Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales

Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.
Overcoming COVID-19 Vaccine Hesitancy: Insights from an Online Population-Based Survey in the United States

This study sought to identify individual-level determinants of COVID-19 vaccine hesitancy based on the Health Belief Model (HBM) and Theory of Planned Behavior (TPB). An online population-based survey was distributed in English and Spanish. Data were derived from 1208 U.S. adults (52% female; 38.7% minorities), 43.5% of whom reported vaccine hesitancy. Multivariable analysis revealed that unemployed individuals were more likely (OR = 1.78, 95% CI: 1.16–2.73, p = 0.009) and married (OR = 0.57, 95% CI: 0.39–0.81, p = 0.002) and higher income individuals (OR = 0.52, 95% CI 0.32–0.84, p = 0.008) were less likely to be hesitant. Individuals with greater perceived susceptibility to COVID-19 (OR = 0.82, 95% CI: 0.71–0.94, p = 0.006), who perceived vaccination as being convenient (OR = 0.86, 95% CI: 0.74–1.00, p = 0.047), and who afforded greater importance to cues to action from government (OR = 0.84, 95% CI: 0.74–0.95, p = 0.005), public health (OR = 0.70, 95% CI: 0.59–0.82, p < 0.001), and healthcare experts (OR = 0.59, 95% CI: 0.50–0.69, p < 0.001) were also less likely to be hesitant. Findings suggest that HBM and TPB constructs may be useful in informing strategies to improve COVID-19 vaccine uptake. Specifically, framing appeals based on perceptions of COVID-19 susceptibility, making vaccination convenient, and rebuilding trust through unified cues to action may help to overcome vaccine hesitancy.
Pre-Exposure Prophylaxis with Hydroxychloroquine Does Not Prevent COVID-19 nor Virus Related Venous Thromboembolism

Different and several public health strategies have been planned to reduce transmission of pandemic due to SARS-CoV-2 since it started. None drugs have been confirmed as able to prevent viral transmission. Hydroxychloroquine with its immunomodulatory properties has been proposed as potential anti-viral drug in particular for prevention once viral exposure has been happen or in first phases of infection. Furthermore, in several immunological systemic disease hydroxychloroquine was able to reduce the number of thrombotic complications. So, because COVID-19 was associated to immunological imbalance and to thrombotic complications, we retrospectively analyzed the rate of infection in those patients being under treatment with this drug during COVID-19 epidemic outbreak from 8 March until 28 April in particular comparing those with pre-exposure to this treatment and those that were not taking this medication before SARS-CoV-2 viral infections.
Combinatorial F-G Immunogens as Nipah and Respiratory Syncytial Virus Vaccine Candidates

Nipah virus (NiV) and respiratory syncytial virus (RSV) possess two surface glycoproteins involved in cellular attachment and membrane fusion, both of which are potential targets for vaccines. The majority of vaccine development is focused on the attachment (G) protein of NiV, which is the immunodominant target. In contrast, the fusion (F) protein of RSV is the main target in vaccine development. Despite this, neutralising epitopes have been described in NiV F and RSV G, making them alternate targets for vaccine design. Through rational design, we have developed a vaccine strategy applicable to phylogenetically divergent NiV and RSV that comprises both the F and G proteins (FxG). In a mouse immunization model, we found that NiV FxG elicited an improved immune response capable of neutralising pseudotyped NiV and a NiV mutant that is able to escape neutralisation by two known F-specific antibodies. RSV FxG elicited an immune response against both F and G and was able to neutralise RSV; however, this was inferior to the immune response of F alone. Despite this, RSV FxG elicited a response against a known protective epitope within G that is conserved across RSV A and B subgroups, which may provide additional protection in vivo. We conclude that inclusion of F and G antigens within a single design provides a streamlined subunit vaccine strategy against both emerging and established pathogens, with the potential for broader protection against NiV.
Factors Associated with COVID-19 Vaccine Intentions in Eastern Zimbabwe: A Cross-Sectional Study

Vaccines are one of the most effective public health strategies to protect against infectious diseases, yet vaccine hesitancy has emerged as a global health threat. Understanding COVID-19 knowledge and attitudes and their association with vaccine intentions can help the targeting of strategies to increase vaccination uptake and achieve herd immunity. The goal of this study was to assess COVID-19 knowledge, attitudes, and behaviors, and identify factors associated with COVID-19 vaccine intentions among heads of households in Manicaland Province, Zimbabwe. A cross-sectional survey was conducted in May 2021 among 551 randomly selected households. Data were collected on socio-demographic characteristics, and knowledge, attitudes, and behaviors regarding COVID-19 and the vaccines. More than half (55.7%) of the respondents reported intending to vaccinate themselves or their households. Multivariate logistic regression indicated that the likelihood of vaccine intentions was most strongly associated with confidence in vaccine safety. Additionally, the odds of intending to get vaccinated were significantly higher among heads of households who were male, had a higher level of education, and identified vaccination and face mask usage as prevention measures. Among perceived motivators to vaccinate, recommendations from the World Health Organization and availability of the vaccine free of charge increased the likelihood of vaccine intentions, while country of vaccine manufacturer posed a barrier to vaccine intentions. As the vaccine rollout in Zimbabwe continues, efforts to increase COVID-19 vaccination coverage and achieve herd immunity should target females and less educated populations and be tailored to address concerns about vaccine safety and country of manufacturer.
Novel Ratio Soluble Fms-like Tyrosine Kinase-1/Angiotensin-II (sFlt-1/ANG-II) in Pregnant Women Is Associated with Critical Illness in COVID-19

Background: In healthy pregnancies, components of the Renin-Angiotensin system (RAS) are present in the placental villi and contribute to invasion, migration, and angiogenesis. At the same time, soluble fms-like tyrosine kinase 1 (sFlt-1) production is induced after binding of ANG-II to its receptor (AT-1R) in response to hypoxia. As RAS plays an essential role in the pathogenesis of COVID-19, we hypothesized that angiogenic marker (sFlt-1) and RAS components (ANG-II and ACE-2) may be related to adverse outcomes in pregnant women with COVID-19; Methods: Prospective cohort study. Primary outcome was severe pneumonia. Secondary outcomes were ICU admission, intubation, sepsis, and death. Spearman’s Rho test was used to analyze the correlation between sFlt-1 and ANG-II levels. The sFlt-1/ANG-II ratio was determined and the association with each adverse outcome was explored by logistic regression analysis and the prediction was assessed using receiver-operating-curve (ROC); Results: Among 80 pregnant women with COVID-19, the sFlt-1/ANG-II ratio was associated with an increased probability of severe pneumonia (odds ratio [OR]: 1.31; p = 0.003), ICU admission (OR: 1.05; p = 0.007); intubation (OR: 1.09; p = 0.008); sepsis (OR: 1.04; p = 0.008); and death (OR: 1.04; p = 0.018); Conclusion: sFlt-1/ANG-II ratio is a good predictor of adverse events such as pneumonia, ICU admission, intubation, sepsis, and death in pregnant women with COVID-19.
Lack of Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spillover in Free-Living Neotropical Non-Human Primates, Brazil

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), is responsible for the worst pandemic of the 21st century. Like all human coronaviruses, SARS-CoV-2 originated in a wildlife reservoir, most likely from bats. As SARS-CoV-2 has spread across the globe in humans, it has spilled over to infect a variety of non-human animal species in domestic, farm, and zoo settings. Additionally, a broad range of species, including one neotropical monkey, have proven to be susceptible to experimental infection with SARS-CoV-2. Together, these findings raise the specter of establishment of novel enzootic cycles of SARS-CoV-2. To assess the potential exposure of free-living non-human primates to SARS-CoV-2, we sampled 60 neotropical monkeys living in proximity to Manaus and São José do Rio Preto, two hotspots for COVID-19 in Brazil. Our molecular and serological tests detected no evidence of SAR-CoV-2 infection among these populations. While this result is reassuring, sustained surveillance efforts of wildlife living in close association with human populations is warranted, given the stochastic nature of spillover events and the enormous implications of SARS-CoV-2 spillover for human health.
Recent Issues in Varicella-Zoster Virus Latency

Varicella-zoster virus (VZV) is a human herpes virus which causes varicella (chicken pox) as a primary infection, and, following a variable period of latency in neurons in the peripheral ganglia, may reactivate to cause herpes zoster (shingles) as well as a variety of neurological syndromes. In this overview we consider some recent issues in alphaherpesvirus latency with special focus on VZV ganglionic latency. A key question is the nature and extent of viral gene transcription during viral latency. While it is known that this is highly restricted, it is only recently that the very high degree of that restriction has been clarified, with both VZV gene 63-encoded transcripts and discovery of a novel VZV transcript (VLT) that maps antisense to the viral transactivator gene 61. It has also emerged in recent years that there is significant epigenetic regulation of VZV gene transcription, and the mechanisms underlying this are complex and being unraveled. The last few years has also seen an increased interest in the immunological aspects of VZV latency and reactivation, in particular from the perspective of inborn errors of host immunity that predispose to different VZV reactivation syndromes.
Human Rhinoviruses in Adult Patients in a Tertiary Care Hospital in Germany: Molecular Epidemiology and Clinical Significance

Rhinoviruses (RVs) constitute a substantial public health burden. To evaluate their abundance and genetic diversity in adult patients, RV RNA in respiratory samples was assessed using real-time RT-PCR and the partial nucleic acid sequencing of viral genomes. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of adult RV infections. In total, the respiratory specimens of 284 adult patients (18–90 years), collected from 2013 to 2017, were analyzed. Infections occurred throughout the entire year, with peaks occurring in fall and winter, and showed a remarkably high intra- and interseasonal diversity of RV genotypes. RV species were detected in the following ratios: 60.9% RV-A 173, 12.7% RV-B, and 26.4% RV-C. No correlations between RV species and underlying comorbidities such as asthma (p = 0.167), COPD (p = 0.312) or immunosuppression (p = 0.824) were found. However, 21.1% of the patients had co-infections with other pathogens, which were associated with a longer hospital stay (p = 0.024), LRTI (p < 0.001), and pneumonia (p = 0.01). Taken together, this study shows a pronounced genetic diversity of RV in adults and underlines the important role of co-infections. No correlation of specific RV species with a particular clinical presentation could be deduced.
Determinants of COVID-19 Vaccine Hesitancy in Portuguese-Speaking Countries: A Structural Equations Modeling Approach

COVID-19 vaccine hesitancy (VH) has caused concerns due to the possible fluctuations that may occur directly impacting the control of the pandemic. In this study, we aimed to estimate the prevalence and factors associated with COVID-19 VH in Portuguese-speaking countries. We developed a web survey (N:6,843) using an online, structured, and validated questionnaire. We used Measurement Models, Exploratory Factor Analysis, Exploratory Structural Equation Models, and Confirmatory Factor Analysis for the data analysis. The overall prevalence of COVID-19 VH in Portuguese-speaking countries was 21.1%. showed a statistically significant direct effect for VH: vaccine-related conspiracy beliefs (VB) (β = 0.886), perceived stress (PS) (β = 0.313), COVID-19 Misinformation (MIS) (β = 0.259) and individual responses to COVID-19 (CIR) (β = −0.122). The effect of MIS and CIR for VH was greater among men and of PS and VB among women; the effect of PS was greater among the youngest and of VB and CIR among the oldest. No discrepant differences were identified in the analyzed education strata. In conclusion, we found that conspiracy beliefs related to the vaccine strongly influence the decision to hesitate (not to take or to delay the vaccine). Specific characteristics related to gender, age group, social and cognitive vulnerabilities, added to the knowledge acquired, poorly substantiated and/or misrepresented about the COVID-19 vaccine, need to be considered in the planning of vaccination campaigns. It is necessary to respond in a timely, fast, and accurate manner to the challenges posed by vaccine hesitancy.
A Mixed-Methods Study to Evaluate Elementary School Staff’s Acceptability, Delivery Challenges, and Communication Regarding the Implementation of School-Located Influenza Vaccination Program in Hong Kong

This was a mixed-methods study comprising a questionnaire-based survey, a qualitative study, and analysis of school newsletters to evaluate elementary school staff’s acceptability, delivery challenges and communication about school-located influenza vaccination program (SIVP) in Hong Kong. We found that school staff with lower intention to implement SIVP perceived greater logistical difficulties in arranging SIVP. Challenges regarding program delivery included schools’ limited infrastructure, the burden of paperwork, the fear of being overwhelmed by multiple school-based vaccination schedules, lacking confidence in communicating with parents about influenza vaccines, and the difficulties in managing vaccination-related anxiety among children with intellectual disability. School staff were generally passive in communicating with parents and students about influenza vaccines. We also found that schools may use the school newsletters as a substitute of the formal informed consent forms. Good partnerships among government, service providers and schools should be established to minimize the burden of paperwork for school staff, facilitate early planning of SIVP, and support schools with limited infrastructure and the vaccination of children with intellectual disabilities. Training is needed to enhance school staff’s confidence in communicating with parents and students about influenza vaccines and improve information delivery to support parents’ informed decisions for children’s vaccination.
An Update on Innate Immune Responses during SARS-CoV-2 Infection

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the Coronaviridae family, which is responsible for the COVID-19 pandemic followed by unprecedented global societal and economic disruptive impact. The innate immune system is the body’s first line of defense against invading pathogens and is induced by a variety of cellular receptors that sense viral components. However, various strategies are exploited by SARS-CoV-2 to disrupt the antiviral innate immune responses. Innate immune dysfunction is characterized by the weak generation of type I interferons (IFNs) and the hypersecretion of pro-inflammatory cytokines, leading to mortality and organ injury in patients with COVID-19. This review summarizes the existing understanding of the mutual effects between SARS-CoV-2 and the type I IFN (IFN-α/β) responses, emphasizing the relationship between host innate immune signaling and viral proteases with an insight on tackling potential therapeutic targets.
SDAV, the Rat Coronavirus—How Much Do We Know about It in the Light of Potential Zoonoses

Sialodacryoadenitis virus (SDAV) is known to be an etiological agent, causing infections in laboratory rats. Until now, its role has only been considered in studies on respiratory and salivary gland infections. The scant literature data, consisting mainly of papers from the last century, do not sufficiently address the topic of SDAV infections. The ongoing pandemic has demonstrated, once again, the role of the Coronaviridae family as extremely dangerous etiological agents of human zoonoses. The ability of coronaviruses to cross the species barrier and change to hosts commonly found in close proximity to humans highlights the need to characterize SDAV infections. The main host of the infection is the rat, as mentioned above. Rats inhabit large urban agglomerations, carrying a vast epidemic threat. Of the 2277 existing rodent species, 217 are reservoirs for 66 zoonotic diseases caused by viruses, bacteria, fungi, and protozoa. This review provides insight into the current state of knowledge of SDAV characteristics and its likely zoonotic potential.
Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities

High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection – often in the absence of disease symptoms – and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.
COVID-19 Vaccination in Patients with Myasthenia Gravis: A Single-Center Case Series

In this study, we report the safety of coronavirus disease 2019 (COVID-19) vaccine in patients with myasthenia gravis (MG). Patients who were vaccinated against COVID-19 were included. Demographics, clinical characteristics, medications, and vaccination information were collected. The main observation outcome is the worsening of MG symptoms within 4 weeks following COVID-19 vaccination. A total of 22 patients with MG vaccinated for COVID-19 were included. Ten (45.5%) patients had ocular MG (OMG), and 12 (55.5%) patients had generalized MG (GMG). Six (27.3%) patients were female, and the mean (SD) onset age was 45.4 (11.8) years. Nineteen (86.4%) patients were seropositive for acetylcholine receptors (AChR) antibody. Seven (31.8%) patients underwent thymectomy, and four of them confirmed thymoma pathologically. Twenty-one patients were administrated with inactivated vaccines, and the remaining one was administrated with recombinant subunit vaccine. Twenty (90.9%) patients did not present MG symptom worsening within 4 weeks of COVID-19 vaccination, and two (9.1%) patients reported slight symptom worsening but resolved quickly within a few days. Our findings suggest inactivated COVID-19 vaccines might be safe in MG patients with Myasthenia Gravis Foundation of America (MGFA) classification I to II, supporting the recommendation to promote vaccination for MG patients during the still expanding COVID-19 pandemic.
Encoder-Decoder Architecture for Ultrasound IMC Segmentation and cIMT Measurement

Cardiovascular diseases (CVDs) have shown a huge impact on the number of deaths in the world. Thus, common carotid artery (CCA) segmentation and intima-media thickness (IMT) measurements have been significantly implemented to perform early diagnosis of CVDs by analyzing IMT features. Using computer vision algorithms on CCA images is not widely used for this type of diagnosis, due to the complexity and the lack of dataset to do it. The advancement of deep learning techniques has made accurate early diagnosis from images possible. In this paper, a deep-learning-based approach is proposed to apply semantic segmentation for intima-media complex (IMC) and to calculate the cIMT measurement. In order to overcome the lack of large-scale datasets, an encoder-decoder-based model is proposed using multi-image inputs that can help achieve good learning for the model using different features. The obtained results were evaluated using different image segmentation metrics which demonstrate the effectiveness of the proposed architecture. In addition, IMT thickness is computed, and the experiment showed that the proposed model is robust and fully automated compared to the state-of-the-art work.