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The COVID-19 pandemic highlighted the need for a rapid, convenient, and scalable diagnostic method for detecting a novel pathogen amidst a global pandemic. While command-line interface tools offer automation for SARS-CoV-2 Oxford Nanopore Technology sequencing data analysis, they are inapplicable to users with limited programming skills. A solution is to establish such automated workflows within a graphical user interface software. We developed two workflows in the software Geneious Prime 2022.1.1, adapted for data obtained from the Midnight and Artic's nCoV-2019 sequencing protocols. Both workflows perform trimming, read mapping, consensus generation, and annotation on SARS-CoV-2 Nanopore sequencing data. Additionally, one workflow includes phylogenetic assignment using the bioinformatic tools pangolin and Nextclade as plugins. The basic workflow was validated in 2020, adhering to the requirements of the European Centre for Disease Prevention and Control for SARS-CoV-2 sequencing and analysis. The enhanced workflow, providing phylogenetic assignment, underwent validation at Uppsala University Hospital by analysing 96 clinical samples. It provided accurate diagnoses matching the original results of the basic workflow while also reducing manual clicks and analysis time. These bioinformatic workflows streamline SARS-CoV-2 Nanopore data analysis in Geneious Prime, saving time and manual work for operators lacking programming knowledge.

Infectious diseases manifesting in the form of epidemics or pandemics do not only cause devastating impacts on public health systems but also disrupt the functioning of the socio-economic structure. Further, risks associated with pandemics and epidemics become exacerbated with coincident compound hazards. This study aims to develop a framework that captures key elements and components of epidemic and pandemic preparedness and response systems, focusing on a multi-hazard context. A systematic literature review was used to collect data through peer-reviewed journal articles using three electronic databases, and 17 experts were involved in the validation. Epidemiological surveillance and early detection, risk and vulnerability assessments, preparedness, prediction and decision making, alerts and early warning, preventive strategies, control and mitigation, response, and elimination were identified as key elements associated with epidemic and pandemic preparedness and response systems in a multi-hazard context. All elements appear integrated within three interventional phases: upstream, interface, and downstream. A holistic approach focusing on all interventional phases is required for preparedness and response to pandemics and epidemics to counter their cascading and systemic effects. Further, a paradigm shift in the preparedness for multi-hazards during an epidemic or pandemic is essential due to the multiple challenges posed by concurrent hazards.

The development of vaccine candidates for COVID-19 has been rapid, and those that are currently approved display high efficacy against the original circulating strains. However, recently, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged with increased transmission rates and less susceptibility to vaccine induced immunity. A greater understanding of protection mechanisms, including antibody longevity and cross-reactivity towards the variants of concern (VoCs), is needed. In this study, samples collected in Denmark early in the pandemic from paucisymptomatic subjects ( n = 165) and symptomatic subjects ( n = 57) infected with SARS-CoV-2 were used to assess IgG binding and inhibition in the form of angiotensin-converting enzyme 2 receptor (ACE2) competition against the wild-type and four SARS-CoV-2 VoCs (Alpha, Beta, Gamma, and Omicron). Antibodies induced early in the pandemic via natural infection were cross-reactive and inhibited ACE2 binding of the VoC, with reduced inhibition observed for the Omicron variant. When examined longitudinally, sustained cross-reactive inhibitory responses were found to exist in naturally infected paucisymptomatic subjects. After vaccination, receptor binding domain (RBD)-specific IgG binding increased by at least 3.5-fold and inhibition of ACE2 increased by at least 2-fold. When vaccination regimens were compared (two doses of Pfizer-BioNTech BNT162b2 ( n = 50), or one dose of Oxford-AstraZeneca ChAdOx1 nCoV-19 followed by Pfizer-BioNTech BNT162b2 (ChAd/BNT) ( n = 15)), higher levels of IgG binding and inhibition were associated with mix and match (ChAd/BNT) prime-boosting and time since vaccination. These results are particularly relevant for countries where vaccination levels are low.

An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country's genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.

UK National Health Service (NHS) Clinical Virology Departments provide a repertoire of tests on clinical samples to detect the presence of viral genomic material or host immune responses to viral infection. In December 2019, a novel coronavirus (SARS-CoV-2) emerged which quickly developed into a global pandemic; NHS laboratories responded rapidly to upscale their testing capabilities. To date, there is little information on the impact of increased SARS-CoV-2 screening on non-SARS-CoV-2 testing within NHS laboratories. This report details the virology test requests received by the Leicester-based NHS Virology laboratory from January 2018 to May 2022. Data show that in spite of a dramatic increase in screening, along with multiple logistic and staffing issues, the Leicester Virology Department was mostly able to maintain the same level of service for non-respiratory virus testing while meeting the new increase in SARS-CoV-2 testing.

The association between mean air temperature and new SARS-CoV-2 case numbers throughout the ongoing coronavirus disease 2019 (COVID-19) pandemic was investigated to identify whether diverse SARS-CoV-2 lineages may exhibit diverse environmental behaviors. The number of new COVID-19 daily cases in the province of Verona was obtained from the Veneto Regional Healthcare Service, whilst the mean daily air temperature during the same period was retrieved from the Regional Agency for Ambient Prevention and Protection of Veneto. A significant inverse correlation was found between new COVID-19 daily cases and mean air temperature in Verona up to Omicron BA.1/BA.2 predominance (correlation coefficients between -0.79 and -0.41). The correlation then became positive when the Omicron BA.4/BA.5 lineages were prevalent (r = 0.32). When the median value (and interquartile range; IQR) of new COVID-19 daily cases recorded during the warmer period of the year in Verona (June-July) was compared across the three years of the pandemic, a gradual increase could be seen over time, from 1 (IQR, 0-2) in 2020, to 22 (IQR, 11-113) in 2021, up to 890 (IQR, 343-1345) in 2022. These results suggest that measures for preventing SARS-CoV-2 infection should not be completely abandoned during the warmer periods of the year.

The aim of the study was to investigate the real-life experience of persons infected with SARS-CoV-2 in Slovenia in the first pandemic wave and how the buffering effect of social and informational support affected negative feelings. We used a self-administrated questionnaire. There were 1182 eligible notified cases with the response rate 64.9%. At least 62% of responders were able to follow the isolation rules, while 21.1% did not or could not organize their living separately from other household members. The main providers during the isolation period were close family members. The most prevalent emotion in our study was worry (70.3%) and fear (37.6%). Worry and fear during the illness were less probable for men than women, but more probable for older patients. Participants with strong emotional support had lower odds of being sad. Those who were exposed to a larger number of sources of information had higher odds of being worried. Those patients who used a higher number of more credible sources of information had higher odds of being afraid during illness. Pets did not play a special role in psychological well-being. The role of the media and public health communications should be explored further to achieve an improved response.

Literature on the impact of the SARS-CoV-2 pandemic on the mental health of Health Care Workers (HCWs) is mostly based on cross-sectional surveys. We designed a longitudinal study to assess work-related stress and mental health before and after the pandemic onset in a university-hospital in Lombardia region, Italy. We report on sample representativeness and structural validity of questionnaires assessing work stress (HSE Indicator Tool, HSE-IT) and work satisfaction (WS), which were not validated in the HCWs population. n = 1287 HCWs from 67 hospital wards/offices were invited to an online survey in summer 2019 (pre-COVID-19 wave) and again during winter 2020 (COVID-19 wave). Selected hospital wards/offices did not differ from the remaining wards for turn-over and down-sizing rates, overload, sick leaves, and night shifts (Wilcoxon rank tests p-values > 0.05). Participation rates were 70% (n = 805) and 60% (n = 431) in the pre-COVID-19 and COVID-19 waves, respectively. Socio-demographic and work-related characteristics did not impact data completeness nor participation to the COVID-19 wave. While confirming a 7-component structure for HSE-IT, we identified a new factor related to participation in work organization. A one-factor model for WS had satisfactory fit. Our longitudinal study based on a representative sample and adopting validated questionnaires is well-suited to elucidate the role of work conditions on the development of mental health disorders in HCWs.

Background: Limited access to SARS-CoV-2 testing has been identified as a potential source of anxiety among healthcare workers (HCWs), but the impact of repeated testing on pandemic-related anxiety in pediatric HCWs has not been examined. We sought to understand the impact of repeated SARS-CoV-2 antibody testing on pediatric HCWs’ COVID-19 anxiety. Methods: This longitudinal cohort study was conducted between April and July 2020. Participants, 362 pediatric HCWs, underwent rapid SARS-CoV-2 antibody testing either every 96 h or weekly and were asked to rate their COVID-19 anxiety on a visual analog scale. Changes in self-reported anxiety from the study baseline were calculated for each testing day response. Bivariate analyses, repeated measures, and logistic regression analyses were performed to examine demographics associated with changes in anxiety. Results: Baseline COVID-19 anxiety was significantly higher in HCWs with less than 10 years of experience (Z = −2.63, p = 0.009), in females compared to males (Z = −3.66 p < 0.001), and in nurses compared to other HCWs (F (3,302) = 6.04, p = 0.003). After excluding participants who received a positive test result, repeated measures analyses indicated that anxiety decreased over time (F (5,835) = 3.14, p = 0.008). Of the HCWs who reported decreased anxiety, 57 (29.8%) had a clinically meaningful decrease (≥30%) and Emergency Department (ED) HCWs were 1.97 times more likely to report a clinically meaningful decrease in anxiety (X2 (1) = 5.05, p = 0.025). Conclusions: The results suggest that repeated SARS-CoV-2 antibody serology testing is associated with decreased COVID-19 anxiety in HCWs. Routine screening for the disease may be a helpful strategy in attenuating pandemic-related anxiety in pediatric HCWs.

SARS-CoV-2 variants pose a significant threat to global public health. However, their influence on disease severity, especially among young adults who may exhibit different clinical characteristics, is debatable. In this retrospective study of 229 young adults hospitalized with COVID-19, we investigated the differences between Poland's second and third waves of the pandemic. To identify potential predictors of severe COVID-19 in young adults, we analyzed patient characteristics and laboratory findings between survivors and non-survivors and we performed logistic regression to assess the risk of death, mechanical ventilation, and intensive care unit treatment. We found no increase in COVID-19 severity comparing the third and second waves of the pandemic, indicating that the alpha variant had no influence on disease severity. In addition, we found that factors, such as obesity, comorbidities, lung involvement, leukocytosis, neutrophilia, lymphopenia, higher IG count, the neutrophil-to-lymphocyte ratio, C-reactive protein, procalcitonin, interleukin-6, D-Dimer, lactate dehydrogenase, high-sensitive troponin I, creatine kinase-myocardial band, myoglobin, N-terminal-pro-B-type natriuretic peptide, creatinine, urea and gamma-glutamyl transferase, lower estimated glomerular filtration rate, albumin, calcium and vitamin D3, possibly a decrease in red blood cell counts, hemoglobin and hematocrit, and an increase in creatine kinase during hospitalization may be associated with poor outcomes of COVID-19.

The male sex, due to the presence of genetic, immunological, hormonal, social, and environmental factors, is associated with higher severity and death in Coronavirus Disease (COVID)-19. We conducted an epidemiological study to characterize the COVID-19 clinical profile, severity, and outcome according to sex in patients with the severe acute respiratory syndrome (SARS) due to the fact of this disease. We carried out an epidemiological analysis using epidemiological data made available by the OpenDataSUS, which stores information about SARS in Brazil. We recorded the features of the patients admitted to the hospital for SARS treatment due to the presence of COVID-19 (in the absence of comorbidities) and associated these characteristics with sex and risk of death. The study comprised 336,463 patients, 213,151 of whom were men. Male patients presented a higher number of clinical signs, for example, fever (OR = 1.424; 95%CI = 1.399−1.448), peripheral arterial oxygen saturation (SpO2) < 95% (OR = 1.253; 95%CI = 1.232−1.274), and dyspnea (OR = 1.146; 95%CI = 1.125−1.166) as well as greater need for admission in intensive care unit (ICU, OR = 1.189; 95%CI = 1.168−1.210), and the use of invasive ventilatory support (OR = 1.306; 95%CI = 1.273−1.339) and noninvasive ventilatory support (OR = 1.238; 95%CI = 1.216−1.260) when compared with female patients. Curiously, the male sex was associated only with a small increase in the risk of death when compared with the female sex (OR = 1.041; 95%CI = 1.023−1.060). We did a secondary analysis to identify the main predictors of death. In that sense, the multivariate analysis enabled the prediction of the risk of death, and the male sex was one of the predictors (OR = 1.101; 95%CI = 1.011−1.199); however, with a small effect size. In addition, other factors also contributed to this prediction and presented a great effect size, they are listed below: older age (61−72 years old (OR = 15.778; 95%CI = 1.865−133.492), 73−85 years old (OR = 31.978; 95%CI = 3.779−270.600), and +85 years old (OR = 68.385; 95%CI = 8.164−589.705)); race (Black (OR = 1.247; 95%CI = 1.016−1.531), Pardos (multiracial background; OR = 1.585; 95%CI = 1.450−1.732), and Indigenous (OR = 3.186; 95%CI = 1.927−5.266)); clinical signs (for instance, dyspnea (OR = 1.231; 95%CI = 1.110−1.365) and SpO2 < 95% (OR = 1.367; 95%CI = 1.238−1.508)); need for admission in the ICU (OR = 3.069; 95%CI = 2.789−3.377); and for ventilatory support (invasive (OR = 10.174; 95%CI = 8.803−11.759) and noninvasive (OR = 1.609; 95%CI = 1.438−1.800)). In conclusion, in Brazil, male patients tend to present the phenotype of higher severity in COVID-19, however, with a small effect on the risk of death.

Background: The Grand Hôpital de Charleroi is a large non-academic Belgian hospital that treated a large number of COVID-19 inpatients. In the context of this pandemic, all professions-combined healthcare workers (HCWs), and not only direct caregivers, are a frontline workforce in contact with suspected and confirmed COVID-19 cases and seem to be a high-risk group for exposure. The aim of our study was to estimate the prevalence of anti-SARS-CoV-2 antibodies in HCWs in our hospital after the first and second pandemic waves and to characterize the distribution of this seroprevalence in relation to various criteria. Methods: At the end of the two recruitment periods, a total of 4008 serological tests were performed in this single-center cross-sectional study. After completing a questionnaire including demographic and personal data, possible previous COVID-19 diagnostic test results and/or the presence of symptoms potentially related to COVID-19, the study participants underwent blood sampling and serological testing using DiaSorin's LIAISON ® SARS-CoV-2 S1/S2 IgG test for the first phase and LIAISON ® SARS-CoV-2 TrimericS IgG test for the second phase of this study. Results: In total, 302 study participants (10.72%) in the first round of the study and 404 (33.92%) in the second round were positive for SARS-CoV-2-IgG antibodies. The prevalence of seropositivity observed after the second wave was 3.16 times higher than after the first wave. We confirmed that direct, prolonged, and repeated contact with patients or their environment was a predominant seroconversion factor, but more unexpectedly, that this was the case for all HCWs and not only caregivers. Finally, the notion of high-risk contact seemed more readily identifiable in one's workplace than in one's private life. Conclusions: Our study confirmed that HCWs are at a significantly higher risk of contracting COVID-19 than the general population, and suggests that repeated contacts with at-risk patients, regardless of the HCWs' professions, represents the most important risk factor for seroconversion (Clinicaltrials.gov number, NCT04723290).

Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.

The aim of this study is to investigate the impact of the COVID-19 pandemic on the surgical treatment of lung cancer patients. Data from patients who underwent surgery during the pandemic were analyzed and compared to pre-pandemic and post-pandemic periods. Multiple parameters were examined, and their changes yielded significant results compared to other periods of the study. The statistical analysis revealed a significant decrease in the number of surgical interventions during the pandemic ( p < 0.001), followed by a significant rebound thereafter. During this period, there was a significant increase in the T stage of cancer compared to both pre-pandemic and post-pandemic periods ( p = 0.027). Additionally, the mean Charlson comorbidity index score was significantly higher during the pandemic compared to the pre-pandemic period ( p = 0.042). In this crisis period, a significant decrease was recorded in both the total hospitalization duration ( p = 0.015) and the pre-operative hospitalization duration ( p = 0.006). These findings provide evidence of significant changes in clinical and therapeutic strategies applied to lung cancer surgery patients during the study period. The pandemic has had a substantial and complex impact, the full extent of which remains to be fully understood.

This work presents a retrospective analysis of indoor CO 2 measurements obtained with a mobile robot in an educational building after the COVID-19 lockdown (May 2021), at a time when public activities resumed with mandatory local pandemic restrictions. The robot-based CO 2 measurement system was assessed as an alternative to the deployment of a net of sensors in a building in the pandemic period, in which there was a global stock outage of CO 2 sensors. The analysis of the obtained measurements confirms that a mobile system can be used to obtain interpretable information on the CO 2 levels inside the rooms of a building during a pandemic outbreak.

As the COVID-19 pandemic revealed, rapid development of vaccines and therapeutic antibodies are crucial to guarantee a quick return to the status quo of society. In early 2020, we deployed our droplet microfluidic single-cell-based platform DROPZYLLA ® for the generation of cognate antibody repertoires of convalescent COVID-19 donors. Discovery of SARS-CoV-2-specific antibodies was performed upon display of antibodies on the surface of HEK293T cells by antigen-specific sorting using binding to the SARS-CoV-2 spike and absence of binding to huACE2 as the sort criteria. This efficiently yielded antibodies within 3-6 weeks, of which up to 100% were neutralizing. One of these, MTX-COVAB, displaying low picomolar neutralization IC50 of SARS-CoV-2 and with a neutralization potency on par with the Regeneron antibodies, was selected for GMP manufacturing and clinical development in June 2020. MTX-COVAB showed strong efficacy in vivo and neutralized all identified clinically relevant variants of SARS-CoV-2 at the time of its selection. MTX-COVAB completed GMP manufacturing by the end of 2020, but clinical development was stopped when the Omicron variant emerged, a variant that proved to be detrimental to all monoclonal antibodies already approved. The present study describes the capabilities of the DROPZYLLA ® platform to identify antibodies of high virus-neutralizing capacity rapidly and directly.

We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. The here described genomic combination was not detectable with the common fasta file-based Pango-lineage analysis, hence increasing the probability of the true global prevalence to be higher.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein D614G mutation became the predominant globally circulating variant after its emergence in the early coronavirus disease 2019 (COVID-19) pandemic. Studies showed that this mutation results in an open conformation of the S glycoprotein receptor-binding domain (RBD), and increased angiotensin 1-converting enzyme 2 (ACE2) binding and fusion, which result in an increase in SARS-CoV-2 transmissibility and infectivity. Dynamic tracking of SARS-CoV-2 showed that the D614G variant became predominant after emergence in Europe and North America, but not in China. The current absence of selective pressures from antiviral treatment suggests that the driving force for viral evolution could be variations in human population genetics. Results show that ACE2 expression is higher in Asian populations than that in European, North American, and African populations. This supports the idea that lower ACE2 expression is a driving force in the positive selection for the D614G mutation. This study suggests that the dynamics of the SARS-CoV-2 D614G mutation during the early-to-mid pandemic is associated with enhanced transmission efficiency in populations with lower ACE2 expression. Understanding the role that human genetic diversity plays in the adaptive evolution of SARS-CoV-2 may have an important impact on public health and measures to control the pandemic.

Botulinum neurotoxin type A (BoNT/A) injections have to be administered repeatedly to achieve a rather stable, high level of improvement. This study aimed to take a look at changes in the daily routine of a BoNT/A outpatient clinic due to the SARS-CoV-2 pandemic lockdown, analyze the impact of SARS-CoV-2-induced re-injection delay on outcomes in patients with cervical dystonia (CD) ( n = 36) and four other disease entities ( n = 58), and study the influence of covariables, including previous injections and doses. For the present observational study, the first 100 patients who were scheduled to have an appointment between April 20 and May 18 during the partial lockdown and also had been treated regularly before the lockdown were recruited. Clinical and demographical characteristics and treatment-related data from the previous visits were extracted from charts. Time delay, symptom severity assessment, and TSUI score (if applicable) were gathered at the first coronavirus pandemic lockdown emergency visit for each patient. Of the 94 patients who could come to the clinic, 48 reported a delay and 44 reported worsening during the delay. Delays ranged from 1 to 63 days, the mean delay was 23 days, and the mean worsening was 26% compared to the previous visit. A significant correlation was found between the duration of the delay and the patient's rating of worsening (PwP). In CD patients, the physician´s rating of CD worsening by the TSUI score (ATUSI-PTSUI) was significantly correlated with general worsening (DwP) and the TSUI at the last visit (PTSUI). A small delay of a few weeks led to a similar worsening of symptoms in CD and all other disease entities and to relapse on a higher level of severity. This relapse can only be compensated by continuous treatment up to at least 1 year until patients reach the same level of treatment efficacy as that before the SARS-CoV-2 pandemic.

With the COVID-19 pandemic having disrupted economies, businesses, and individual activities, it is important to examine how different forms of work affect employee behaviour. This study applies work engagement (the key construct in organisational psychology) as the dependent variable and considers its determinants in the form of stress factors and attitudes toward remote work. A cross-sectional study was conducted. A total of 544 (Female = 58.5%) workers were surveyed: remote ( n = 144), hybrid ( n = 142), and on-site ( n = 258). The selection for the study was purposive. Standardised survey questionnaires were used in the study: UWES-9, Stress Management Standards, and Attitudes toward Remote Work. The obtained results indicate that there were no significant differences between groups in terms of the intensity of work engagement, but work engagement was explained by other variables that are different in each of the studied groups. Relationships and use of social media were the most important factors among remote workers. For on-site workers, the most important factors were control and role definition. For practitioners, the results indicate which aspects of work should be considered in order to maintain high levels of work engagement when employees are transferring to other forms of work.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3' untranslated region (UTR) of this β-CoV contains essential cis -acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3' UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis -acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3' UTRs in the infectious virions and the minigene-transfected cells are almost identical.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). This respiratory illness was declared a pandemic by the world health organization (WHO) in March 2020, just a few weeks after being described for the first time. Since then, global research effort has considerably increased humanity's knowledge about both viruses and disease. It has also spawned several vaccines that have proven to be key tools in attenuating the spread of the pandemic and severity of COVID-19. However, with vaccine-related skepticism being on the rise, as well as breakthrough infections in the vaccinated population and the threat of a complete immune escape variant, alternative strategies in the fight against SARS-CoV-2 are urgently required. Calcium signals have long been known to play an essential role in infection with diverse viruses and thus constitute a promising avenue for further research on therapeutic strategies. In this review, we introduce the pivotal role of calcium signaling in viral infection cascades. Based on this, we discuss prospective calcium-related treatment targets and strategies for the cure of COVID-19 that exploit viral dependence on calcium signals.

Considering the lack of effective treatments against COVID-19, wastewater-based epidemiology (WBE) is emerging as a cost-effective approach for real-time population-wide SARS-CoV-2 monitoring. Here, we report novel molecular assays for sensitive detection and mutational/variant analysis of SARS-CoV-2 in wastewater. Highly stable regions of SARS-CoV-2 RNA were identified by RNA stability analysis and targeted for the development of novel nested PCR assays. Targeted DNA sequencing (DNA-seq) was applied for the analysis and quantification of SARS-CoV-2 mutations/variants, following hexamers-based reverse transcription and nested PCR-based amplification of targeted regions. Three-dimensional (3D) structure models were generated to examine the predicted structural modification caused by genomic variants. WBE of SARS-CoV-2 revealed to be assay dependent, and significantly improved sensitivity achieved by assay combination (94%) vs. single-assay screening (30%-60%). Targeted DNA-seq allowed the quantification of SARS-CoV-2 mutations/variants in wastewater, which agreed with COVID-19 patients' sequencing data. A mutational analysis indicated the prevalence of D614G (S) and P323L (RdRP) variants, as well as of the Β.1.1.7/alpha variant of concern, in agreement with the frequency of Β.1.1.7/alpha variant in clinical samples of the same period of the third pandemic wave at the national level. Our assays provide an innovative cost-effective platform for real-time monitoring and early-identification of SARS-CoV-2 variants at community/population levels.

We introduced the mixed-methods Data-Powered Positive Deviance (DPPD) framework as a potential addition to the set of tools used to search for effective response strategies against the SARS-CoV-2 pandemic. For this purpose, we conducted a DPPD study in the context of the early stages of the German SARS-CoV-2 pandemic. We used a framework of scalable quantitative methods to identify positively deviant German districts that is novel in the scientific literature on DPPD, and subsequently employed qualitative methods to identify factors that might have contributed to their comparatively successful reduction of the forward transmission rate. Our qualitative analysis suggests that quick, proactive, decisive, and flexible/pragmatic actions, the willingness to take risks and deviate from standard procedures, good information flows both in terms of data collection and public communication, alongside the utilization of social network effects were deemed highly important by the interviewed districts. Our study design with its small qualitative sample constitutes an exploratory and illustrative effort and hence does not allow for a clear causal link to be established. Thus, the results cannot necessarily be extrapolated to other districts as is. However, the findings indicate areas for further research to assess these strategies' effectiveness in a broader study setting. We conclude by stressing DPPD's strengths regarding replicability, scalability, adaptability, as well as its focus on local solutions, which make it a promising framework to be applied in various contexts, e.g., in the context of the Global South.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is posing a global public health burden. These consequences have been shown to increase the risk of mental distress, but the underlying protective and risk factors for mental distress and trends over different waves of the pandemic are largely unknown. Furthermore, it is largely unknown how mental distress is associated with individual protective behavior. Three quota samples, weighted to represent the population forming the German COVID-19 Snapshot Monitoring study (24 March and 26 May 2020, and 9 March 2021 with >900 subjects each), were used to describe the course of mental distress and resilience, to identify risk and protective factors during the pandemic, and to investigate their associations with individual protective behaviors. Mental distress increased slightly during the pandemic. Usage of cognitive reappraisal strategies, maintenance of a daily structure, and usage of alternative social interactions decreased. Self-reported resilience, cognitive reappraisal strategies, and maintaining a daily structure were the most important protective factors in all three samples. Adherence to individual protective behaviors (e.g., physical distancing) was negatively associated with mental distress and positively associated with frequency of information intake, maintenance of a daily structure, and cognitive reappraisal. Maintaining a daily structure, training of cognitive reappraisal strategies, and information provision may be targets to prevent mental distress while assuring a high degree of individual protective behaviors during the COVID-19 pandemic. Effects of the respective interventions have to be confirmed in further studies.

Background and Objectives : The incidence of osteoporotic hip fractures in Niigata Prefecture, Japan, has been studied approximately every 5 years since 1985. In 2020, as in previous surveys, a prefecture-wide survey was initiated as planned; however, the global outbreak of the coronavirus disease 2019 (COVID-19) began simultaneously. This study aimed to compare the results of the 2015 and 2020 Niigata Prefecture Fragility Hip Fracture Surveys to determine whether the COVID-19 pandemic affected the occurrence and treatment of proximal femoral fractures throughout Niigata Prefecture. Materials and Methods : In this study, data from the 2015 and 2020 Niigata Prefecture Fragility Hip Fracture Surveys were used. Data were obtained from registration forms returned by hospitals and clinics in Niigata Prefecture for patients living therein who were diagnosed with osteoporotic hip fractures over a 1-year period in 2015 and 2020. Results : In Niigata Prefecture, the total annual number of fractures increased from 3181 in 2015 to 3369 in 2020, whereas the age-adjusted fracture rate decreased. Regarding the location of the fractures, the proportion of outdoor fractures was lower than that of indoor fractures. The proportion of outdoor fractures decreased over the year as a whole, but in particular, the proportion of outdoor fractures decreased significantly under the issued emergency declarations. The most common reasons for delayed surgery related to COVID-19 were "waiting for PCR results" and "quarantine for fever," accounting for approximately 1.9% of all causes. Conclusions : In Niigata Prefecture, Japan, the effect of the COVID-19 pandemic on the number and rate of fractures was minuscule. The proportion of indoor fractures to outdoor fractures increased during the emergency declaration period. Considering that the number of fragility fractures remains the same during an infectious disease pandemic such as COVID-19, it is necessary to ensure that healthcare resources are available to deal with them.

Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are currently administered in South Korea; however, vaccine supply is limited. Considering constraints in vaccine supply and the emergence of variant strains, we evaluated the impact of coronavirus disease (COVID-19) vaccination program in reducing incidence, ICU hospitalization, and deaths in South Korea. We developed an age-structured model of SARS-CoV-2 transmission parameterized with Korean demographics and age-specific COVID-19 outcomes. Using our model, we analyzed the impact of the COVID-19 vaccination program during the fourth wave of the pandemic in South Korea in reducing disease burden. We projected that the vaccination program can reduce the overall attack rate to 3.9% from 6.9% without vaccination, over 150 days, starting from 5 July 2021. The highest relative reduction (50%) was observed among individuals aged 50-59 years. Vaccination markedly reduced adverse outcomes, such as ICU hospitalizations and deaths, decreasing them by 45% and 43%, respectively. In the presence of the Delta variant, vaccination is expected to reduce the overall attack rate to 11.9% from 26.9%. Our results indicate that the impact of vaccination can be substantially affected by the emergence of SARS-CoV-2 variants. Furthermore, herd immunity is unlikely to be achieved with the potential emergence of the Delta variant, inconsistent with the blueprint of the South Korean government.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic started in December 2019 and still is a major global health challenge. Lockdown measures and social distancing sparked a global shift towards online learning, which deeply impacted universities' daily life, and the University of Barcelona (UB) was not an exception. Accordingly, we aimed to determine the impact of the SARS-CoV-2 pandemic at the UB. To that end, we performed a cross-sectional study on a sample of 2784 UB members ( n = 52,529). Participants answered a brief, ad hoc, online epidemiological questionnaire and provided a nasal swab for reverse transcription polymerase chain reaction (RT-PCR) SARS-CoV-2 analysis and a venous blood sample for SARS-CoV-2 IgG antibody assay. Total prevalence of SARS-CoV-2 infection (positive RT-PCR or positive IgG) was 14.9% (95%CI 13.3 to 17.0%). Forty-four participants (1.6%, 95%CI: 1.2-2.1%) were positive for SARS-CoV-2 RT-PCR. IgG against SARS-CoV-2 was observed in 12.8% (95%CI: 11.6-14.1%) of participants. Overall, while waiting for population vaccination and/or increased herd immunity, we should concentrate on identifying and isolating new cases and their contacts.

Background and Objectives : Action, not fear, is the path forward in the coronavirus infectious disease 2019 (COVID-19) pandemic. Since early 2020, the world's nations have faced conundrums over severe acute respiratory syndrome corona virus type 2 (SARS-CoV-2) infections resulting in COVID-19 resulting in national closures, and thus, a clear understandable plan that nations can implement is required to reopen. The healthcare benefits of reopening a nation more likely than not exceed the benefits of continued pandemic-related closure. Pandemic-related closures have resulted in countless delayed or avoided urgent care evaluations. Furthermore, routine care of acute and chronic illnesses, including evaluations, diagnoses, and treatments, has also been delayed. Isolation, loss of income, and fear have resulted in mental health conditions or exacerbated existing conditions. The magnitude of untoward ramifications is unknown and may ultimately represent an inestimable degree of danger and morbidity, and even death. The pandemic of SARS-CoV-2 has created an atmosphere of fear of COVID-19 that has directly and indirectly injured the world's population. Since this has resulted in increasing morbidity and mortality, creating economic chaos, and near systemic collapse of educational systems with no well described plan forward, it is the purpose of this study to provide guidelines that provide a path forward to safely open a nation. Physicians often equipped by their education, training, and experiences across disciplines are uniquely positioned to comprehend, coordinate, and teach other physicians, business owners, and municipal and government leaders from guidelines. As such, physicians may take the lead in a path forward to reopening a nation, including opening businesses, educational facilities, and religious establishments, while minimizing the risk of SARS-CoV-2 infection. Materials and Methods : Reviews of the literature among the disciplines of environmental air, sanitation, social interaction, medical testing, vaccination, protection, and disease prevention and safety allowed for the conceptualization and eventual genesis of identifiable interventions which either reduce the viral load in the environment or inactivate the virus from replication. Each of the guidelines was selected based on the principle that it involved the elimination or inactivation of the viral particle. With a reduction in viral load or inactivation of replication, the implementation of these guidelines is expected to allow for reopening a nation with an increased level of safety. Results : The guidelines identified, including air exchange (ventilation), air filtration, personal protective filtering devices (masks), hand hygiene, social distancing, screening and testing, vaccines, high-risk patient protection, medical management, and adjunctive therapies, are described and referenced. Conclusions : In that the pandemic is primarily a public health issue, the path forward is best coordinated by local, regional, and national physicians. Many physicians with a breadth of experiences are uniquely positioned to coordinate the implementation of these interdisciplinary guidelines. Using these guidelines as a planned, coordinated action, not fear, is a path forward. Nations have a decision to make: closuring versus opening.

We aimed to explore university students' perceptions and experiences of SARS-CoV-2 mass asymptomatic testing, social distancing and self-isolation, during the COVID-19 pandemic. This qualitative study comprised of four rapid online focus groups conducted at a higher education institution in England, during high alert (tier 2) national COVID-19 restrictions. Participants were purposively sampled university students ( n = 25) representing a range of gender, age, living circumstances (on/off campus), and SARS-CoV-2 testing/self-isolation experiences. Data were analysed using an inductive thematic approach. Six themes with 16 sub-themes emerged from the analysis of the qualitative data: 'Term-time Experiences', 'Risk Perception and Worry', 'Engagement in Protective Behaviours', 'Openness to Testing', 'Barriers to Testing' and 'General Wellbeing'. Students described feeling safe on campus, believed most of their peers are adherent to protective behaviours and were positive towards asymptomatic testing in university settings. University communications about COVID-19 testing and social behaviours need to be timely and presented in a more inclusive way to reach groups of students who currently feel marginalised. Barriers to engagement with SARS-CoV-2 testing, social distancing and self-isolation were primarily associated with fear of the mental health impacts of self-isolation, including worry about how they will cope, high anxiety, low mood, guilt relating to impact on others and loneliness. Loneliness in students could be mitigated through increased intra-university communications and a focus on establishment of low COVID-risk social activities to help students build and enhance their social support networks. These findings are particularly pertinent in the context of mass asymptomatic testing programmes being implemented in educational settings and high numbers of students being required to self-isolate. Universities need to determine the support needs of students during self-isolation and prepare for the long-term impacts of the pandemic on student mental health and welfare support services.

Background and Objectives : Sentinel surveillance in the early stage of the COVID-19 pandemic in Mexico represented a significant cost reduction and was useful in estimating the population infected with SARS-CoV-2. However, it also implied that many patients were not screened and therefore had no accurate diagnosis. In this study, we carried out a population-based SARS-CoV-2 screening in Mexico to evaluate the COVID-19-related symptoms and their weighting in predicting SARS-CoV-2 infection. We also discuss this data in the context of the operational definition of suspected cases of COVID-19 established by the Mexican Health Authority's consensus. Materials and Methods : One thousand two hundred seventy-nine subjects were included. They were screened for SARS-CoV-2 using RT-PCR. The weighting of COVID-19 symptoms in predicting SARS-CoV-2 infection was evaluated statistically. Results : Three hundred and twenty-five patients were positive for SARS-CoV-2 and 954 were negative. Fever, asthenia, dysgeusia, and oxygen saturation predicted SARS-CoV-2 infection (odds ratios ranged from 1.74 to 4.98; p < 0.05). The percentage of asymptomatic COVID-19 patients was 36% and only 38.15% met the Mexican operational definition. Cq-values for the gene N of SARS-CoV-2 were significantly higher in asymptomatic subjects than in the groups of COVID-19 patients with neurological, respiratory, and/or musculoskeletal manifestations ( p < 0.05). Conclusions : Dysgeusia, fever, and asthenia increased the odds of a positive result for COVID-19 1.74-4.98-fold among the study population. Patients with neurological, respiratory, and/or musculoskeletal manifestations had higher viral loads at COVID-19 diagnosis than those observed in asymptomatic patients. A high percentage of the participants in the study (61.85%) did not meet the operational definition for a suspected case of COVID-19 established by the Mexican Health Authority's consensus, representing a high percentage of the population that could have remained without a COVID-19 diagnosis, so becoming a potential source of virus spread.

Cats are susceptible to infection with severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Whilst a number of studies have been performed worldwide on owned cats, limited data are available on stray, colony or shelter cats. We investigated SARS-CoV-2 infection in a stray cat population before and during human outbreaks of SARS-CoV-2 in cities in the Lombardy region in northern Italy, a high endemic region for SARS-CoV-2, using serological and molecular methods. A cohort of different samples were collected from 241 cats, including frozen archived serum samples from 136 cats collected before the 2019 coronavirus disease (COVID-19) pandemic and serum, pharyngeal and rectal swab samples from 105 cats collected during the SARS-CoV-2 outbreak. All pre-pandemic samples tested seronegative for antibodies against the nucleocapsid of SARS-CoV-2 using indirect enzyme linked immunosorbent assay (ELISA) test, while one serum sample collected during the pandemic was seropositive. No serological cross-reactivity was detected between SARS-CoV-2 antibodies and antibodies against feline enteric (FECV) and infectious peritonitis coronavirus (FIPC), Feline Immunodeficiency Virus (FIV), Feline Calicivirus (FCV), Feline Herpesvirus-1 (FHV-1), Feline Parvovirus (FPV), Leishmania infantum , Anaplasma phagocytophilum , Rickettsia spp., Toxoplasma gondii or Chlamydophila felis . No pharyngeal or rectal swab tested positive for SARS-CoV-2 RNA on real time reverse transcription-polymerase chain reaction (rRT-PCR). Our data show that SARS-CoV-2 did infect stray cats in Lombardy during the COVID-19 pandemic, but with lower prevalence than found in owned cats. This should alleviate public concerns about stray cats acting as SARS-CoV-2 carriers.

Face mask use is a critical behavior to prevent the spread of SARS-CoV-2. We aimed to evaluate the association between social integration and face mask use during the COVID-19 pandemic in a random sample of households in Utsunomiya City, Greater Tokyo, Japan. Data included 645 adults in the Utsunomiya COVID-19 seROprevalence Neighborhood Association (U-CORONA) study, which was conducted after the first wave of the pandemic, between 14 June 2020 and 5 July 2020, in Utsunomiya City. Social integration before the pandemic was assessed by counting the number of social roles, based on the Cohen's social network index. Face mask use before and during the pandemic was assessed by questionnaire, and participants were categorized into consistent mask users, new users, and current non-users. Multinomial logistic regression analysis was used to examine the association between lower social integration score and face mask use. To account for possible differential non-response bias, non-response weights were used. Of the 645 participants, 172 (26.7%) were consistent mask users and 460 (71.3%) were new users, while 13 (2.0%) were current non-users. Lower social integration level was positively associated with non-users (RRR: 1.76, 95% CI: 1.10, 2.82). Social integration may be important to promote face mask use.

Background: The COVID-19 pandemic has hit both the Spanish economy and the population's health hard. The result is an unprecedented economic and social crisis due to uncertainty about the remedy and the socioeconomic effects on people's lives., Methods: We performed a retrospective analysis of the macroeconomic impact of the COVID-19 pandemic in 2020 using key indicators of the Spanish economy for the 17 Autonomous Communities (ACs) of the country. National statistics were examined in the search for impacts or anomalies occurring since the beginning of the pandemic. To estimate the strength of the impact on each of the indicators analyzed, we used Bayesian structural time series. We also calculated the correlation between the rate of GDP decline during 2020 and the cumulative incidence of COVID-19 cases per 100,000 inhabitants in the ACs., Results: In 2020, the cumulative impact on the gross domestic product was of -11.41% (95% credible interval: -13.46; -9.29). The indicator for business turnover changed by -9.37% (-12.71; -6.07). The Spanish employment market was strongly affected; our estimates showed a cumulative increase of 11.9% (4.27; 19.45) in the rate of unemployment during 2020. The worst indicators were recorded in the ACs most economically dependent on the services sector. There was no statistical association between the incidence of COVID-19 in 2020 and the fall in GDP in the ACs., Conclusions: Our estimates portray a dramatic situation in Spain, where the COVID-19 crisis has had more serious economic and health consequences than in other European countries. The productive system in Spain is too dependent on sectors vulnerable to the pandemic, and it is necessary to design and implement profound changes through the European Next Generation program.

Recently, the outbreak of the SARS-CoV-2 virus and the COVID-19 pandemic significantly affected the health situation of the entire society and necessitated reorganization of health care including oncology. The objective of this study was to examine the perception of medical services by cancer patients during the pandemic and to identify the key elements influencing the level of satisfaction with oncological care. Of note, 394 patients diagnosed with cancer treated in inpatient oncology wards participated in the study (Poland). The diagnostic survey method was used. A survey questionnaire developed by the authors was used and validated the EORTC IN-PATSAT32 questionnaire. The calculations were made in Statistica 10.0 (Statsoft; 2011, Dell Inc., Round Rock, TX, USA). The average general level of satisfaction with oncological care in the study group was 80.77 out of a total score of 100, representing the highest level of satisfaction. Levels of satisfaction varied according to time since diagnosis (longer time-greater satisfaction) and were lower where treatment was delayed or perceived as disorganised. Nearly half of the respondents felt the threat of the SARS-CoV-2 infection, despite the fact that most of them believed that the hospital was well prepared to diagnose and treat cancer patients during the COVID-19 pandemic. Convincing patients about the proper preparation of health care for diagnostics and therapy is an important element influencing patient satisfaction with oncological care.

Background: The COVID-19 pandemic has had global effects; cases have been counted in the tens of millions, and there have been over two million deaths throughout the world. Health systems have been stressed in trying to provide a response to the increasing demand for hospital beds during the different waves. This paper analyzes the dynamic response of the hospitals of the Community of Madrid (CoM) during the first wave of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the period between 18 March and 31 May 2020. The aim was to model the response of the CoM's health system in terms of the number of available beds. Methods: A research design based on a case study of the CoM was developed. To model this response, we use two concepts: "bed margin" (available beds minus occupied beds, expressed as a percentage) and "flexibility" (which describes the ability to adapt to the growing demand for beds). The Linear Hinges Model allowed a robust estimation of the key performance indicators for capturing the flexibility of the available beds in hospitals. Three new flexibility indicators were defined: the Average Ramp Rate Until the Peak (ARRUP), the Ramp Duration Until the Peak (RDUP), and the Ramp Growth Until the Peak (RGUP). Results: The public and private hospitals of the CoM were able to increase the number of available beds from 18,692 on 18 March 2020 to 23,623 on 2 April 2020. At the peak of the wave, the number of available beds increased by 160 in 48 h, with an occupancy of 90.3%. Within that fifteen-day period, the number of COVID-19 inpatients increased by 200% in non-intensive care unit (non-ICU) wards and by 155% in intensive care unit (ICU) wards. The estimated ARRUP for non-ICU beds in the CoM hospital network during the first pandemic wave was 305.56 beds/day, the RDUP was 15 days, and the RGUP was 4598 beds. For the ICU beds, the ARRUP was 36.73 beds/day, the RDUP was 20 days, and the RGUP was 735 beds. This paper includes a further analysis of the response estimated for each hospital. Conclusions: This research provides insights not only for academia, but also for hospital management and practitioners. The results show that not all of the hospitals dealt with the sudden increase in bed demand in the same way, nor did they provide the same flexibility in order to increase their bed capabilities. The bed margin and the proposed indicators of flexibility summarize the dynamic response and can be included as part of a hospital's management dashboard for monitoring its behavior during pandemic waves or other health crises as a complement to other, more steady-state indicators.

In the context of the ongoing coronavirus disease 2019 (COVID-19) pandemic, numerous attempts have been made to discover new potential antiviral molecules against its causative agent, SARS-CoV-2, many of which focus on its main protease (M pro ). We hereby used two approaches based on molecular docking simulation to explore the interaction of four libraries of semisynthetic nitrogenous heterocyclic compounds with M pro . Libraries L1 and L2 contain 52 synthetic derivatives of the natural compound 2-propylquinoline, whereas libraries L3 and L4 contain 65 compounds synthesized using the natural compound physostigmine as a precursor. Validation through redocking suggested that the rigid receptor and flexible receptor approaches used for docking were suitable to model the interaction of this type of compounds with the target protein, although the flexible approach seemed to provide a more realistic representation of interactions within the active site. Using empirical energy score thresholds, we selected 58 compounds from the four libraries with the most favorable energy estimates. Globally, favorable estimates were obtained for molecules with two or more substituents, putatively accommodating in three or more subsites within the M pro active site. Our results pave the way for further experimental evaluation of the selected compounds as potential antiviral agents against SARS-CoV-2.

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 and its associated pathology, COVID-19, have been of particular concerns these last months due to the worldwide burden they represent. The number of cases requiring intensive care being the critical point in this epidemic, a better understanding of the pathophysiology leading to these severe cases is urgently needed. Tissue lesions can be caused by the pathogen or can be driven by an overwhelmed immune response. Focusing on SARS-CoV-2, we and others have observed that this virus can trigger indeed an immune response that can be dysregulated in severe patients and leading to further injury to multiple organs. The purpose of the review is to bring to light the current knowledge about SARS-CoV-2 virologic and immunologic features. Thus, we address virus biology, life cycle, tropism for many organs and how ultimately it will affect several host biological and physiological functions, notably the immune response. Given that therapeutic avenues are now highly warranted, we also discuss the immunotherapies available to manage the infection and the clinical outcomes.

Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.

The recent outbreak of a novel Coronavirus (SARS-CoV-2) and its rapid spread across the continents has generated an urgent need for assays to detect the neutralising activity of human sera or human monoclonal antibodies against SARS-CoV-2 spike protein and to evaluate the serological immunity in humans. Since the accessibility of live virus microneutralisation (MN) assays with SARS-CoV-2 is limited and requires enhanced bio-containment, the approach based on "pseudotyping" can be considered a useful complement to other serological assays. After fully characterising lentiviral pseudotypes bearing the SARS-CoV-2 spike protein, we employed them in pseudotype-based neutralisation assays in order to profile the neutralising activity of human serum samples from an Italian sero-epidemiological study. The results obtained with pseudotype-based neutralisation assays mirrored those obtained when the same panel of sera was tested against the wild type virus, showing an evident convergence of the pseudotype-based neutralisation and MN results. The overall results lead to the conclusion that the pseudotype-based neutralisation assay is a valid alternative to using the wild-type strain, and although this system needs to be optimised and standardised, it can not only complement the classical serological methods, but also allows serological assessments to be made when other methods cannot be employed, especially in a human pandemic context.

Growing evidence links prenatal exposure to particulate matter (PM2.5) with reduced lung function and incidence of pulmonary diseases in infancy and childhood. However, the underlying biological mechanisms of how prenatal PM2.5 exposure affects the lungs are incompletely understood, which explains the lack of an ideal in vitro lung development model. Human pluripotent stem cells (hPSCs) have been successfully employed for in vitro developmental toxicity evaluations due to their unique ability to differentiate into any type of cell in the body. In this study, we investigated the developmental toxicity of diesel fine PM (dPM2.5) exposure during hPSC-derived alveolar epithelial cell (AEC) differentiation and three-dimensional (3D) multicellular alveolar organoid (AO) development. We found that dPM2.5 (50 and 100 μg/mL) treatment disturbed the AEC differentiation, accompanied by upregulation of nicotinamide adenine dinucleotide phosphate oxidases and inflammation. Exposure to dPM2.5 also promoted epithelial-to-mesenchymal transition during AEC and AO development via activation of extracellular signal-regulated kinase signaling, while dPM2.5 had no effect on surfactant protein C expression in hPSC-derived AECs. Notably, we provided evidence, for the first time, that angiotensin-converting enzyme 2, a receptor to mediate the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) entry into target cells, and the cofactor transmembrane protease serine 2 were significantly upregulated in both hPSC-AECs and AOs treated with dPM2.5. In conclusion, we demonstrated the potential alveolar development toxicity and the increase of SARS-Cov-2 susceptibility of PM2.5. Our findings suggest that an hPSC-based 2D and 3D alveolar induction system could be a useful in vitro platform for evaluating the adverse effects of environmental toxins and for virus research.

The aim of this research was to analyze how the need for psychological support of health workers (HCWs) influenced the beliefs, perceptions and attitudes towards their work during the COVID-19 pandemic and to predict the need of psychological assistance. A descriptive transversal study was conducted based on a self-administered questionnaire distributed to health professionals working in the Canary Islands, Spain. The data were analyzed using Pearson's chi-squared test and the linear trend test. The correlation test between ordinal and frequency variables was applied using Kendall's Tau B. Multiple logistic regression was used to predict dichotomous variables. The sample included 783 health professionals: 17.8% ( n = 139) of them needed psychological or psychiatric support. Being redeployed to other services influenced the predisposition to request psychological help, and HCWs who required psychological support had more negative attitudes and perceptions towards their work. After five waves of COVID-19, these HCWs reported to be physically, psychologically and emotionally exhausted or even "burned out"; they did not feel supported by their institutions. The commitment of health personnel to fight against the COVID-19 pandemic decreased after the five waves, especially among professionals who required psychological support.

We reviewed the association between seasonal influenza vaccination and the risk of SARS-CoV-2 infection or complicated illness or poor outcome (e.g., severe disease, need for hospitalization or ventilatory support, or death) among COVID-19 patients. None of the studies that were reviewed ( n = 12) found a significant increase in the risk of infection or in the illness severity or lethality, and some reported significantly inverse associations. Our findings support measures aimed at raising influenza vaccination coverage in the coming months.

This study calculates and elucidates the minimum size of respiratory particles that are potential carriers of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); furthermore, it evaluates the aerosol generation potential of SARS-CoV-2. The calculations are based on experimental results and theoretical models. In the case of maximum viral-loading derived from experimental data of COVID-19 patients, 8.97 × 10 -5 % of a respiratory fluid particle from a COVID-19 patient is occupied by SARS-CoV-2. Hence, the minimum size of a respiratory particle that can contain SARS-CoV-2 is calculated to be approximately 9.3 μm. The minimum size of the particles can decrease due to the evaporation of water on the particle surfaces. There are limitations to this analysis: (a) assumption that the viruses are homogeneously distributed in respiratory fluid particles and (b) considering a gene copy as a single virion in unit conversions. However, the study shows that high viral loads can decrease the minimum size of respiratory particles containing SARS-CoV-2, thereby increasing the probability of aerosol generation of the viruses. The aerosol generation theory created in this study for COVID-19 has the potential to be applied to other contagious diseases that are caused by respiratory infectious microorganisms.

COVID-19 also affects pregnant and breastfeeding women. Hence, clinicians and policymakers require reliable evidence on COVID-19 epidemiology and consequences in this population. We aimed to assess the susceptibility of pregnant women to SARS-CoV-2 and women's perceived impact of the pandemic on their breastfeeding practices, medical counseling and social support. We performed a cross-sectional study using an online survey in primary care in Belgium. Pregnant and breastfeeding women and women who breastfed in the preceding four weeks were eligible to participate. The survey was distributed through social media in April 2020. In total, 6470 women participated (i.e., 2647 pregnant and 3823 breastfeeding women). Overall, 0.3% of all respondents reported to have tested positive for SARS-CoV-2, not indicating a higher susceptibility of pregnant women to contracting COVID-19. More than 90% refuted that the pandemic affected their breastfeeding practices, nor indicated that the coronavirus was responsible for breastfeeding cessation. Half of the women even considered giving longer breastmilk because of the coronavirus. In contrast, women's medical counseling and social support were negatively affected by the lockdown. Women without previous breastfeeding experience and in the early postpartum period experienced a higher burden in terms of reduced medical counseling and support. In the future, more consideration and alternative supportive measures such as tele-visits by midwives or perinatal organizations are required for these women.

Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden., Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020., Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10 -3 substitutions per year., Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.

A critical point in the management of the SARS-CoV-2 pandemic is the need to promptly identify the greatest number of infected people and to implement strict public health measures. In this study, the performance of a rapid serological test in a clinical setting was evaluated. Samples from 819 consecutive patients (with or without respiratory symptoms) admitted to a large Emergency Department were tested between 23 March and 21 April 2020. Patient samples were tested in a real-time PCR assay and a serological assay. In total, 148/819 patients (18.1%) tested positive for SARS-CoV-2 by real-time PCR. The serological test revealed that 70/819 patients (8.5%) had anti-SARS-CoV-2 IgM and/or IgG. The prevalence of anti-SARS-CoV-2 antibodies was significantly higher in patients with respiratory symptoms lasting for >7 days than in those with respiratory symptoms lasting for 0-7 days ( p < 0.001). The serological assay had an overall sensitivity of 35.1% and an overall specificity of 97.3%. A high negative predictive value (96.7%) was reported for patients without respiratory symptoms. The results confirm that rapid serological assays alone are not sufficient for diagnosis of SARS-CoV-2 infection but can be incorporated into large-scale screening programs during periods in which the virus circulation is low.

An effective vaccine is essential for controlling the spread of the SARS-CoV-2 virus. Here, we describe an influenza virus-based vaccine for SARS-CoV-2. We incorporated a membrane-anchored form of the SARS-CoV-2 spike receptor binding domain (RBD) in place of the neuraminidase (NA) coding sequence in an influenza virus also possessing a mutation that reduces the affinity of hemagglutinin for its sialic acid receptor. The resulting ΔNA(RBD)-Flu virus can be generated by reverse genetics and grown to high titers in cell culture. A single-dose intranasal inoculation of mice with ΔNA(RBD)-Flu elicits serum neutralizing antibody titers against SAR-CoV-2 comparable to those observed in humans following natural infection (~1:200). Furthermore, ΔNA(RBD)-Flu itself causes no apparent disease in mice. It might be possible to produce a vaccine similar to ΔNA(RBD)-Flu at scale by leveraging existing platforms for the production of influenza vaccines.

Background: Since the beginning of SARS-CoV-2 outbreak, a large number of infections have been reported among healthcare workers (HCWs). The aim of this study was to investigate the occurrence of SARS-CoV-2 infection among HCWs involved in the first management of infected patients and to describe the measures adopted to prevent the transmission in the hospital., Methods: This prospective observational study was conducted between February 21 and April 16, 2020, in the Padua University Hospital (north-east Italy). The infection control policy adopted consisted of the following: the creation of the "Advanced Triage" area for the evaluation of SARS-CoV-2 cases, and the implementation of an integrated infection control surveillance system directed to all the healthcare personnel involved in the Advance Triage area. HCWs were regularly tested with nasopharyngeal swabs for SARS-CoV-2; body temperature and suggestive symptoms were evaluated at each duty. Demographic and clinical data of both patients and HCWs were collected and analyzed; HCWs' personal protective equipment (PPE) consumption was also recorded. The efficiency of the control strategy among HCWs was evaluated identifying symptomatic infection (primary endpoint) and asymptomatic infection (secondary endpoint) with confirmed detection of SARS-CoV-2., Results: 7595 patients were evaluated in the Advanced Triage area: 5.2% resulted positive and 72.4% was symptomatic. The HCW team was composed of 60 members. A total of 361 nasopharyngeal swabs were performed on HCWs. All the swabs resulted negative and none of the HCWs reached the primary or the secondary endpoint., Conclusions: An integrated hospital infection control strategy, consisting of dedicated areas for infected patients, strict measures for PPE use and mass surveillance, is successful to prevent infection among HCWs.