Immunoinformatics Identification of the Conserved and Cross-Reactive T-Cell Epitopes of SARS-CoV-2 with Human Common Cold Coronaviruses, SARS-CoV, MERS-CoV and Live Attenuated Vaccines Presented by HLA Alleles of Indonesian Population.

Reports on T-cell cross-reactivity against SARS-CoV-2 epitopes in unexposed individuals have been linked with prior exposure to the human common cold coronaviruses (HCCCs). Several studies suggested that cross-reactive T-cells response to live attenuated vaccines (LAVs) such as BCG (Bacillus Calmette-Guérin), OPV (Oral Polio Vaccine), and MMR (measles, mumps, and rubella) can limit the development and severity of COVID-19. This study aims to identify potential cross-reactivity between SARS-CoV-2, HCCCs, and LAVs in the context of T-cell epitopes peptides presented by HLA (Human Leukocyte Antigen) alleles of the Indonesian population. SARS-CoV-2 derived T-cell epitopes were predicted using immunoinformatics tools and assessed for their conservancy, variability, and population coverage. Two fully conserved epitopes with 100% similarity and nine heterologous epitopes with identical T-cell receptor (TCR) contact residues were identified from the ORF1ab fragment of SARS-CoV-2 and all HCCCs. Cross-reactive epitopes from various proteins of SARS-CoV-2 and LAVs were also identified (15 epitopes from BCG, 7 epitopes from MMR, but none from OPV). A majority of the identified epitopes were observed to belong to ORF1ab, further suggesting the vital role of ORF1ab in the coronaviruses family and suggesting it as a candidate for a potential universal coronavirus vaccine that protects against severe disease by inducing cell mediated immunity.

Role of hepatitis B virus in development of hepatocellular carcinoma: Focus on covalently closed circular DNA.

Chronic infection with hepatitis B virus (HBV) remains a major global health problem, especially in developing countries. It may lead to prolonged liver damage, fibrosis, cirrhosis, and hepatocellular carcinoma. Persistent chronic HBV infection is related to host immune response and the stability of the covalently closed circular DNA (cccDNA) in human hepatocytes. In addition to being essential for viral transcription and replication, cccDNA is also suspected to play a role in persistent HBV infections or hepatitis relapses since cccDNA is very stable in non-dividing human hepatocytes. Understanding the pathogenicity and oncogenicity of HBV components would be essential in the development of new diagnostic tools and treatment strategies. This review summarizes the role and molecular mechanisms of HBV cccDNA in hepatocyte transformation and hepatocarcinogenesis and current efforts to its detection and targeting.

Evaluation of antiplasmodial properties of a cyanobacterium, Spirulina platensis and its mechanism of action.

The rapid emergence of antimalarial drug resistance necessitates a continual effort on novel drug discovery. A cyanobacterium, Spirulina platensis, is a potential antimalarial agent that has been widely consumed as food supplement in the form of crude extract. It is known to possess antiviral, antibacterial and antifungi activities. This study examined the antimalarial activities of several Spirulina formulas against Plasmodium falciparum 3D7, in vitro. The tested Spirulina formulas included commercially available capsule, crude extract and alkaloid fraction. Results showed that all tested formula possessed antimalarial activities with the Spirulina capsule exhibited the highest activities (IC50 = 2.16 µg/mL). Light and electron microscopies revealed interference of the Spirulina with the parasite hemozoin formation. In conclusion, all tested Spirulina formulas and fraction exhibited moderate to high antimalarial activities.

Factors affecting signal strength in spectral-domain optical coherence tomography.

PURPOSE: To identify ocular factors that affect signal strength in spectral-domain optical coherence tomography (SD-OCT). METHODS: Data from 1312 participants of the population-based Singapore Malay Eye Study-2 (SiMES-2) were included in the analysis. All participants underwent standardized ophthalmic examination, including measurements of best-corrected visual acuity (BCVA), refractive error, axial length, corneal curvature and presence of cataracts. Optic disc and macular cube scans were acquired using the Cirrus HD-OCT (software version 6.0, Carl Zeiss Meditec, Dublin, CA, USA). Signal strength of the optical coherence tomography (OCT) scan was recorded for each study eye. Multivariable linear regression analyses were performed to evaluate the associations between ocular factors and signal strength of the OCT scans. RESULTS: The mean (±SD) age of our study participants was 61 ± 9 years, and 44.6% were male. Mean optic disc scan signal strength was 7.90 ± 1.25, range = 0-10, while mean macular scan signal strength was 8.80 ± 1.27, range = 0-10. In multivariable regression analyses, poorer signal strength in optic disc and macular cube scans was each associated with older age (per decade, ß = -0.373, p < 0.001; ß = -0.373, p < 0.001, respectively), poorer BCVA (per logMAR line; ß = -0.123, p < 0.001; ß = -0.156, p < 0.001, respectively), greater degree of myopia (per negative dioptre of spherical equivalent; ß = -0.112, p < 0.001; ß = -0.117, p < 0.001, respectively), presence of cortical cataracts (ß = -0.331, p < 0.001; ß = -0.314, p < 0.001, respectively) and presence of posterior subcapsular cataracts (ß = -0.910, p < 0.001; ß = -0.797, p < 0.001, respectively). CONCLUSION: We found that older age, poorer BCVA, greater degree of myopia and presence of cortical and posterior subcapsular cataracts were associated with reduced signal strength in Cirrus SD-OCT. Our findings provide information on the barriers to obtaining good image quality when using SD-OCT, and allow clinicians to potentially identify individuals who are more likely to have unreliable OCT measurements.

Association of iris surface features with iris parameters assessed by swept-source optical coherence tomography in Asian eyes.

BACKGROUND/AIMS: To characterise the association of iris surface features (crypts, furrows and colour) with iris volume and curvature assessed by swept-source optical coherence tomography (SSOCT) in Asian eyes. METHODS: Iris crypts (by number and size) and furrows (by number and circumferential extent) were graded from iris photographs. Iris colour was measured by a customised algorithm written on MATLAB (MathWorks, Natick, Massachusetts, USA). The iris was imaged by SSOCT (SS-1000, CASIA, Tomey, Nagoya, Japan). The associations of surface features with iris parameters were analysed using a generalised estimating equation. RESULTS: A total of 1704 subjects (3297 eyes) were included in the analysis. The majority was Chinese (86.4%), and 63.2% were females, and their mean age (±SD) was 61.4±6.6 years. After adjusting for age, sex, ethnicity, pupil size and corneal arcus, higher iris crypt grade was independently associated with smaller iris volume (ß=-0.54, p<0.001), whereas darker irides and higher iris furrow grade were associated with larger iris volume (ß=-0.041, p<0.001) and (ß=0.233, p<0.001), respectively. Lighter coloured irides with more crypts and/or more furrows were also associated with less convexity (crypts: ß=-0.003, p=0.03; furrows: ß=-0.004, p=0.007; and colour: ß=-0.001, p=0.005). CONCLUSIONS: Iris surface features were highly correlated with iris volume and curvature. Irides with more crypts have a smaller volume; and darker irides with more furrows have a larger volume. Lighter irides with more crypts and/or furrows have less convexity.

Relationship between iris surface features and angle width in Asian eyes.

PURPOSE: To examine the associations between iris surface features with anterior chamber angle width in Asian eyes. METHODS: In this prospective cross-sectional study, we recruited 600 subjects from a large population-based study, the Singapore Epidemiology of Eye Diseases (SEED) study. We obtained standardized digital slit-lamp iris photographs and graded the iris crypts (by number and size), furrows (by number and circumferential extent), and color (higher grade denoting darker iris). Vertical and horizontal cross-sections of anterior chamber were imaged using anterior segment optical coherence tomography. Angle opening distance (AOD), angle recess area (ARA), and trabecular-iris space area (TISA) were measured using customized software. Associations of the angle width with the iris surface features in the subject's right eyes were assessed using linear regression analysis. RESULTS: A total of 464 eyes of the 464 subjects (mean age: 57.5 ± 8.6 years) had complete and gradable data for crypts and color, and 423 eyes had gradable data for furrows. After adjustment for age, sex, ethnicity, pupil size, and corneal arcus, higher crypt grade was independently associated with wider AOD750 (ß [change in angle width per grade higher] = 0.018, P = 0.023), ARA750 (ß = 0.022, P = 0.049), and TISA750 (ß = 0.011, P = 0.019), and darker iris was associated narrower ARA750 (ß = -0.025, P = 0.044) and TISA750 (ß = -0.013, P = 0.011). CONCLUSIONS: Iris surface features, assessed and measured from slit-lamp photographs, correlated well with anterior chamber angle width; irises with more crypts and lighter color were associated with wider angle. These findings may provide another imaging modality to assess angle closure risk based on iris surface features.

A simplified method to measure choroidal thickness using adaptive compensation in enhanced depth imaging optical coherence tomography.

PURPOSE: To evaluate a simplified method to measure choroidal thickness (CT) using commercially available enhanced depth imaging (EDI) spectral domain optical coherence tomography (SD-OCT). METHODS: We measured CT in 31 subjects without ocular diseases using Spectralis EDI SD-OCT. The choroid-scleral interface of the acquired images was first enhanced using a post-processing compensation algorithm. The enhanced images were then analysed using Photoshop. Two graders independently graded the images to assess inter-grader reliability. One grader re-graded the images after 2 weeks to determine intra-grader reliability. Statistical analysis was performed using intra-class correlation coefficient (ICC) and Bland-Altman plot analyses. RESULTS: Using adaptive compensation both the intra-grader reliability (ICC: 0.95 to 0.97) and inter-grader reliability (ICC: 0.93 to 0.97) were perfect for all five locations of CT. However, with the conventional technique of manual CT measurements using built-in callipers provided with the Heidelberg explorer software, the intra- (ICC: 0.87 to 0.94) and inter-grader reliability (ICC: 0.90 to 0.93) for all the measured locations is lower. Using adaptive compensation, the mean differences (95% limits of agreement) for intra- and inter-grader sub-foveal CT measurements were -1.3 (-3.33 to 30.8) µm and -1.2 (-36.6 to 34.2) µm, respectively. CONCLUSIONS: The measurement of CT obtained from EDI SD-OCT using our simplified method was highly reliable and efficient. Our method is an easy and practical approach to improve the quality of choroidal images and the precision of CT measurement.

Assessment of iris surface features and their relationship with iris thickness in Asian eyes.

PURPOSE: To assess iris surface features in Asian eyes and examine their associations with iris thickness measured by anterior segment optical coherence tomography (AS OCT). DESIGN: Cross-sectional study. PARTICIPANTS: We recruited 250 subjects from the Singapore Malay Eye Study. METHODS: We obtained standardized slit-lamp photographs and developed a grading system assessing iris crypts (by number and size), furrows (by number and circumferential extent), and color (higher grade denoting darker iris). Vertical and horizontal cross-sections of the anterior chamber were imaged using AS OCT. Intragrader and intergrader agreements in the grading of iris surface were assessed by weighted κ (κ(w)) statistic. Associations of the average iris thickness with the grade of iris features were assessed using linear regression analysis. MAIN OUTCOME MEASURES: Frequency and size of iris crypts, furrows, and color; iris thickness at 750 µm (IT750) and 2000 µm (IT2000) from the scleral spur; and maximum iris thickness (ITM) averaged from the 4 quarters. RESULTS: Three hundred sixty-four eyes had complete and gradable data for crypts and color; 330 eyes were graded for furrows. The grading scheme showed good intragrader (crypt κ(w) = 0.919, furrow κ(w) =0.901, color κ(w) = 0.925) and intergrader (crypt κ(w) = 0.775, furrow κ(w) = 0.836, color κ(w) = 0.718) agreements. Higher crypt grade was associated independently with thinner IT750 (ß [change in iris thickness per grade higher] = -0.007; P = 0.029), IT2000 (ß = -0.018; P < 0.001), and ITM (ß = -0.012; P < 0.001). More extensive furrows were associated with thicker IT750 (ß = 0.022; P < 0.001). Darker iris was also associated with thicker IT750 (ß = 0.014; P = 0.001). CONCLUSIONS: Iris surface features, assessed and measured from slit-lamp photographs, correlate well with iris thickness. Irises with more crypts are thinner; irises with more extensive furrows and darker color are thicker peripherally. These findings may provide another means to assess angle closure risk based on iris features.

Determinants of macular thickness using spectral domain optical coherence tomography in healthy eyes: the Singapore Chinese Eye study.

PURPOSE: We determined ocular and systemic factors influencing macular thickness measured by spectral-domain optical coherence tomography (SD-OCT) in a population-based sample of healthy eyes. METHODS: We recruited 490 healthy Chinese adults, aged 40 to 80 years, from the Singapore Chinese Eye Study, a population-based survey. All participants underwent a comprehensive eye examination and a standardized interview. The SD-OCT (Cirrus HD-OCT, software version 6.0) was used to measure a range of macular thickness parameters (central foveal subfield thickness, average inner macular thickness, average outer macular thickness, overall average macular thickness, and overall macular cube volume). Linear regression analyses were performed to examine the effects of various ocular and systemic factors on macular thickness. RESULTS: The mean (standard deviation) age of the subjects was 53.17 (6.14) years and 50.0% of them were male. The mean central foveal subfield, average inner, and average outer macular thicknesses were 250.38 (20.58), 319.33 (14.40), and 276.67 (11.94) µm, respectively. The overall average macular thickness was 280.25 (11.42) µm and overall macular cube volume was 10.09 (0.41) mm(3). Sex, age, and axial length (AL) are the factors that influenced macular thicknesses. Thinner overall average macular thickness was associated with female sex (4.46 µm thinner compared to males, P < 0.001), older age (0.38 µm decrease per each year increase in age, P < 0.001), and longer AL (2.34-µm decrease per each mm increase in AL, P < 0.001), whereas thinner central foveal subfield thickness was associated with female sex (13.5 µm thinner compared to males, P < 0.001) and shorter AL (3.33-µm decrease per each mm increase in AL, P < 0.001). CONCLUSIONS: Female sex, older age, and longer AL were associated independently with thinner overall average macular thickness, whereas female sex and shorter AL were associated with thinner central foveal thickness in ethnic Chinese. These factors should be taken into consideration when interpreting macular thickness measurements with SD-OCT.

Relationship between ganglion cell-inner plexiform layer and optic disc/retinal nerve fibre layer parameters in non-glaucomatous eyes.

AIMS: To determine the relationship between macular ganglion cell-inner plexiform layer (GC-IPL) thickness and optic disc/retinal nerve fibre layer (RNFL) parameters in non-glaucomatous eyes measured by spectral-domain optical coherence tomography (SD-OCT). METHODS: 491 non-glaucomatous Chinese aged 40-80 years were recruited from a population-based study and underwent standardised ophthalmic examination. SD-OCT was used to measure GC-IPL thickness, optic disc parameters and RNFL thickness. Univariate and multiple linear regression analyses were performed to assess the association between GC-IPL and optic disc/RNFL parameters. RESULTS: In univariate analyses, all RNFL parameters and rim area were significantly correlated with all macular GC-IPL parameters (p<0.001, r=0.12-0.56). In multiple regression analyses, after adjusting for age, gender, disc area, signal strength and axial length, average RNFL thickness (per µm decrease) was most strongly correlated with average GC-IPL thickness (ß=-0.30, standardised ß=-0.499, p<0.001) compared with other optic disc/RNFL parameters. CONCLUSIONS: Our study demonstrated only fair correlations between macular GC-IPL and optic disc/RNFL parameters measured by SD-OCT. This information is important for further evaluation of macular GC-IPL thickness as an additional marker in detecting glaucomatous damage and progression.