Original Hosts, Clinical Features, Transmission Routes, and Vaccine Development for Coronavirus Disease (COVID-19)

Self- and informant-reported personality traits and vaccination against COVID-19

As COVID-19 vaccines' accessibility has grown, so has the role of personal choice in vaccination, and not everybody is willing to vaccinate. Exploring personality traits' associations with vaccination could highlight some person-level drivers of, and barriers to, vaccination. We used self- and informant-ratings of the Five-Factor Model domains and their subtraits (a) measured approximately at the time of vaccination with the 100 Nuances of Personality (100NP) item pool (N = 56,575) and (b) measured on average ten years before the pandemic with the NEO Personality Inventory-3 (NEO-PI-3; N = 3,168). We tested individual domains' and either items' (in the 100NP sample) or facets' (in the NEO-PI-3 sample) associations with vaccination, as well as their collective ability to predict vaccination using elastic net models trained and tested in independent sample partitions. Although the NEO-PI-3 domains and facets did not predict vaccination ten years later, the domains correlated with vaccination in the 100NP sample, with vaccinated people scoring slightly higher on neuroticism and agreeableness and lower on openness, controlling for age, sex, and education. Collectively, the five domains predicted vaccination with an accuracy of r = .08. Associations were stronger at the item level. Vaccinated people were, on average, more science-minded, politically liberal, respectful of rules and authority, and anxious but less spiritual, religious, and self-assured. The 100NP items collectively predicted vaccination with r = .31 accuracy. We conclude that unvaccinated people may be a psychologically heterogeneous group and highlight some potential areas for action in vaccination campaigns.

Stability of SARS-CoV-2 and persistence of viral nucleic acids on common foods and widely used packaging material surfaces

SARS-CoV-2 is still spreading globally. Studies have reported the stability of SARS-CoV-2 in aerosols and on surfaces under different conditions. However, studies on the stability of SARS-CoV-2 and viral nucleic acids on common food and packaging material surfaces are insufficient. The study evaluated the stability of SARS-CoV-2 using TCID₅₀ assays and the persistence of SARS-CoV-2 nucleic acids using droplet digital polymerase chain reaction on various food and packaging material surfaces. Viral nucleic acids were stable on food and material surfaces under different conditions. The viability of SARS-CoV-2 varied among different surfaces. SARS-CoV-2 was inactivated on most food and packaging material surfaces within 1 day at room temperature but was more stable at lower temperatures. Viruses survived for at least 1 week on pork and plastic at 4°C, while no viable viruses were detected on hairtail, orange, or carton after 3 days. There were viable viruses and a slight titer decrease after 8 weeks on pork and plastic, but titers decreased rapidly on hairtail and carton at -20°C. These results highlight the need for targeted preventive and disinfection measures based on different types of foods, packaging materials, and environmental conditions, particularly in the cold-chain food trade, to combat the ongoing pandemic.

Identification of new dihydrophenanthrene derivatives as promising anti-SARS-CoV-2 drugs through in silico investigations

To research, evaluate, and invent novel compounds that inhibit SARS-CoV-2 activity, a series of reported 39 substituted 9, 10-dihydrophenanthrene derivatives were subjected to a quantitative structure-activity relationship (QSAR) study. Gaussian 09 and ChemOffice programs were used to calculate the molecular descriptors employed to determine their impact on the studied activity. Then we reduced the number of descriptors by eliminating the redundant information using principal component analysis (PCA). The creation of molecular models was done by using multiple linear regression (MLR) according to the principles established by the Organization for Economic Co-operation and Development (OECD) and the validation by using external and internal validation, Y-randomization tests, and domain of applicability. Moreover, we evaluated the toxicity of developed compounds using ADMET and Molecular docking to determine their optimal position to form a stable complex. As a result, four molecules may be used to develop a novel drug that can inhibit SARS-CoV-2 without causing the side effect.

CO2 Concentrations and Thermal Comfort Analysis at Onsite and Online Educational Environments

In building areas with high occupancy, such as classrooms, transmission routes of SARS-CoV-2 are increased when indoor air quality is deficient. Under this scenario, universities have adopted ventilation measures to mitigate contagious environments. However, the lack of adequate equipment or designs in old educational buildings is a barrier to reach minimum requirements. This study aims to quantify the indoor air quality and thermal comfort at universities and compare it to conditions in students' households. In this regard, several classrooms in buildings of the Polytechnic University of Catalonia were monitored for temperature, CO₂ concentration and relative humidity. The people who used these classrooms were surveyed about their comfort perceptions. A sample of students was also monitored at their homes where they reported to studying during the exam period. By means of point-in-time surveys, students reported their daily comfort, for comparison with the monitored data. The results show that the recommendations for CO₂ concentration, temperature, and relative humidity are not always met in any of the study spaces. These factors are more critical at universities due to the high occupancy. In addition, the surveys highlighted the perception that the environment is better at home than at university.

Can the COVID-19 Pandemic Improve the Management of Solid Organ Transplant Recipients?

Increased mortality due to SARS-CoV-2 infection was observed among solid organ transplant patients. During the pandemic, in order to prevent and treat COVID-19 infections in this context, several innovative procedures and therapies were initiated within a short period of time. A large number of these innovations can be applied and expanded to improve the management of non-COVID-19 infectious diseases in solid organ transplant patients and in the case of a future pandemic. In this vein, the present paper reviews and discusses medical care system adaptation, modification of immunosuppression, adjuvant innovative therapies, the role of laboratory expertise, and the prevention of infections as examples of such innovations.

The CRISPR-Cas system as a tool for diagnosing and treating infectious diseases

Emerging and relapsing infectious diseases pose a huge health threat to human health and a new challenge to global public health. Rapid, sensitive and simple diagnostic tools are keys to successful management of infectious patients and containment of disease transmission. In recent years, international research on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-related proteins (Cas) has revolutionized our understanding of biology. The CRISPR-Cas system has the advantages of high specificity, high sensitivity, simple, rapid, low cost, and has begun to be used for molecular diagnosis and treatment of infectious diseases. In this paper, we described the biological principles, application fields and prospects of CRISPR-Cas system in the molecular diagnosis and treatment of infectious diseases, and compared it with existing molecular diagnosis methods, the advantages and disadvantages were summarized.

Rational identification of small molecules derived from 9,10-dihydrophenanthrene as potential inhibitors of 3CLpro enzyme for COVID-19 therapy: a computer-aided drug design approach

Small molecules such as 9,10-dihydrophenanthrene derivatives have remarkable activity toward inhibition of SARS-CoV-2 3CL^pro and COVID-19 proliferation, which show a strong correlation between their structures and bioactivity. Therefore, these small compounds could be suitable for clinical pharmaceutical use against COVID-19. The objective of this study was to remodel the structures of 9,10-dihydrophenanthrene derivatives to achieve a powerful biological activity against 3CL^pro and favorable pharmacokinetic properties for drug design and discovery. Therefore, by the use of bioinformatics techniques, we developed robust 3D-QSAR models that are capable of describing the structure–activity relationship for 46 molecules based on 9,10-dihydrophenanthrene derivatives using CoMFA/SE (R² = 0.97, Q² = 0.81, R²_pred = 0.95, ^cR²_p = 0.71) and CoMSIA/SEHDA (R² = 0.94, Q² = 0.76, R²_pred = 0.91, ^cR²_p = 0.65) techniques. Accordingly, 96 lead compounds were generated based on a template molecule that showed the highest observed activity in vitro (T40, pIC₅₀ = 5.81) and predicted their activities and bioavailability in silico. The rational screening outputs of 3D-QSAR, Molecular docking, ADMET, and MM-GBSA led to the identification of 9 novel modeled molecules as potent noncovalent drugs against SARS-CoV-2-3CL^pro. Finally, by molecular dynamics simulations, the stability and structural dynamics of 3CL^pro free and complex (PDB code: 6LU7) were discussed in the presence of samples of 9,10-dihydrophenanthrene derivative in an aqueous environment. Overall, the retrosynthesis of the proposed drug compounds in this study and the evaluation of their bioactivity in vitro and in vivo may be interesting for designing and discovering a new drug effective against COVID-19.

Real-Word Effectiveness of Global COVID-19 Vaccines Against SARS-CoV-2 Variants: A Systematic Review and Meta-Analysis

Background

Currently, promoted vaccinations against SARS-CoV-2 are being given out globally. However, the occurrence of numerous COVID-19 variants has hindered the goal of rapid mitigation of the COVID-19 pandemic by effective mass vaccinations. The real-word effectiveness of the current vaccines against COVID-19 variants has not been assessed by published reviews. Therefore, our study evaluated the overall effectiveness of current vaccines and the differences between the various vaccines and variants.

Methods

PubMed, Embase, Cochrane Library, medRxiv, bioRxiv, and arXiv were searched to screen the eligible studies. The Newcastle-Ottawa scale and the Egger test were applied to estimate the quality of the literature and any publication bias, respectively. The pooled incident rates of different variants after vaccination were estimated by single-arm analysis. Meanwhile, the pooled efficacies of various vaccines against variants were evaluated by two-arm analysis using odds ratios (ORs) and vaccine effectiveness (VE).

Results

A total of 6,118 studies were identified initially and 44 articles were included. We found that the overall incidence of variants post first/second vaccine were 0.07 and 0.03, respectively. The VE of the incidence of variants post first vaccine between the vaccine and the placebo or unvaccinated population was 40% and post second vaccine was 96%, respectively. The sub-single-arm analysis showed a low prevalence rate of COVID-19 variants after specific vaccination with the pooled incidence below 0.10 in most subgroups. Meanwhile, the sub-two-arm analysis indicated that most current vaccines had a good or moderate preventive effect on certain variants considering that the VE in these subgroups was between 66 and 95%, which was broadly in line with the results of the sub-single-arm analysis.

Conclusion

Our meta-analysis shows that the current vaccines that are used globally could prevent COVID-19 infection and restrict the spread of variants to a great extent. We would also support maximizing vaccine uptake with two doses, as the effectiveness of which was more marked compared with one dose. Although the mRNA vaccine was the most effective against variants according to our study, specific vaccines should be taken into account based on the local dominant prevalence of variants.

SARS-CoV-2 cold-chain transmission: Characteristics, risks and strategies

Low temperature and certain humidity are conducive to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) for long‐time survival and long‐distance spread during logistics and trades. Contaminated cold‐chain or frozen products and outer packaging act as the carrier of SARS‐CoV‐2, that infects the high‐risk population who works in the ports, cold storage or seafood market. Since the coronavirus disease 2019 (COVID‐19) pandemic worldwide, multiple localized outbreaks caused by SARS‐CoV‐2 contaminated imported cold‐chain products have been reported in China, which brought challenges to COVID‐19 prevention and control. Here, we review the evidences of SARS‐CoV‐2 cold‐chain transmission from six confirmed cold‐chain related COVID‐19 outbreaks in China, especially in terms of SARS‐CoV‐2 whole‐genome sequencing and virus isolation. In addition, we summarize the characteristics and mode of SARS‐CoV‐2 cold‐chain transmission from both six COVID‐19 outbreaks in China and the outbreaks suspected cold‐chain transmission in other countries. Finally, we analyze the underlying risks of SARS‐CoV‐2 cold‐chain transmission and propose the preventive countermeasures.

SARS‐CoV‐2 contaminated cold‐chain products can infect high‐risk populations and subsequently cause community transmission

Specific locations, such as seafood market stalls, can amplify outbreaks

Cold‐chain fomites accelerate global spread of SARS‐CoV‐2 and cause “silent transmission”

Rational sampling, comprehensive disinfection, protection of high‐risk groups and pollution classification are the main strategies

Zika Virus Infection During Research Vaccine Development: Investigation of the Laboratory-Acquired Infection via Nanopore Whole-Genome Sequencing

Zika virus (ZIKV) emerged as a serious public health problem since the first major outbreak in 2007. Current ZIKV diagnostic methods can successfully identify known ZIKV but are impossible to track the origin of viruses and pathogens other than known ZIKV strains. We planned to determine the ability of Whole Genome Sequencing (WGS) in clinical epidemiology by evaluating whether it can successfully detect the origin of ZIKV in a suspected case of laboratory-acquired infection (LAI). ZIKV found in the patient sample was sequenced with nanopore sequencing technology, followed by the production of the phylogenetic tree, based on the alignment of 38 known ZIKV strains with the consensus sequence. The closest viral strain with the consensus sequence was the strain used in the laboratory, with a percent identity of 99.27%. We think WGS showed its time-effectiveness and ability to detect the difference between strains to the level of a single base. Additionally, to determine the global number of LAIs, a literature review of articles published in the last 10 years was performed, and 53 reports of 338 LAIs were found. The lack of a universal reporting system was worrisome, as in the majority of cases (81.1%), the exposure route was unknown.

Discovery of 9,10-dihydrophenanthrene derivatives as SARS-CoV-2 3CLpro inhibitors for treating COVID-19

The epidemic coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread worldwide and efficacious therapeutics are urgently needed. 3-Chymotrypsin-like cysteine protease (3CL^pro) is an indispensable protein in viral replication and represents an attractive drug target for fighting COVID-19. Herein, we report the discovery of 9,10-dihydrophenanthrene derivatives as non-peptidomimetic and non-covalent inhibitors of the SARS-CoV-2 3CL^pro. The structure-activity relationships of 9,10-dihydrophenanthrenes as SARS-CoV-2 3CL^pro inhibitors have carefully been investigated and discussed in this study. Among all tested 9,10-dihydrophenanthrene derivatives, C1 and C2 display the most potent SARS-CoV-2 3CL^pro inhibition activity, with IC₅₀ values of 1.55 ± 0.21 μM and 1.81 ± 0.17 μM, respectively. Further enzyme kinetics assays show that these two compounds dose-dependently inhibit SARS-CoV-2 3CL^provia a mixed-inhibition manner. Molecular docking simulations reveal the binding modes of C1 in the dimer interface and substrate-binding pocket of the target. In addition, C1 shows outstanding metabolic stability in the gastrointestinal tract, human plasma, and human liver microsome, suggesting that this agent has the potential to be developed as an orally administrated SARS-CoV-2 3CL^pro inhibitor.