Integrated immunoinformatics and subtractive proteomics approach for multi-epitope vaccine designing to combat S. pneumoniae TIGR4

Streptococcus pneumoniae is one of the major precarious pathogens accountable for over 1.2 million fatalities annually. The key drivers for pneumococcal vaccine development involve high morbidity and mortality in over one million cases, especially in very young children and the elderly. In this study, immunoinformatics was integrated with subtractive proteomics to find antigenic proteins for designing a multi-epitope vaccine against S. pneumoniae. As prospective vaccine targets, the developed pipeline identified two antigenic proteins, i.e., penicillin-binding protein and ATP synthase subunit. Several immunoinformatics and bioinformatics resources were used to forecast T- and B-cell epitopes from specific proteins. By employing a mixture of five cytotoxic T-cell lymphocytes, six helper T-cell lymphocytes, and seven linear B-cell lymphocyte epitopes, a 392 amino acid-long vaccine was designed. To enhance immune responses, the designed vaccine was coupled with a cholera enterotoxin subunit B adjuvant. The designed vaccine was highly antigenic, non-allergenic, and stable for human usage. The stability of the vaccine with toll-like receptor-4 was evaluated by molecular docking and molecular dynamic simulation. In addition, immunological simulation was performed to test its real-world potency. The vaccine codon was then cloned in silico. Overall, this study paves the way for the development of a multi-epitope S. pneumoniae vaccine under laboratory conditions. Furthermore, the current findings warrant for the experimental validation of the final multi-epitope vaccine construct to demonstrate its immunological reinforcing capability and clinical applicability.

Development and optimization of nanoparticles loaded with erucin, a dietary isothiocyanate isolated from Eruca sativa: Antioxidant and antiproliferative activities in ehrlich-ascites carcinoma cell line

The study on Erucin (ER) has gained interest of nutraceutical and pharmaceutical industries because of its anti-cancer properties. Erucin is an isothiocyanate obtained from the seeds of Eruca sativa which possess certain drawbacks such as poor aqueous solubility and bioavailability. Therefore, the present study aimed at developing ER-cubosomes (CUB) by solvent evaporation technique followed by applying Central Composite Design to optimize ER loaded cubosomes. For this purpose, independent variables selected were Monoolein (MO) as lipid and Pluronic-84 (P-84) as a stabilizer whereas dependent variables were particle size, percentage of ER loading and percentage of its entrapment efficiency. The cubosomal nanocarriers exhibited particle size in the range of 26 nm, entrapment efficiency of 99.12 ± 0.04% and drug loading of 3.96 ± 0.0001%. Furthermore, to investigate the antioxidant potential, we checked the effect of ER and ER-CUB by DNA nicking assay, DDPH assay and Phosphomolybdate assay, and results showed significant improvement in antioxidant potential for ER-CUB than ER. Similarly, ER-CUB showed enhanced anticancer activity with a marked reduction in IC50 value than ER in MTT assay. These results suggested that ER-CUB produced notable escalation in antioxidant potential and enhanced anticancer activity than ER.

COVID-19 Knowledge, Attitudes, and Preventive Measures of University Students in Bahrain

BACKGROUND

The severe, acute respiratory syndrome COVID-19 that was first reported in China in December 2019 quickly became a global pandemic that has resulted in over 100 million infections and more than 2 million deaths.

STUDY DESIGN

This study aimed to assess the awareness level of university students regarding the possibility of becoming infected with COVID-19. In order to achieve this objective, we assessed the students' knowledge, attitudes, and behaviors using an online survey questionnaire offered to a total of 300 students.

RESULTS

A positive response regarding awareness of COVID-19 symptoms was registered by more than 70% of the students, whereas 62% felt that wearing a mask did not give full protection against infection, approximately 30% agreed that antibiotics and antivirals did not treat COVID-19, and 62% agreed that vitamin C was helpful in treating common symptoms of COVID-19. Moreover, around 31% of the students believed that COVID-19 is a man-made virus. Students who had gotten infected with SARS-CoV-2 believed that wearing a mask gives full protection (p=0.018). In response to survey questions related to attitude, 80% of students cancelled and postponed meetings with friends, and 90% agreed that mask-wearing is the most precautionary measure used to prevent the infection. In addition, 82% avoided coughing in public, 82% avoided contact if they felt flu-like symptoms and 80% washed their hands far more often due to the pandemic. Interestingly, 76% carried hand sanitizer, 66.5% avoided shaking hands, and 42.7% were taking vitamin C supplements.

CONCLUSIONS

This study showed that the participants had a positive awareness of COVID-19 transmission, symptoms, and treatments misconceptions and mistaken beliefs related to treatments and the origin of the virus were also common and should be addressed. This study thus provides a baseline for a population-based surveillance program that could help local authorities to improve pandemic preparation plans, particularly with regard to governmental education and media campaigns.

A cross-sectional analysis of post-acute COVID-19 symptoms

OBJECTIVES

The severe acute respiratory syndrome (COVID-19) due to SARS-CoV-2 was first reported in China in December 2019 and has generated a worldwide pandemic. The objective of the research is to examine and describe (a) the symptoms that persist after the end of the acute stage and (b) their relationship with the severity of the disease.

STUDY DESIGN

This study is a cross-sectional study conducted in the Kingdom of Bahrain on COVID-19 infected patients using an online survey questionnaire with a total number of 52 patient responses (29 females and 23 males).

METHOD

A scale (0 no symptoms to 10 very high symptoms intensity) was assessed in patients after 3 months to detect the relevance of specific symptoms post-COVID-19 such as emotional and physical health, headache, dyspnoea, pain (muscles/joints/chest), anosmia, vertigo, neurologic symptoms, sarcopenia, delirium.

RESULTS

The most common COVID-19 symptoms were reported to be fever (69.2%), headache (59.6%), and cough (50.0%). Data analysis showed that BMI was not correlated with any post-acute COVID-19 symptoms. Regarding the post-acute COVID-19 symptoms, this study showed that an increase of intensity of headache was associated with an increase of delirium; an increase of intensity of dyspnoea was associated with an increase of pulmonary dysfunction. The increase of anosmia and dysgeusia was associated with an increase in delirium. In addition, the increase of neurological symptoms and delirium were associated with the increase of sarcopenia. The most common persistent post-COVID-19 symptoms observed in this study were emotional stress, followed by loss of smell and taste, and neurological symptoms.

CONCLUSIONS

Therefore, follow-up and rehabilitation care for COVID-19 patients must be focused on addressing the needs of these people in the longer term.

Clearing the air about airborne transmission of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has created the current pandemic, has caused a worldwide worry. Different countries have since enforced varying levels of lockdowns and guidelines for their populations to follow in a serious effort to mitigate the spread. Up until recently, the majority of these regulations and policies were established on the assumption that the dominant routes of transmission of this virus are through droplets and fomite contact. However, there is now a substantial amount of research pointing towards the strong possibility that SARS-CoV-2 can spread through airborne means. The World Health Organization (WHO) and the Center for Disease Control and Prevention (CDC) have recently recognized this, which poses the question of whether our collective methods of lessening transmission risk and keeping people safe have been sufficient. This paper is a comprehensive review of the evidence on SARS-CoV-2 being an airborne disease, through different epidemiological, experimental, and animal-model based published research. Studies opposing this evidence have also been discussed. The majority of these studies are favoring the high plausibility of SARS-CoV-2 aerosol transmission, and therefore the many implications of aerosol transmission have been discussed in this paper to suggest effective mitigation and control strategies.

Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies

OBJECTIVE: The current study reviewed Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) variants for their effects on infection, transmission and neutralization by vaccine-induced antibodies. MATERIALS AND METHODS: The research articles for the current study were searched over PubMed, Google Scholar, EMBASE and Web of Science online databases. The keywords used were: (("SARS-CoV-2" OR "COVID-19") AND ("mutation" OR "variant") AND ("death" OR "hospitalization" OR "infection" OR "transmission") AND ("antibody" OR "neutralize" OR "vaccine")). A total of 333 research articles were retrieved through online-database search. These articles were further scrutinized for their relevancy. Additionally, searches were performed to find the latest relevant information over Google search engine and relevant news browsers. Finally, around 35 germane articles were considered for scripting the current report. RESULTS: The mutations have changed amino acids at key positions in spike protein viz. S477N, E484K, Q677H, E484Q, L452R, K417T, K417N and N501Y. These mutations are relevant for different characteristics and are present in newly evolved strains of SARS-CoV-2 like E484K in B.1.526, B.1.525, P.2, B.1.1.7, P.1 and B.1.351. Mutations have increased the immune escape potential leading to 3.5-6.5-folds decrease in neutralization of antibodies (Pfizer and Moderna vaccines). The variant, B.1.617 circulating in India and many other countries (double variant) having E484Q and L452R mutations, has raised the infection rate and decreased the neutralization capacity of the vaccine-induced antibodies. Deadly K417N+E484K+N501Y triplet mutations found in B.1.351 and P.1 have increased the transmission ability of these strains by 50% leading to greater COVID-19 hospitalization, ICU admissions and deaths. CONCLUSIONS: The new SARS-CoV-2 variants have compromised the neutralization potential of the currently used vaccines, but still, they have considerable efficacy to reduce infection and mortality.

Graphical Abstract

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Association between RT-PCR Ct values and COVID-19 new daily cases: a multicenter cross-sectional study

Proactive prediction of the epidemiologic dynamics of viral diseases and outbreaks of the type of COVID-19 has remained a difficult pursuit for scientists, public health researchers, and policymakers. It is unclear whether RT-PCR Cycle Threshold (Ct) values of COVID-19 - or any other virus - as indicator of viral load, could represent a possible predictor for underlying epidemiologic changes on a population level. The study objective is thus to investigate whether population-wide changes in SARS-CoV-2 RT-PCR Ct values over time are associated with the daily fraction of positive COVID-19 tests. In addition, this study analyses the factors that could influence RT-PCR Ct values. A retrospective cross-sectional study was conducted on 63,879 patients from May 4, 2020 to September 30, 2020, in all COVID-19 facilities in the Kingdom of Bahrain. Data collected included number of tests and newly diagnosed cases, as well as Ct values, age, sex nationality, and symptomatic status. Ct values were found to be negatively and very weakly correlated with the fraction of daily positive tests in the population r = -0.06 (CI 95%: -0.06; -0.05; p=0.001). The R-squared for the regression model (adjusting for age and number of daily tests) showed an accuracy of 45.3%. Ct Values showed an association with nationality (p=0.012). After the stratification, the association between Ct values and the fraction of daily positive cases was only maintained for the female sex and Bahraini-nationality. Symptomatic presentation was significantly associated with lower Ct values (higher viral loads). Ct values do not show any correlation with age (p=0.333) or sex (p=0.522). We report one of the first and largest studies to investigate the epidemiologic associations of Ct values with COVID-19. Although changes in Ct values showed a moderate association with daily cases, our results indicate that it may not be as predictive within a simple model. More population studies and models from global cohorts are necessary.

Detection of Enteric Viruses and Bacterial Indicators in a Sewage Treatment Center and Shallow Water Bay

The incidence of enteric viruses in treated wastewater and their potential release into the environment or use for agriculture are very critical matters in public health. In our study, PCR (polymerase chain reaction) analysis of enteric viruses was performed on 59 samples of influents and effluents collected from Tubli wastewater treatment plant (Water Pollution Control Center (WPCC)) and Tubli Bay, where the effluents were discharged, in Kingdom of Bahrain during two sampling periods. Four clinically essential waterborne enteric viruses were examined: enterovirus (EV), hepatitis A virus (HAV), astroviruses (AV), and rotaviruses (RV) and compared to standard bacterial and bacteriophages indicators of fecal pollution. Detection rates of EV, AV, HAV, and RV in the influent samples were 100%, 75%, 12.5%, and 12.5%, respectively, while 50% of the effluent samples from Tubli WPCC contained only EV RNA. None of the tested enteric viruses could be detected in any of the samples collected directly from Tubli Bay. Effluent samples from Tubli plant did not show significant seasonal differences. Since detection of enteric viruses genome does not necessarily indicate infectivity, the infectivity of these viruses was evaluated through isolation and growth of indictor bacteria and bacteriophages. High concentration of fecal bacteriological indicators was detected in all effluents samples (100%): 3.20 × 10³ cfu/mL for E. coli, 1.32 × 10³ cfu/mL for Salmonella spp., and 1.92 × 10³ cfu/mL for Shigella spp. E. coli and Salmonella specific bacteriophages were also detected in the effluent samples in high titers. The combined results of PCR and bacterial enumeration point to a probable public health risk via the use of these wastewaters in agriculture or their discharge into the sea. Continuous surveillance of viral and bacterial prevalence and their resistance to sewage disinfection procedures could contribute to a better control of risks associated with the recycling of effluent wastewater and its release into the environment.

Implications of Hepatitis E Virus in Blood Transfusions, Hemodialysis, and Solid Organ Transplants

Hepatitis E Virus (HEV) is emerging as the primary cause of acute viral hepatitis in humans. The virus is commonly transmitted by the fecal-oral route via contaminated water in endemic regions or through the consumption of inadequately cooked swine products or game meats in industrialized regions. HEV genotypes 1 and 2 are predominantly associated with waterborne transmission in developing countries, whereas HEV3 and HEV4 are mainly zoonotically transmitted in industrialized countries. Seroprevalence in populations determined by detecting anti-HEV antibodies and serum HEV RNA is commonly used to analyze the presence of HEV. Although HEV RNA-based detection is now standardized, there is a lack of agreement between the assaying methods used for gathering seroprevalence data. Since 2004, HEV has been considered as a transmissible infectious agent through blood transfusion. Recent seroprevalence studies in European countries indicate an underestimated risk for blood transfusion and hence warrant testing the blood supply. HEV infection is usually self-limiting and spontaneously cleared. However, in about 60% of recipients of solid organ transplants, HEV progresses to chronic hepatitis. Immunosuppressive drugs such as tacrolimus are a major cause of chronic hepatitis and reducing its dosage results in viral clearance in about 30% of patients. In hemodialysis patients, the parenteral route is implicated as an important mechanism of transmission. In this review, we explore the clinical and epidemiological characteristics of various HEV genotypes in blood donors, hemodialysis patients, and transplant recipients.

Perceptions and Attitudes Towards HIV/AIDS Patients among General Public in Bahrain

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Distribution of Hepatitis C Virus Genotypes in Bahrain

BACKGROUND

Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide, making it one of the world's major infectious diseases. There are no published population based studies about the prevalence of HCV genotypes in Bahrain.

OBJECTIVES

Therefore, the aim of the present study was to investigate the prevalence and distribution of HCV genotypes and subtypes among a large sample of patients with chronic HCV infection in Bahrain.

PATIENTS AND METHODS

Serum samples were collected from 202 HCV positive patients; of them 128 had a viral load (> 500 IU/mL) suitable for the type-specific genotyping assay. Gender-wise and age-wise differences in the distribution of HCV genotypes were determined by Chi Square and Fisher's Exact tests.

RESULTS

The predominant genotype among Bahraini patients was type 1 (36.71%), followed by genotypes 3 and 4 (15.6% each) and the lowest frequency was found for genotype 2 (3.9%). Among genotype 1, subtype 1b had the highest frequency (21.09%), followed by subtype 1a (14.06%). Among genotype 3, subtype 3a had the highest frequency (11.72%), while among genotype 4, most of subtypes were undetermined. The frequency of all different HCV genotypes was higher in male patients compared to female patients. Genotype 1 was most common in the age group of 51 - 60 years (38.3%), genotype 2 in 21 - 30 years (60%) and genotype 3 in 51 - 60 years (30%), while genotype 4 was most frequent among the age group > 61 (40%).

CONCLUSIONS

The most common HCV genotype in Bahrain was subtype 1b followed by 1a and 3a. Further studies involving sources of transmission in Bahrain are required to enhance control measures for HCV infection.

Prevalence and risk factors of hepatitis B virus infection in Bahrain, 2000 through 2010

Hepatitis B infection is one of the world's major infectious diseases with about 350 million chronic carriers. Because no data is published on the prevalence and risk factors of this important disease in Bahrain, this article evaluates the available data from 2000 to 2010 to estimate the prevalence of the infection and to evaluate the risk factors. Epidemiologic data on HBV cases were collected from the major hospitals and health centers in Bahrain and statistically analyzed. Over this indicated decade, 877,892 individuals were screened for HBV infection and 5055 positive cases were reported in Bahrain. The prevalence of HBV infection during that period was 0.58%. Although there was no significant difference in the prevalence over the period of 10 years, the actual number of positive cases has almost doubled in the later years especially in 2007 and 2008. The prevalence was significantly higher among males (62.3%; P<0.01). Most cases were associated with non Bahrainis and the prevalence was significantly higher among them (68.3%; P<0.01) than it was among Bahrainis (31.7%). Seventy eight percent (2877/3690) of non Bahraini cases were for citizens of six countries which are highly endemic for HBV, namely India, Pakistan, Bangladesh, Philippines, Indonesia and Ethiopia. Dental procedures and surgical operations were the main risk factors of infection as 37.2% and 35.6% of the patients were probably infected through this route. The prevalence of hepatitis B virus infection in Bahrain indicates that Bahrain had low HBV endemicity for the last 10 years (2000–2010). Our study verifies the significant role played by expatriates/immigrants in the present epidemiology of hepatitis B in Bahrain. Increasing HBV vaccination of high risk groups, active educational and media campaign, screening HBV infection during pregnancy, and surveillance of hepatitis B infected individuals will further decrease the prevalence of the disease in Bahrain.

The inhibition of hepatitis B virus by APOBEC cytidine deaminases

APOBEC3 (A3) cytidine deaminases are a family of enzymes that have been shown to inhibit the replication of HIV-1 and other retroviruses as part of the innate immune responses to virus infection. They can also hyperedit HBV DNA and inhibit HBV replication. Although A3 proteins are present at low levels in normal liver, A3 gene expression is highly stimulated by both interferon-α and interferon-γ. A3 deaminases are incorporated into nascent HBV capsids where they cleave amino groups from cytidine bases converting them to uracil in newly synthesized DNA following reverse transcription of pregenomic RNA. This modified HBV DNA is susceptible to degradation, or alternatively, numerous G-to-A nucleotide mutations are incorporated into positive-strand viral DNA disrupting coding sequences. A3 proteins in which the cytidine deaminase activity has been lost can also inhibit HBV replication, suggesting that there may be more than one way in which inhibition can occur. There is also evidence that A3 proteins might play a role in the development of hepatocellular carcinoma during chronic HBV infection.