COVID-19: Structural Considerations for Virus Pathogenesis, Therapeutic Strategies and Vaccine Design in the Novel SARS-CoV-2 Variants Era

Immediate Adverse Reaction and SARS-CoV-2 Anti-Spike Receptor Binding Domain IgG of COVID-19 Vaccines Among Health Staffs

OBJECTIVE

To contain the spread of coronavirus disease 2019 (COVID-19), several vaccines have been developed. This study is intended to elucidate the level of anti-severe acute respiratory syndrome coronavirus 2 immunoglobulin G (anti-SARS-CoV-2-IgG) antibodies for COVID-19 vaccines (Pfizer BioNTech [BNT162b2], Oxford/AstraZeneca [ChAdOx1], and Sinopharm [BBIBP-CorV]) among health staff from health facilities in Duhok province, and it explored the immediate adverse reactions of COVID-19 vaccines among participants.

METHODS

A longitudinal study was conducted from June 1, 2021, to June 30, 2022, and 300 participants were included through simple random sampling.

RESULTS

The immune response 1 mo after the second dose was significantly higher than the sustained immune after 5 and 9 mo as results revealed that, in 100% of study samples who had (ChAdOx1) vaccine, their antibody titers exceeded the positivity threshold of 1 AU/m, while 96% for (BNT162b2) and 90% for (BBIBP-CorV) for the first test after 1 mo from the second dose of the COVID-19 vaccine, and these rates were reduced to 94.6% for (ChAdOx1), 97.8% for (BNT162b2), and 81.9% for (BBIBP-CorV) at 5 mo after the second dose, while simultaneously the seropositivity rates were more reduced at 9 mo to 46.5% for (ChAdOx1), 67.5% for (BNT162b2), and 9.20% for (BBIBP-CorV). In terms of adverse reactionsss, fever was reported as the most prevalent after the first dose in 58% for ChAdOx1, 43% for BNT162b2, and 23% for BBIBP-CorV, followed by muscle pain, joint pain, and shoulder pain for both doses.

CONCLUSIONS

The implications of the findings from this study are that higher and potentially longer antibody responses can be obtained if the BNT162b2 is given as compared with the other 2 vaccines. Moreover, the booster doses of the COVID-19 vaccine are highly recommended because more than 50% of the participants either have become anti-spike protein negative or have a deficient level of anti-spike protein against COVD-19 vaccines.

T cell receptor β repertoires in patients with COVID-19 reveal disease severity signatures

Background

The immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are crucial in maintaining a delicate balance between protective effects and harmful pathological reactions that drive the progression of coronavirus disease 2019 (COVID-19). T cells play a significant role in adaptive antiviral immune responses, making it valuable to investigate the heterogeneity and diversity of SARS-CoV-2-specific T cell responses in COVID-19 patients with varying disease severity.

Methods

In this study, we employed high-throughput T cell receptor (TCR) β repertoire sequencing to analyze TCR profiles in the peripheral blood of 192 patients with COVID-19, including those with moderate, severe, or critical symptoms, and compared them with 81 healthy controls. We specifically focused on SARS-CoV-2-associated TCR clonotypes.

Results

We observed a decrease in the diversity of TCR clonotypes in COVID-19 patients compared to healthy controls. However, the overall abundance of dominant clones increased with disease severity. Additionally, we identified significant differences in the genomic rearrangement of variable (V), joining (J), and VJ pairings between the patient groups. Furthermore, the SARS-CoV-2-associated TCRs we identified enabled accurate differentiation between COVID-19 patients and healthy controls (AUC > 0.98) and distinguished those with moderate symptoms from those with more severe forms of the disease (AUC > 0.8). These findings suggest that TCR repertoires can serve as informative biomarkers for monitoring COVID-19 progression.

Conclusions

Our study provides valuable insights into TCR repertoire signatures that can be utilized to assess host immunity to COVID-19. These findings have important implications for the use of TCR β repertoires in monitoring disease development and indicating disease severity.

Association between serologically confirmed COVID-19 infection and cognitive functioning in community dwelling older adults

Introduction

COVID-19 infection can impact the central nervous system, and is often associated with cognitive decline. However, there are no studies linking serologically confirmed COVID-19 infection with objectively assessed cognitive functioning. We explored whether presence of SARS-CoV-2 antibodies account for variability in participants' scores on a neuropsychological assessment.

Methods

In this cross-sectional study participants were 657 (mean age = 72.97; SD = 6.07 years; women = 47.7%) individuals randomly selected from the general population of the canton of Zurich and included in the Corona Immunitas study. We conducted serological tests between October 2020 and May 2021 to detect and quantify SARS-CoV-2 antibodies in peripheral venous blood samples. We assessed cognitive function, vaccination status (vaccinated; not vaccinated), number of health conditions, and demographic variables between January and August 2021. We studied the association between seropositivity and global cognitive function and five cognitive domains (language expression, language comprehension, temporal orientation, spatial orientation, and memory) with linear regression models. Based on SARS-CoV-2 antibodies and vaccination status, we stratified participants into three groups: No SARS-CoV-2 antibodies (N = 402); SARS-CoV-2 antibodies due to vaccination (N = 218); history of SARS-CoV-2 infection and no vaccination (N = 37).

Results

In the regression model adjusted for age, sex, educational level, and number of health conditions, compared to those without SARS-CoV-2 antibodies, those with SARS-CoV-2 antibodies due to vaccination had better global cognitive functioning (Standardized beta = 0.10; 95% CI = 0.02; 0.17), and those with SARS-CoV-2 antibodies due to infection had poorer cognitive functioning (Standardized beta = -0.10; 95% CI = -0.18; -0.03). Regarding cognitive domains, compared to those without SARS-CoV-2 antibodies, those with SARS-CoV-2 antibodies due to infection scored more poorly on language comprehension and temporal orientation, and those with SARS-CoV-2 antibodies due to vaccination scored better on memory.

Discussion

By linking serologically confirmed presence of SARS-CoV-2 antibodies to poorer global cognitive functioning in community dwelling older adults we strengthen existing evidence in support of cognitive decline related to COVID-19. Given the large number of infected older adults, and the endurance of the pandemic, our results highlight the need to address COVID-19 related cognitive decline in the clinical and public health areas of prevention, diagnosis, and treatment.

The "vaccine" hubbub: Viral load comparisons of SARS-CoV-2 Delta and Omicron variants against different vaccine-booster vaccine combinations

There is a significant body of evidence showing that efficient vaccination schemes against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is helping control the coronavirus disease 2019 (COVID-19) pandemic. However, this goal cannot be achieved without real world data highlighting the impact of vaccines against viral spread. In this study, we have aimed at differentially investigating the impact of COVID-19 vaccines (CoronaVac, Pfizer/BioNTech, Astra/Zeneca Oxford, Janssen) used in North Cyprus in limiting the viral load of Delta and Omicron variants of SARS-COV-2. We have utilized real-time quantitative polymerase chain reaction cycle threshold values (Ct values) as a proxy of viral load of the two SARS-CoV-2 variants. Our results indicate that the administration of at least two doses of the messenger RNA-based Pfizer/BioNTech vaccine leads to the lowest viral load (highest Ct values) obtained for both Omicron and Delta variants. Interestingly, regardless of the vaccine type used, our study revealed that Delta variant produced significantly higher viral loads (lower Ct values) compared with the Omicron variant, where the latter was more commonly associated with younger patients. Viral spread is a crucial factor that can help determine the future of the pandemic. Thus, prioritizing vaccines that will play a role in not only preventing severe disease but also in limiting viral load and spread may contribute to infection control strategies.

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus 2 variants toward the host cell. Diversity of these variants challenges the development of effective general therapies, their transmissibility relying either on an increased affinity toward their dedicated human receptor, the angiotensin-converting enzyme 2 (ACE2), or on escaping the immune response. Now that robust structural data are available, we have determined with utmost accuracy the standard binding free energy of the receptor-binding domain to the most widespread variants, namely, Alpha, Beta, Delta, and Omicron BA.2, as well as the wild type (WT) in complex either with ACE2 or with antibodies, namely, S2E12 and H11-D4, using a rigorous theoretical framework that combines molecular dynamics and potential-of-mean-force calculations. Our results show that an appropriate starting structure is crucial to ensure appropriate reproduction of the binding affinity, allowing the variants to be compared. They also emphasize the necessity to apply the relevant methodology, bereft of any shortcut, to account for all the contributions to the standard binding free energy. Our estimates of the binding affinities support the view that while the Alpha and Beta variants lean on an increased affinity toward the host cell, the Delta and Omicron BA.2 variants choose immune escape. Moreover, the S2E12 antibody, already known to be active against the WT (Starr et al., 2021; Mlcochova et al., 2021), proved to be equally effective against the Delta variant. In stark contrast, H11-D4 retains a low affinity toward the WT compared to that of ACE2 for the latter. Assuming robust structural information, the methodology employed herein successfully addresses the challenging protein-protein binding problem in the context of coronavirus disease 2019 while offering promising perspectives for predictive studies of ever-emerging variants.

Comparison of SARS-CoV-2 anti-spike receptor binding domain IgG antibody responses after CoronaVac, BNT162b2, ChAdOx1 COVID-19 vaccines, and a single booster dose: a prospective, longitudinal population-based study

BACKGROUND

Vaccination is an efficient strategy to control the COVID-19 pandemic. In north Cyprus, vaccine distribution started with CoronaVac followed by BNT162b2, and ChAdOx1 vaccines. An option to obtain a third booster dose with BNT162b2 or CoronaVac was later offered to people fully inoculated with CoronaVac. There are few simultaneous and comparative real-world antibody data for these three vaccines as well as boosters after CoronaVac vaccination. Our study was aimed at evaluating antibody responses after these vaccination schemes.

METHODS

We did a prospective, longitudinal population-based study to measure SARS-CoV-2 anti-spike receptor binding domain (RBD) IgG concentrations, assessed by assaying blood samples collected, in participants in north Cyprus who had received the BNT162b2, ChAdOx1, or CoronaVac vaccine at 1 month and 3 months after the second dose. Participants were recruited when they voluntarily came to the laboratory for testing after vaccination, solicited from health-care access points, or from the general population. We also evaluated antibody responses 1 month after a booster dose of BNT162b2 or CoronaVac after primary CoronaVac regimen. Demographics, baseline characteristics, vaccination reactions, and percentage of antibody responders were collected by phone interviews or directly from the laboratory summarised by vaccine and age group. Antibody levels were compared between groups over time by parametric and non-parametric methods.

FINDINGS

Recruitment, follow-up, and data collection was done between March 1 and Sept 30, 2021. BNT162b2 induced the highest seropositivity and anti-spike RBD IgG antibody titres, followed by ChAdOx1, and then by CoronaVac. In addition, the rate of decline of antibodies was fastest with CoronaVac, followed by ChAdOx1, and then by BNT162b2. For the older age group, the rate of seropositivity at 3 months after the second dose was 100% for BNT162b2, 90% for ChAdOx1, and 60% for CoronaVac. In the multivariate repeated measures model, lower antibody titres were also significantly associated with male sex, older age, and time since vaccination. Boosting a two-dose CoronaVac regimen at 6 months with a single BNT162b2 dose led to significantly increased titres of IgG compared with boosting with CoronaVac; for the 60 years and older age group, the geometric mean fold rise in antibody titre after the booster relative to 1 month post-baseline was 7·9 (95% CI 5·8-10·8) in the BNT162b2 boost group versus 2·8 (1·6-5·0) in the CoronaVac group.

INTERPRETATION

These longitudinal data can help shape vaccination strategies. Given the low antibody titres and fast decline in the CoronaVac group in individuals 60 years or older, more potent vaccine options could be considered as the primary vaccination or booster dose in these high-risk populations to sustain antibody responses for longer.

FUNDING

Crowdfunded in north Cyprus.

A systematic review of Vaccine Breakthrough Infections by SARS-CoV-2 Delta Variant

Vaccines are proving to be highly effective in controlling hospitalization and deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as shown by clinical trials and real-world evidence. However, a deadly second wave of coronavirus disease 2019 (COVID-19), infected by SARS-CoV-2 variants, especially the Delta (B.1.617.2) variant, with an increased number of post-vaccination breakthrough infections were reported in the world recently. Actually, Delta variant not only resulted in a severe surge of vaccine breakthrough infections which was accompanied with high viral load and transmissibility, but also challenged the development of effective vaccines. Therefore, the biological characteristics and epidemiological profile of Delta variant, the current status of Delta variant vaccine breakthrough infections and the mechanism of vaccine breakthrough infections were discussed in this article. In addition, the significant role of the Delta variant spike (S) protein in the mechanism of immune escape of SARS-CoV-2 was highlighted in this article. In particular, we further discussed key points on the future SARS-CoV-2 vaccine research and development, hoping to make a contribution to the early, accurate and rapid control of the COVID-19 epidemic.

The Influence of the COVID-19 Pandemic on the Stress Levels and Occurrence of Stomatoghnatic System Disorders (SSDs) among Physiotherapy Students in Poland

Background: This study is a quantitative analysis examining the impact of the COVID-19 pandemic on the occurrence of stress and stomatognathic system disorders (SSDs) among students of physiotherapy. Objective: To assess stress severity, strategies of coping with stress and the presence of type D personality among physiotherapy students including those with symptoms of stomatognathic system disorders. Material and Methods: The research was conducted from October to December 2020 on a sample of 188 students of physiotherapy. The data were collected using a survey form related to the occurrence of SS disorders symptoms and standardized psychological questionnaires, such as the Perceived Stress Scale (PSS)-10, Mini-Cope, and the type-D Scale (DS14), developed for the purpose of this study. Results: Women experiencing at least one of the SS disorder-related symptoms were characterized by a significantly higher level of stress and a type D personality (p < 0.05). Among men, these differences were not statistically significant (p > 0.05). On the basis of the strategies of coping with stress, i.e., positive self-reevaluation, discharging and blaming oneself, and taking psychoactive substances, it is possible to predict the intensity of stress during the pandemic in the group of the examined students. Among the reported symptoms of SS, headache was a significant predictor of stress, which was accompanied by an increase in the intensity of stress by nearly 0.2 measurement points. Students with higher levels of stress showed more symptoms of type D personality, and those with more severe symptoms of SS showed higher levels of stress. Conclusions: People prone to stress and having type D personality traits should be assessed for the presence of SS disorders.