods studies. Numerical data were summarised using descriptive statistics, while a thematic framework was used to categorise and identify themes for qualitative data. Results We found 42 of the retrieved 360 articles eligible, mainly from South Africa, Ethiopia and Ghana (73.4%). COVID-19 increased the risk of death (OR 1.30,9.0, 95% CI), hospitalisation (OR 3.30,3.73: 95% CI), and severity (OR: 1.30,4.05, 95% CI) in persons with diabetes mellitus. COVID-19 also increased the risk of developing diabetes mellitus in hospitalised cases. The pandemic, on the other hand, was associated with disruptions in patient self-management routine and diabetes mellitus care service delivery. Three major themes emerged, namely, (i) patient-related health management challenges, (ii) diabetes mellitus care service delivery challenges, and (iii) reorganisation of diabetes mellitus care delivery. Conclusion COVID-19 increased mortality and morbidity among people living with diabetes mellitus. In addition, the COVID-19 pandemic worsened diabetes mellitus care management. Sub-Saharan African countries should, therefore, institute appropriate policy considerations for persons with diabetes mellitus during widespread emergencies.