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1.
Vaccines (Basel) ; 10(1)2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-1614026

ABSTRACT

The Bacillus Calmette-Guérin (BCG) vaccine affords indirect protection against COVID-19, which is presumably due to priming of the innate immune system. It was hypothesized that the live attenuated Varicella Zoster (LAVZ) vaccine, recommended for the elderly population, would also protect against COVID-19 infection. A retrospective population-based cross-sectional study was conducted using the Leumit Health Services (LHS) database. LAVZ-vaccinated patients were matched with controls based on a propensity score model using 1:9 nearest-neighbor matching. Matching was based on age, gender, and the presence of some chronic disorders, which were selected according to their association with COVID-19 infection. Multivariate logistic regression analyses, adjusted for sex, age, smoking status, comorbidities, and chronic medications associated with COVID-19 risk, were used to estimate the association between LAVZ vaccination and COVID-19 RT-PCR results. Subjects (625) vaccinated with LAVZ and RT-PCR-tested for COVID-19 were identified. After 1:9 matching of subjects who received the LAVZ vaccine, 6250 subjects were included in the study. Multivariate logistic regression analysis demonstrated a significant and independent negative association between having received the LAVZ vaccine and the likelihood of COVID-19 infection (adjusted OR = 0.47 (95% CI 0.33-0.69, p < 0.001)). This association was further strengthened after separate analysis based on the time of LAVZ vaccination before COVID-19 RT-PCR testing. Individuals aged ≥50 years vaccinated with LAVZ had a decreased likelihood of being tested positive for COVID-19.

4.
Neuromolecular Med ; 23(4): 561-571, 2021 12.
Article in English | MEDLINE | ID: covidwho-1525619

ABSTRACT

The current SARS-CoV-2 outbreak, which causes COVID-19, is particularly devastating for individuals with chronic medical conditions, in particular those with Down Syndrome (DS) who often exhibit a higher prevalence of respiratory tract infections, immune dysregulation and potential complications. The incidence of Alzheimer's disease (AD) is much higher in DS than in the general population, possibly increasing further the risk of COVID-19 infection and its complications. Here we provide a biological overview with regard to specific susceptibility of individuals with DS to SARS-CoV-2 infection as well as data from a recent survey on the prevalence of COVID-19 among them. We see an urgent need to protect people with DS, especially those with AD, from COVID-19 and future pandemics and focus on developing protective measures, which also include interventions by health systems worldwide for reducing the negative social effects of long-term isolation and increased periods of hospitalization.

5.
FEBS Open Bio ; 2021 Oct 05.
Article in English | MEDLINE | ID: covidwho-1449903

ABSTRACT

Several recent studies have demonstrated that low plasma 25(OH) vitamin D levels are associated with the risk of COVID-19 infection. The primary source of vitamin D production in humans is environmental UV radiation. In many viral respiratory diseases, peak infection rates are observed during winter due to reduced UV exposure and low temperatures. In Europe, the second wave of COVID-19 began early in the winter of 2020. Investigating the impact of seasonal temperature and UV exposure on COVID-19 transmission could thus aid in prevention and intervention. As such, we first performed a comprehensive meta-analysis of all related published literature based on the association between vitamin D and COVID-19, which supported the hypothesis that the low vitamin D level is a critical risk factor for COVID-19 infection. Next, to understand the potential impact of seasonal UV and temperature levels on COVID-19 cases, we analyzed meteorological data and daily COVID-19 cases per million in the populations of 26 European countries. We observed that low temperature, UV index, and cloud-free vitamin D UV dose (UVDVF) levels are negatively correlated with COVID-19 prevalence in Europe. Furthermore, a distributed lag nonlinear model was used to assess the nonlinear delayed effects of individual seasonal factors on COVID-19 cases. Such analysis highlighted the significantly delayed impact of UVDVF on the cumulative relative risk of COVID-19 infection. The findings of this study suggest that low UV exposure can affect the required production of vitamin D in the body, which substantially influences the dynamics of COVID-19 transmission and severity.

7.
FEBS J ; 288(17): 5201-5223, 2021 09.
Article in English | MEDLINE | ID: covidwho-1146926

ABSTRACT

Circulating animal coronaviruses occasionally infect humans. The SARS-CoV-2 is responsible for the current worldwide outbreak of COVID-19 that has resulted in 2 112 844 deaths as of late January 2021. We compared genetic code preferences in 496 viruses, including 34 coronaviruses and 242 corresponding hosts, to uncover patterns that distinguish single- and 'promiscuous' multiple-host-infecting viruses. Based on a codon usage preference score, promiscuous viruses were shown to significantly employ nonoptimal codons, namely codons that involve 'wobble' binding to anticodons, as compared to single-host viruses. The codon adaptation index (CAI) and the effective number of codons (ENC) were calculated for all viruses and hosts. Promiscuous viruses were less adapted hosts vs single-host viruses (P-value = 4.392e-11). All coronaviruses exploit nonoptimal codons to infect multiple hosts. We found that nonoptimal codon preferences at the beginning of viral coding sequences enhance the translational efficiency of viral proteins within the host. Finally, coronaviruses lack endogenous RNA degradation motifs to a significant degree, thereby increasing viral mRNA burden and infection load. To conclude, we found that promiscuously infecting coronaviruses prefer nonoptimal codon usage to remove degradation motifs from their RNAs and to dramatically increase their viral RNA production rates.


Subject(s)
COVID-19/genetics , Codon Usage/genetics , Evolution, Molecular , SARS-CoV-2/genetics , Animals , COVID-19/virology , Codon/genetics , Computational Biology , Genetic Code/genetics , Genome, Viral/genetics , Humans , Phylogeny , RNA, Messenger/genetics , SARS-CoV-2/pathogenicity , Viral Proteins/genetics
8.
Nucleic Acids Res ; 49(D1): D1113-D1121, 2021 01 08.
Article in English | MEDLINE | ID: covidwho-1139997

ABSTRACT

The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-related articles are currently listed in PubMed. It has been shown in clinical settings that the analysis of past research results and the mining of available data can provide novel opportunities for the successful application of currently approved therapeutics and their combinations for the treatment of conditions caused by a novel SARS-CoV-2 infection. As such, effective responses to the pandemic require the development of efficient applications, methods and algorithms for data navigation, text-mining, clustering, classification, analysis, and reasoning. Thus, our COVID19 Drug Repository represents a modular platform for drug data navigation and analysis, with an emphasis on COVID-19-related information currently being reported. The COVID19 Drug Repository enables users to focus on different levels of complexity, starting from general information about (FDA-) approved drugs, PubMed references, clinical trials, recipes as well as the descriptions of molecular mechanisms of drugs' action. Our COVID19 drug repository provide a most updated world-wide collection of drugs that has been repurposed for COVID19 treatments around the world.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19/drug therapy , Databases, Pharmaceutical/statistics & numerical data , Drug Repositioning/statistics & numerical data , SARS-CoV-2/drug effects , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , Clinical Trials as Topic/methods , Clinical Trials as Topic/statistics & numerical data , Data Mining/methods , Data Mining/statistics & numerical data , Drug Approval/statistics & numerical data , Drug Repositioning/methods , Epidemics , Humans , Machine Learning , SARS-CoV-2/physiology
9.
Viruses ; 13(3)2021 03 03.
Article in English | MEDLINE | ID: covidwho-1125782

ABSTRACT

The recently emerged SARS-CoV-2 virus is responsible for the ongoing COVID-19 pandemic that has rapidly developed into a global public health threat. Patients severely affected with COVID-19 present distinct clinical features, including acute respiratory disorder, neutrophilia, cytokine storm, and sepsis. In addition, multiple pro-inflammatory cytokines are found in the plasma of such patients. Transcriptome sequencing of different specimens obtained from patients suffering from severe episodes of COVID-19 shows dynamics in terms of their immune responses. However, those host factors required for SARS-CoV-2 propagation and the underlying molecular mechanisms responsible for dysfunctional immune responses during COVID-19 infection remain elusive. In the present study, we analyzed the mRNA-long non-coding RNA (lncRNA) co-expression network derived from publicly available SARS-CoV-2-infected transcriptome data of human lung epithelial cell lines and bronchoalveolar lavage fluid (BALF) from COVID-19 patients. Through co-expression network analysis, we identified four differentially expressed lncRNAs strongly correlated with genes involved in various immune-related pathways crucial for cytokine signaling. Our findings suggest that the aberrant expression of these four lncRNAs can be associated with cytokine storms and anti-viral responses during severe SARS-CoV-2 infection of the lungs. Thus, the present study uncovers molecular interactions behind the cytokine storm activation potentially responsible for hyper-inflammatory responses in critical COVID-19 patients.


Subject(s)
COVID-19/genetics , COVID-19/immunology , RNA, Long Noncoding/genetics , RNA, Messenger/genetics , SARS-CoV-2/physiology , Bronchoalveolar Lavage Fluid/immunology , COVID-19/virology , Cytokines/genetics , Cytokines/immunology , Gene Regulatory Networks , Humans , Lung/immunology , Lung/virology , RNA, Long Noncoding/immunology , RNA, Messenger/immunology , SARS-CoV-2/genetics
10.
FEBS J ; 288(17): 5179-5189, 2021 09.
Article in English | MEDLINE | ID: covidwho-1096764

ABSTRACT

Acetylsalicylic acid (aspirin) is commonly used for primary and secondary prevention of cardiovascular diseases. Aspirin use is associated with better outcomes among COVID-19 positive patients. We hypothesized that the aspirin use for primary cardiovascular disease prevention might have a protective effect on COVID-19 susceptibility and disease duration. We conducted a retrospective population-based cross-sectional study, utilizing data from the Leumit Health Services database. The proportion of patients treated with aspirin was significantly lower among the COVID-19-positive group, as compared to the COVID-19-negative group [73 (11.03%) vs. 1548 (15.77%); P = 0.001]. Aspirin use was associated with lower likelihood of COVID-19 infection, as compared to nonusers (adjusted OR 0.71 (95% CI, 0.52 to 0.99; P = 0.041). Aspirin users were older (68.06 ± 12.79 vs. 56.63 ± 12.28 years of age; P < 0.001), presented a lower BMI (28.77 ± 5.4 vs. 30.37 ± 4.55; P < 0.0189), and showed higher prevalence of hypertension (56, 76.71%), diabetes (47, 64.38%), and COPD (11, 15.07%) than the aspirin nonusers (151, 25.64%, P < 0.001; 130, 22.07%, P < 0.001; and 43, 7.3%, P = 0.023, respectively). Moreover, COVID-19 disease duration (considered as the time between the first positive and second negative COVID-19 RT-PCR test results) among aspirin users was significantly shorter, as compared to aspirin nonusers (19.8 ± 7.8 vs. 21.9 ± 7.9 P = 0.045). Among hospitalized COVID-positive patients, a higher proportion of surviving subjects were treated with aspirin (20, 19.05%), as opposed to 1 dead subject (14.29%), although this difference was not significant (P = 0.449). In conclusion, we observed an inverse association between the likelihood of COVID-19 infection, disease duration and mortality, and aspirin use for primary prevention.


Subject(s)
Aspirin/administration & dosage , COVID-19/drug therapy , Cardiovascular Diseases/drug therapy , SARS-CoV-2/drug effects , Adult , Aged , Aspirin/adverse effects , COVID-19/complications , COVID-19/virology , Cardiovascular Diseases/complications , Cardiovascular Diseases/virology , Diabetes Mellitus/drug therapy , Diabetes Mellitus/virology , Humans , Hypertension/complications , Hypertension/drug therapy , Hypertension/virology , Male , Middle Aged , Primary Prevention , Retrospective Studies , Risk Factors , SARS-CoV-2/pathogenicity
11.
J Am Med Inform Assoc ; 27(11): 1721-1726, 2020 11 01.
Article in English | MEDLINE | ID: covidwho-1024117

ABSTRACT

Global pandemics call for large and diverse healthcare data to study various risk factors, treatment options, and disease progression patterns. Despite the enormous efforts of many large data consortium initiatives, scientific community still lacks a secure and privacy-preserving infrastructure to support auditable data sharing and facilitate automated and legally compliant federated analysis on an international scale. Existing health informatics systems do not incorporate the latest progress in modern security and federated machine learning algorithms, which are poised to offer solutions. An international group of passionate researchers came together with a joint mission to solve the problem with our finest models and tools. The SCOR Consortium has developed a ready-to-deploy secure infrastructure using world-class privacy and security technologies to reconcile the privacy/utility conflicts. We hope our effort will make a change and accelerate research in future pandemics with broad and diverse samples on an international scale.


Subject(s)
Biomedical Research , Computer Security , Coronavirus Infections , Information Dissemination , Pandemics , Pneumonia, Viral , Privacy , COVID-19 , Humans , Information Dissemination/ethics , Internationality , Machine Learning
12.
FEBS J ; 287(17): 3693-3702, 2020 09.
Article in English | MEDLINE | ID: covidwho-960855

ABSTRACT

Vitamin D deficiency is a worldwide pandemic. The aim of this study was to evaluate associations of plasma 25(OH)D levels with the likelihood of coronavirus disease 2019 (COVID-19) infection and hospitalization. The study population included the 14 000 members of Leumit Health Services, who were tested for COVID-19 infection from February 1st to April 30th , 2020, and who had at least one previous blood test for the plasma 25(OH)D level. 'Suboptimal' or 'low' plasma 25(OH)D level was defined as plasma 25-hydroxyvitamin D, or 25(OH)D, concentration below the level of 30 ng/mL. Of 7807 individuals, 782 (10.02%) were COVID-19-positive, and 7025 (89.98%) COVID-19-negative. The mean plasma vitamin D level was significantly lower among those who tested positive than negative for COVID-19 [19.00 ng/mL (95% confidence interval (CI) 18.41-19.59) vs. 20.55 (95% CI: 20.32-20.78)]. Univariate analysis demonstrated an association between the low plasma 25(OH)D level and increased likelihood of COVID-19 infection [crude odds ratio (OR) of 1.58 (95% CI: 1.24-2.01, P < 0.001)], and of hospitalization due to the SARS-CoV-2 virus [crude OR of 2.09 (95% CI: 1.01-4.30, P < 0.05)]. In multivariate analyses that controlled for demographic variables, and psychiatric and somatic disorders, the adjusted OR of COVID-19 infection [1.45 (95% CI: 1.08-1.95, P < 0.001)] and of hospitalization due to the SARS-CoV-2 virus [1.95 (95% CI: 0.98-4.845, P = 0.061)] were preserved. In the multivariate analyses, age over 50 years, male gender and low-medium socioeconomic status were also positively associated with the risk of COVID-19 infection; age over 50 years was positively associated with the likelihood of hospitalization due to COVID-19. We concluded that low plasma 25(OH)D levels appear to be an independent risk factor for COVID-19 infection and hospitalization.


Subject(s)
COVID-19/epidemiology , Pandemics , SARS-CoV-2/pathogenicity , Vitamin D Deficiency/epidemiology , Vitamin D/analogs & derivatives , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Body Mass Index , COVID-19/blood , COVID-19/complications , COVID-19/virology , Child , Child, Preschool , Female , Hospitalization/statistics & numerical data , Humans , Infant , Israel/epidemiology , Male , Middle Aged , Odds Ratio , Prevalence , Risk Factors , Severity of Illness Index , Social Class , Vitamin D/blood , Vitamin D Deficiency/blood , Vitamin D Deficiency/complications , Vitamin D Deficiency/virology
13.
Vaccines (Basel) ; 8(2)2020 Jun 09.
Article in English | MEDLINE | ID: covidwho-591334

ABSTRACT

A new coronavirus infection, COVID-19, has recently emerged, and has caused a global pandemic along with an international public health emergency. Currently, no licensed vaccines are available for COVID-19. The identification of immunodominant epitopes for both B- and T-cells that induce protective responses in the host is crucial for effective vaccine design. Computational prediction of potential epitopes might significantly reduce the time required to screen peptide libraries as part of emergent vaccine design. In our present study, we used an extensive immunoinformatics-based approach to predict conserved immunodominant epitopes from the proteome of SARS-CoV-2. Regions from SARS-CoV-2 protein sequences were defined as immunodominant, based on the following three criteria regarding B- and T-cell epitopes: (i) they were both mapped, (ii) they predicted protective antigens, and (iii) they were completely identical to experimentally validated epitopes of SARS-CoV. Further, structural and molecular docking analyses were performed in order to understand the binding interactions of the identified immunodominant epitopes with human major histocompatibility complexes (MHC). Our study provides a set of potential immunodominant epitopes that could enable the generation of both antibody- and cell-mediated immunity. This could contribute to developing peptide vaccine-based adaptive immunotherapy against SARS-CoV-2 infections and prevent future pandemic outbreaks.

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