Immune and bioinformatics identification of T cell and B cell epitopes in the protein structure of SARS-CoV-2: A systematic review

The beginning of 2020 was marked as the emergence of a COVID-19 outbreak caused by a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, there is no vaccine or approved treatment for this infectious virus so the invention of an efficient vaccine is certainly a high priority. Some studies have employed several techniques to facilitate the combination of the immunoinformatics approach and comparative genomic approach in order to determine the potential peptides for designing the T-cell epitope-based peptide vaccine using the 2019-nCoV envelope protein as a target. Via screening the bioimmunoinformatic SARS-CoV2 derived B-cell and T-cell epitopes within the basic immunogenic of SARS-CoV2 proteins, we presented a set of inferred B-cell and T-cell epitopes from the spike (S) and nucleocapsid (N) proteins with high antigenicity and without allergenic property or toxic effects. Our findings provide a screened set of epitopes that can be introduced as potential targets for developing peptide vaccines against the SARS-CoV-2 virus

The association of cancer survival with four socioeconomic indicators: a longitudinal study of the older population of England and Wales 1981–2000

BACKGROUND: Many studies have found socioeconomic differentials in cancer survival. Previous studies have generally demonstrated poorer cancer survival with decreasing socioeconomic status but mostly used only ecological measures of status and analytical methods estimating simple survival. This study investigate socio-economic differentials in cancer survival using four indicators of socioeconomic status; three individual and one ecological. It uses a relative survival method which gives a measure of excess mortality due to cancer. METHODS: This study uses prospective record linkage data from The Office for National Statistics Longitudinal Study for England and Wales. The participants are Longitudinal Study members, recorded at census in 1971 and 1981 and with a primary malignant cancer diagnosed at age 45 or above, between 1981 and 1997, with follow-up until end 2000. The outcome measure is relative survival/excess mortality, compared with age and sex adjusted survival of the general population. Relative survival and Poisson regression analyses are presented, giving models of relative excess mortality, adjusted for covariates. RESULTS: Different socioeconomic indicators detect survival differentials of varying magnitude and definition. For all cancers combined, the four indicators show similar effects. For individual cancers there are differences between indicators. Where there is an association, all indicators show poorer survival with lower socioeconomic status. CONCLUSION: Cancer survival differs markedly by socio-economic status. The commonly used ecological measure, the Carstairs Index, is adequate at demonstrating socioeconomic differentials in survival for combined cancers and some individual cancers. A combination of car access and housing tenure is more sensitive than the ecological Carstairs measure at detecting socioeconomic effects on survival – confirming Carstairs effects where they occur but additionally identifying effects for other cancers. Social class is a relatively weak indicator of survival differentials

Prognosis of screen-detected breast cancers: results of a population based study

BACKGROUND: The reduced mortality rate from breast carcinoma among women offered screening mammography is demonstrated after 15–20 years of follow-up. However, the assessment of 5-year overall and event-free survival could represent an earlier measure of the efficacy of mammography screening program (MSP). METHODS: All cases of breast cancer diagnosed in the Province of Modena between years 1996 and 2000 in women aged 50 to 69 years, were identified through the Modena Cancer Registry (MCR). Stage of disease and treatment information were obtained from clinical records. All the events occurring up to June 30, 2003 were retrieved by experienced monitors. Five-year overall and event-free survival were the principal end-points of the study. RESULTS: During a 5-year period, 587 primary breast cancers were detected by the MSP and 471 primary breast cancers were diagnosed out of the MSP. The screen-detected breast cancers were smaller, more likely node negative, with low histological grade, low proliferative activity and positive receptors status. Furthermore, the breast cancer diagnosed through the MSP more frequently received a conservative surgery. The 5-year survival rate was 94% in the screen-detected group, versus 84% in the other group (p = 0.0001). The rate of 5-year event-free survival was 89% and 75% for the MSP participants and not participants, respectively (p = 0.0001). CONCLUSIONS: Our data confirm a favourable outcome of screen-detected breast cancers in terms of five-year overall and event-free survival, which reflect the good quality assurance parameters of the MSP. Finally, a cancer registry should be implemented in every area covered by screening programs

The relation between socioeconomic and demographic factors and tumour stage in women diagnosed with breast cancer in Denmark, 1983–1999

The authors investigated the association between socioeconomic position and stage of breast cancer at the time of diagnosis in a nationwide Danish study. All 28 765 women with a primary invasive breast cancer diagnosed between 1983 and 1999 were identified in a nationwide clinical database and information on socioeconomic variables was obtained from Statistics Denmark. The risk of being diagnosed with a high-risk breast cancer, that is size >20 mm, lymph-node positive, ductal histology/high histologic grade and hormone receptor negative, was analysed by multivariate logistic regression. The adjusted odds ratio (OR) for high-risk breast cancer was reduced with longer education with a 12% reduced risk (95% confidence interval (CI), 0.80,0.96) in women with higher education and increased with reduced disposable income (low income group: OR, 1.22; 95% CI, 1.10,1.34). There was an urban–rural gradient, with higher risk among rural women (OR 1.10; 95 % CI, 1.02, 1.18) and lower risk among women in the capital suburbs (OR, 0.85; 95% CI, 0.78, 0.93) and capital area (OR, 0.93; 95% CI, 0.84–1.02). These factors were significant only for postmenopausal women, although similar patterns were observed among the premenopausal women, suggesting a subgroup of aggressive premenopausal breast cancers less influenced by socioeconomic factors

The status of hepatitis C virus infection among people who inject drugs in the Middle East and North Africa.

BACKGROUND AND AIMS: People who inject drugs (PWID) are a key population at high risk of hepatitis C virus (HCV) infection. The aim of this study was to delineate the epidemiology of HCV in PWID in the Middle East and North Africa (MENA). METHODS: Syntheses of data were conducted on the standardized and systematically assembled databases of the MENA HCV Epidemiology Synthesis Project, 1989-2018. Random-effects meta-analyses and meta-regressions were performed. Meta-regression variables included country, study site, year of data collection and year of publication [to assess trends in HCV antibody prevalence over time], sample size and sampling methodology. Numbers of chronically infected PWID across MENA were estimated. The Shannon Diversity Index was calculated to assess genotype diversity. RESULTS: Based on 118 HCV antibody prevalence measures, the pooled mean prevalence in PWID for all MENA was 49.3% [95% confidence interval (CI) = 44.4-54.1%]. The country-specific pooled mean ranged from 21.7% (95% CI = 4.9-38.6%) in Tunisia to 94.2% (95% CI = 90.8-96.7%) in Libya. An estimated 221 704 PWID were chronically infected, with the largest numbers found in Iran at 68 526 and in Pakistan at 46 554. There was no statistically significant evidence for a decline in HCV antibody prevalence over time. Genotype diversity was moderate (Shannon Diversity Index of 1.01 out of 1.95; 52.1%). The pooled mean percentage for each HCV genotype was highest in genotype 3 (42.7%) and in genotype 1 (35.9%). CONCLUSION: Half of people who inject drugs in the Middle East and North Africa appear to have ever been infected with hepatitis C virus, but there are large variations in antibody prevalence among countries. In addition to > 200 000 chronically infected current people who inject drugs, there is an unknown number of people who no longer inject drugs who may have acquired hepatitis C virus during past injecting drug use. Harm reduction services must be expanded, and innovative strategies need to be employed to ensure accessibility to hepatitis C virus testing and treatment

Socioeconomic background in relation to stage at diagnosis, treatment and survival in women with breast cancer

In a large population-based series of invasive breast cancer patients, we investigated socioeconomic background (SEB) in relation to (a) stage at diagnosis; (b) treatment pattern; and (c) 5-year survival. Women diagnosed during 1998–2000 and resident in the Northern and Yorkshire regions of England were identified from the cancer registry database (N=12 768). Logistic regression and Cox proportional hazards analyses were used to estimate associations between SEB (defined using the Townsend Index for area of residence) and tumour stage, treatment pattern, and survival. Living in a more deprived area was associated with increased likelihood of being diagnosed with stage III or IV disease (age-adjusted odds ratio (OR) 1.13; 95% confidence interval (CI) 1.08–1.18 per quartile increase in Townsend score), and, after adjustment for age and stage, reduced odds of having surgery (OR 0.85; 95% CI 0.80–0.91), and receiving radiotherapy (OR 0.91; 95% CI 0.88–0.94). Amongst patients receiving surgery, those living in more deprived areas had decreased odds of having breast conserving surgery (age plus stage-adjusted OR 0.92; 95% CI 0.89–0.95). Living in a more deprived area was also associated with increased mortality (age- plus stage-adjusted hazard ratio 1.08; 95% CI 1.05–1.11). These effects may operate through several pathways, such as later presentation leading to advanced disease

Socio-economic status and overall and cause-specific mortality in Sweden

<p>Abstract</p> <p>Background</p> <p>Previous studies have reported discrepancies in cause-specific mortality among groups of individuals with different socio-economic status. However, most of the studies were limited by the specificity of the investigated populations and the broad definitions of the causes of death. The aim of the present population-based study was to explore the dependence of disease specific mortalities on the socio-economic status in Sweden, a country with universal health care. Another aim was to investigate possible gender differences.</p> <p>Methods</p> <p>Using the 2006 update of the Swedish Family-Cancer Database, we identified over 2 million individuals with socio-economic data recorded in the 1960 national census. The association between mortality and socio-economic status was investigated by Cox's proportional hazards models taking into account the age, time period and residential area in both men and women, and additionally parity and age at first birth in women.</p> <p>Results</p> <p>We observed significant associations between socio-economic status and mortality due to cardiovascular diseases, respiratory diseases, to cancer and to endocrine, nutritional and metabolic diseases. The influence of socio-economic status on female breast cancer was markedly specific: women with a higher socio-economic status showed increased mortality due to breast cancer.</p> <p>Conclusion</p> <p>Even in Sweden, a country where health care is universally provided, higher socio-economic status is associated with decreased overall and cause-specific mortalities. Comparison of mortality among female and male socio-economic groups may provide valuable insights into the underlying causes of socio-economic inequalities in length of life.</p

Serum magnesium and calcium levels in relation to ischemic stroke : Mendelian randomization study

ObjectiveTo determine whether serum magnesium and calcium concentrations are causally associated with ischemic stroke or any of its subtypes using the mendelian randomization approach.MethodsAnalyses were conducted using summary statistics data for 13 single-nucleotide polymorphisms robustly associated with serum magnesium (n = 6) or serum calcium (n = 7) concentrations. The corresponding data for ischemic stroke were obtained from the MEGASTROKE consortium (34,217 cases and 404,630 noncases).ResultsIn standard mendelian randomization analysis, the odds ratios for each 0.1 mmol/L (about 1 SD) increase in genetically predicted serum magnesium concentrations were 0.78 (95% confidence interval [CI] 0.69-0.89; p = 1.3 7 10-4) for all ischemic stroke, 0.63 (95% CI 0.50-0.80; p = 1.6 7 10-4) for cardioembolic stroke, and 0.60 (95% CI 0.44-0.82; p = 0.001) for large artery stroke; there was no association with small vessel stroke (odds ratio 0.90, 95% CI 0.67-1.20; p = 0.46). Only the association with cardioembolic stroke was robust in sensitivity analyses. There was no association of genetically predicted serum calcium concentrations with all ischemic stroke (per 0.5 mg/dL [about 1 SD] increase in serum calcium: odds ratio 1.03, 95% CI 0.88-1.21) or with any subtype.ConclusionsThis study found that genetically higher serum magnesium concentrations are associated with a reduced risk of cardioembolic stroke but found no significant association of genetically higher serum calcium concentrations with any ischemic stroke subtype