COVID, Volume 3, Issue 4 (April 2023) – 16 articles

To verify the role played by burnout in the prediction of alcohol consumption, considering the integration of the theory of job demands-resources (JD-R) and sociocognitive theory (SCT), we developed an analytical model in which self-efficacy and depression act as mediators of this relationship. A cross-sectional online survey was taken by 3856 workers enrolled in various public agencies of the Mexican Health Ministry during the COVID-19 pandemic in Mexico. The results indicate that of the three dimensions of burnout, only depersonalization predicts alcohol consumption; however, self-efficacy regulates the effect of emotional exhaustion and achievement dissatisfaction on alcohol consumption. Similarly, the three components of burnout have indirect effects through depression, suggesting that depression and self-efficacy mediate the relationship between burnout and alcohol consumption. Burnout alone cannot explain alcohol consumption, but when depression is present, burnout increases the predisposition to consume alcohol; when self-efficacy is present, the probability of alcohol consumption decreases. Full article

In developing in vitro diagnostic (IVD) tests, in particular at-home/over-the-counter (OTC) tests, one of the generally accepted exclusion criteria in IVD clinical trial protocols has been that of subjects with prior knowledge of their positive status, due to potential bias. With COVID-19 antigen tests now widely available, it is common for individuals to test themselves at home with an antigen test if they have symptoms associated with COVID-19, flu, or the common cold. These subjects would be excluded from participation in COVID-19-related clinical trials (i.e., COVID-19 alone or any multiplex tests that include COVID-19). This study compiled the results of four clinical trials to assesses whether potential bias (positive or negative) exists in at-home antigen COVID-19 testing if someone has a prior diagnostic COVID-19 result. The results clearly demonstrated that knowledge of prior COVID-19 diagnostic results did not affect the accuracy of the test result interpretations nor the clinical performance of the at-home antigen test products. This is an important finding that supports the inclusion of these subjects in future COVID-19 diagnostic clinical trials and the FDA’s recommendation of serial antigen testing to improve antigen test performance. Full article

In the course of SARS-CoV-2 infection, the 3CL or nsp5 protease plays a pivotal role as the most important viral protease required for the maturation of viral proteins during host infection. Herein, we simulated for 500 ns 3CLpro^WT, 3CLpro^H41A, 3CLpro^Beta, and 3CLpro^Omicron, in complex with the substrates nsp 4|5 and nsp 5|6. Our results show that mutations in the 3CLpro present in the SARS-CoV-2 variants of concern (VOCs) did not lead to significant conformational changes or changes in substrate binding affinities. However, significantly high cleavage rates for the boundary between nsp4 and nsp5 were obtained for 3CLpro^Beta and 3CLpro^Omicron and may play a key role in viral replication and virus fitness gain. Our molecular dynamics data suggest that the cleavage rate of nsp4|5 may be related to the increased amount of viral load observed for these VOCs, releasing more nsp4 than other non-structural proteins. This study is limited by being fully computational. However, our results suggest that the cleavage rate may be affected by mutations. Based on our hydrogen bonding analyses, we also discovered that Gly143 and Glu166 are key residues in substrate recognition, suggesting that these residues may be incorporated as pharmacophoric centers for Beta and Omicron variants in drug design. Our results suggest that Gly143 and Glu166 are essential residues to interact with Gln6 of the different substrates and, therefore, are potential broad-spectrum pharmacophoric centers of SARS-CoV-2 3CLpro. Full article

Prior to the emergence of the Omicron variant, we found large regional differences (ƞ² = 0.19) in the frequency of wearing face masks in New Zealand even though the strength of people’s motivation to wear face masks to prevent the spread of COVID-19 was similar across regions. These differences were associated with regional differences (as measured by case numbers) in the risk of COVID-19 infection. The emergence of Omicron and its spread throughout New Zealand in conjunction with the cessation of lockdowns offered the opportunity to test whether regional differences in the frequency of mask wearing disappeared once the risk of COVID-19 infection became uniform across the country. It also created an opportunity to investigate differences in people’s behaviour with respect to wearing masks in private and in public. The results confirmed that regional differences in the frequency of mask wearing disappeared once Omicron spread through the country. We also found that the frequency of wearing masks was significantly lower when with family or friends than when out in public. Full article

Monitored infection and vaccination rates during past past waves of the coronavirus are used to infer a posteriori two-key parameter of the SIRV epidemic model, namely, the real-time variation in (i) the ratio of recovery to infection rate and (ii) the ratio of vaccination to infection rate. We demonstrate that using the classical SIR model, the ratio between recovery and infection rates tends to overestimate the true ratio, which is of relevance in predicting the dynamics of an epidemic in the presence of vaccinations. Full article

The nasal microenvironment plays a crucial role in the transmission, modulation, and clinical progression of COVID-19; however, the immune responses at the site of viral entry remain poorly understood. We deciphered the link between nasopharyngeal (NP) immune and inflammatory response that triggers cytokine/chemokine storms in the nasal route of COVID-19-positive patients. We used RT-PCR, multiplex ELISA, flow cytometry, and LC-MS/MS to decipher nasopharyngeal immune perturbations associated with severe COVID-19. In addition, we performed in vitro assays using cultured human monocytes-derived macrophages trained both in the presence and absence of SARS-CoV-2 trimeric spike protein(s) and co-cultured with and without autologous human peripheral blood mononuclear cells (hPBMCs)/total T-cells/CD8 T-cells. In vitro immune perturbations were examined by flow cytometry and LC-MS/MS assays. Our findings confirm that macrophages orchestrate NP immune inflammatory responses and highlight the cytokine/chemokine storms associated with the increased CD8${}^{+}$T-cells along with Tregs, Th1, and Th17.1 T-helper cells. We observed a correlation between in vitro and nasal findings that trained macrophages, profoundly M2c, differentially promote the inflammatory surfactome on CD8 T-cells, including ITGAM, LGALS3, CD38, TKT, LRPAP1, and SSBP1. The findings of this study conclude that inflammatory lymphocyte perturbations within the nasopharynx of COVID-19 patients may enforce immune homeostasis during SARS-CoV-2-infection and contribute to COVID-19 pathology. This study explored the therapeutic target proteins that could facilitate the development of new medications, which could allow for immediate treatment of possible emerging viral infections. Full article

Objective: To compare the performance of established scoring systems (CURB65, NEWS2, qSOFA, SOFA and REDS) to the newly developed scores (ISARIC 4C, PRIEST and novel COVID-19 severity scores) in mortality prediction for patients with confirmed COVID-19 infection in the emergency department (ED). Method: A retrospective observational cohort study of adult patients attending a teaching hospital ED who fulfilled the criteria for suspected sepsis and tested positive for COVID-19. The scores were calculated for each patient. The primary outcome measure was all-cause in-hospital mortality. Receiver operator characteristic (ROC) curves were generated for each score. The area under the ROC (AUROC) curves were compared to that of the ISARIC 4C score. The cut-off points were determined by the statistical software package. The test characteristics at the cut-off scores were noted. Results: Of the 504 patients studied, 153 (30.5%) died in hospital. The AUROC of the ISARIC 4C score was similar to all of the scores except for the NEWS2 score and qSOFA scores, which were significantly lower. The test characteristics of the different scores were similar. Conclusions: In this single-centre study, the newly developed COVID scores outperformed the NEWS2 and qSOFA scores but did not perform better than the other scores studied. Full article

Recent global changes, including increased health risks and economic instability associated with the coronavirus (COVID-19) pandemic, highlight the need for mental health researchers to regularly and frequently monitor sociodemographic shifts. To minimise the risk of psychological complications arising from adverse events, we need to identify and understand the factors linked to psychological resilience in different populations. To this end, we collected data in Turkey during the third wave of the pandemic (June 2021). The aims were to identify how the level of perceived psychological resilience changed: (1) across sociodemographic groups (age, gender, perceived economic security, caregiver status, perceived socioeconomic status, education level, perceived social isolation, and presence of acquaintances who had contracted COVID-19); (2) across health groups (smoking status, psychological or chronic illness status, and having had COVID-19); and (3) in relation to changes in fear of COVID-19. Regression analyses showed that age, gender, economic security, socioeconomic status, and illness status were factors influencing resilience, and fear of COVID-19 was negatively correlated with resilience. Young adults, females, nonbinary individuals, a low socioeconomic status, and economically insecure groups as well as people with a psychological condition were identified as lower resilience groups. The results provide insights about the predictors of perceived psychological resilience during a global crisis and help identify vulnerable populations. Full article

The continuous emergence of new variants of concern for SARS-CoV-2 has created a challenge for existing therapies. To address this, we developed a series of single-stranded DNA aptamers that not only bind specifically to the trimer S protein of SARS-CoV-2 but also block the interaction between the trimer S protein and ACE2 receptors. The systematic evolution of ligands by exponential enrichment (SELEX) was performed to select the aptamers for SARS-CoV-2 trimer S protein. ELISA-based assay and flow cytometry were performed to test the apatmers’ binding and inhibition of trimer S protein in vitro. Binding affinity was measured using surface plasmon resonance. Significance was determined in Prism 9.0 using the one-way ANOVA test (Dunnett’s multiple comparisons test) or two-way ANOVA test (Tukey’s multiple comparisons test) for comparisons. The p values < 0.05 were considered statistically significant. After 12 rounds of SELEX, eight highly enriched aptamers were able to bind to the trimer S protein of the SARS-CoV-2 Wuhan original strain as well as the trimer S proteins of the Delta, Delta plus, Alpha, Lambda, Mu, and Omicron variants, with affinities in the nM range, while also inhibiting their interaction with ACE2 receptors in Vero E6 cells. Modifications to our best aptamer were made by adding forward and reverse primer sequences and truncation. The modified aptamers AYA2012004_L and AYA2012004_L-M1 showed up to 70% inhibition of the binding of virus-like particles (VLPs) expressing S protein to the ACE2 receptor expressed in HEK293T cells. Our findings imply that the selected aptamers can prevent SARS-CoV-2 from entering host cells and hence suppress the viral infection. In addition, the findings suggest that the selected aptamers might be an innovative therapy for the treatment of COVID-19. Full article

SARS-CoV-2 is a highly contagious and dangerous coronavirus that has been spreading around the world since late December 2019. Severe COVID-19 has been observed to induce severe damage to the alveoli, and the slow loss of lung function led to the deaths of many patients. Scientists from all over the world are now saying that SARS-CoV-2 can spread through the air, which is a very frightening prospect for humans. Many scientists thought that this virus would evolve during the first wave of the pandemic and that the second wave of reinfection with the coronavirus would also be very dangerous. In late 2020 and early 2021, researchers found different genetic versions of the SARS-CoV-2 virus in many places around the world. Patients with different types of viruses had different symptoms. It is now evident from numerous case studies that many COVID-19 patients who are released from nursing homes or hospitals are more prone to developing multi-organ dysfunction than the general population. Understanding the pathophysiology of COVID-19 and its impact on various organ systems is crucial for developing effective treatment strategies and managing long-term health consequences. The case studies highlighted in this review provide valuable insights into the ongoing health concerns of individuals affected by COVID-19. Full article

This study sought to examine the impact of long-COVID symptoms on the occupational status of teachers after recovery. A mixed-methods study was conducted in Israel in June 2022 among teachers who had recovered within the past six months. The quantitative data were collected using a self-report online survey (n = 170) based on questionnaires, and the qualitative data were based on individual semi-structured in-depth online interviews (n = 26). Participants reported the following symptoms: fatigue (43.7%), weakness (32.2%), difficulty sleeping (27.3%), pain or discomfort (22.4%), and anxiety (20.7%). Sense of control, social support, and well-being exhibited negative correlations with long-term symptoms (p < 0.001). A multivariate regression analysis revealed that the model explained 25% of the variance in long-term symptoms and that a greater sense of control and well-being predicted lower levels of long-term symptoms. In the qualitative study, the teachers reported high levels of symptoms that impaired their functioning, including guilt, despair, and lack of work motivation. Some teachers reported that the school staff helped them cope, whereas others described the staff’s alienated attitude. The research found that fatigue, weakness, and difficulty sleeping were the primary long-term symptoms that exerted a significant impact on teachers’ functioning and well-being. Full article

After the spill to humans, in the evolutionary timeline of SARS-CoV-2, several positively selected variants have emerged. A phylogeographic study on these variants can reveal their spatial and temporal distribution. In December 2020, the alpha variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which has been designated as a variant of concern (VOC) by the WHO, was discovered in the south-eastern United Kingdom (UK). Slowly, it expanded across India, with a considerable number of cases, particularly in North India. This study focuses on determining the prevalence and expansion of the Alpha variants in various parts of India mainly by using phylospatial analysis. The genetic diversity estimation has helped us to understand various evolutionary forces that have shaped the spatial distribution of this variant during its peak. Overall, our study paves the way to understanding the evolution and expansion of a virus variant, which may help to mitigate in the case of any future wave. Full article

The Spike (S) protein of the SARS-CoV-2 virus that causes the COVID-19 disease is considered the most important target for vaccine, drug and therapeutic research as it attaches and binds to the ACE2 receptor of the host cells and allows the entry of this virus. Analysis and classification of newly determined S protein structures for SARS-CoV-2 are critical to properly understand their functional, evolutionary and architectural relatedness to already known protein structures. In this paper, first, the comparative analysis of SARS-CoV-2 S protein structures is performed. Through comparative analysis, the S protein structures in the PDB (protein data bank) database are compared and analyzed not only with each other but with the structures of other viruses for various parameters. Second, the S protein structures in PDB are classified into different variants, and the associated published literature is studied to investigate what kind of therapeutics (antibodies, T-cell receptors and small molecules) are used on the structures. This is the first study that classifies the S protein structures of the SARS-CoV-2 in PDB into various variants, and the obtained comparative analysis results could be beneficial to the research community, in general, and to crystallographers and health workers, in particular. Full article

Colonization of SARS-CoV-2 with specific bacteria may either protect or increase the risk of disease severity. This study aimed to identify microbial organisms in the lower respiratory tract and their association with SARS-CoV-2 infection. This was a cross-sectional study conducted between May 2020 and August 2021 at the Tamale Public Health Laboratory in the Northern part of Ghana. RT-PCRs for SARS-CoV-2 and bacteriological cultures were performed on sputum samples collected from suspected COVID-19 patients. Biochemical identification and antimicrobial susceptibility tests were performed on the bacterial isolates. A total of 380 participants were recruited into the study. Most participants were within the 21–30 years age group (29.6%). RT-PCR testing detected SARS-CoV-2 in 118 (31.1%) patients. Headache was found to be associated with SARS-CoV-2 (p = 0.033). Sputum cultures yielded 187 (49.2%) positive bacteria growths. Klebsiella spp. (20.5%), Moraxella catarrhalis (7.9%), and Pseudomonas spp. (6.3%) were the most commonly isolated bacteria. M. catarrhalis, Serratia spp., and Stenotrophomonas maltophilia were significantly associated with SARS-CoV-2 infection. Most of the isolates were resistant to 3rd generation cephalosporins. This study has demonstrated the association between specific bacteria and SARS-CoV-2 infection. Clinicians should investigate possible bacterial co-infections in the management of COVID-19 cases. Full article

Contact tracing outcome indicators, such as symptom development (SD) and secondary attack rate (SAR) among close contacts (CCs), are key to understanding SARS-CoV-2 transmission. This study analyses SD and SAR and estimates the incubation period (IP) from a cohort of 47,729 CCs from 17,679 SARS-CoV-2 cases diagnosed in Catalonia (Spain) from May to August 2020. Globally, 19.4% of the CCs reported symptoms, especially adult women living in urban areas. SAR was 24.5%, notably higher among infants (37.6%), and 45.9% of secondary cases (SCs) were asymptomatic. Household CCs had 98% (OR: 1.98, 95% CI: 1.81–2.18) and 138% (2.38, 2.19–2.58) increased risk of SD and becoming SCs compared to social settings. The IP was 3.42 days, being 4.10 days among social CCs, and only 15.4% and 4.8% of SCs developed symptoms after days 7 and 10 of quarantine, respectively. These results, notably the higher SAR among asymptomatic children, highlight the importance of diligent monitoring to inform SARS-CoV-2 control strategies. Full article

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic. Despite the fact that it affects all ages and profiles, some evidence shows that patients with comorbidities, including diabetes, obesity, and hypertension, are likely to be most affected. For chronic diseases, such as human immunodeficiency virus (HIV), information is scarce, with a few studies from high-income countries. This study reports predictors of SARS-CoV-2 seropositivity (IgG + IgM) among unvaccinated people living with HIV attending Bugando Medical Centre in Mwanza, Tanzania. Methodology: A cross-sectional, hospital-based study involving 150 HIV-infected patients was conducted at Bugando Medical Centre between June and July 2022. A pretested questionnaire was used to collect the participants’ information. Blood samples were collected and used for the detection of SARS-CoV-2 (IgM/IgG) antibodies by immunochromatographic assay. Data were analyzed using STATA version 15. Results: The mean age of the enrolled participants was 46.4 ± 11.1 years. The overall seropositivity (IgG + IgM) of SARS-CoV-2 antibodies was 79/150 (52.7%) [95% CI: 44.4–60.9]. Seropositivity of IgM only was 8/150 (5.3) [95% CI: 1.7–8.8], while that of IgG only was 61/150 (40.6%) [95% CI: 32.7–48.4]. Seropositivity of both IgG and IgM was observed in 10/150 (6.7%) patients. In a multivariate logistic regression analysis, history of sore throat (OR: 6.34, 95% CI: 2.305–18.351, p < 0.001), low CD4 count (OR: 0.99, 95% CI: 0.995–0.999, p = 0.004), and use of pit latrines (OR: 2.30, 95% CI: 1.122–4.738, p = 0.023) were independently associated with SARS-CoV-2 seropositivity. Conclusion: HIV-infected individuals with history of sore throat, low CD4 count, and use of pit latrines were more likely to be SARS-CoV-2 IgG seropositive. There is a need to routinely screen for SARS-CoV-2 infection among HIV-infected individuals to obtain comprehensive data regarding the interactions of the pathogens. Full article