Insights of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) pandemic: a current review

mRNA-Based Nanomedicine: A New Strategy for Treating Infectious Diseases and Beyond

Messenger RNA (mRNA) has emerged as a new therapeutic agent for the prevention and treatment of a wide range of diseases. The recent achievement of the two lipid nanoparticle-mRNA vaccines developed by Moderna and Pfizer-BioNTech against coronavirus 2019 (COVID-19) disease in record time highlights the huge potential of mRNA technology and reshaping the landscape of vaccine development and the future of gene therapies. Challenges related to translational efficacy, mRNA stability, immunogenicity, and ensuring the quality of final products have been significantly improved by recent advancements in mRNA engineering and delivery. Thus, the present review aims to provide the latest innovations that incrementally overcome these issues and future directions in the context of ongoing clinical trials against infectious diseases and beyond.

Analysis of CT signs, radiomic features and clinical characteristics for delta variant COVID-19 patients with different vaccination status

OBJECTIVE

To explore the characteristics of peripheral blood, high resolution computed tomography (HRCT) imaging and the radiomics signature (RadScore) in patients infected with delta variant virus under different coronavirus disease (COVID-19) vaccination status.

METHODS

123 patients with delta variant virus infection collected from November 1, 2021 to March 1, 2022 were analyzed retrospectively. According to COVID-19 vaccination Status, they were divided into three groups: Unvaccinated group, partially vaccinated group and full vaccination group. The peripheral blood, chest HRCT manifestations and RadScore of each group were analyzed and compared.

RESULTS

The mean lymphocyte count 1.22 ± 0.49 × 10^⁹/L, CT score 7.29 ± 3.48, RadScore 0.75 ± 0.63 in the unvaccinated group; The mean lymphocyte count 1.55 ± 0.70 × 10^⁹/L, CT score 5.27 ± 2.72, RadScore 1.03 ± 0.46 in the partially vaccinated group; The mean lymphocyte count 1.87 ± 0.70 × 10^9/L, CT score 3.59 ± 3.14, RadScore 1.23 ± 0.29 in the fully vaccinated group. There were significant differences in lymphocyte count, CT score and RadScore among the three groups (all p < 0.05); Compared with the other two groups, the lung lesions in the unvaccinated group were more involved in multiple lobes, of which 26 cases involved the whole lung.

CONCLUSIONS

Through the analysis of clinical features, pulmonary imaging features and radiomics, we confirmed the positive effect of COVID-19 vaccine on pulmonary inflammatory symptoms and lymphocyte count (immune system) during delta mutant infection.

Theranostic efficiency of biosurfactants against COVID-19 and similar viruses - A review

The world has witnessed an extreme vulnerability of a pandemic during 2020; originated from China. The coronavirus disease 2019 (COVID-19) is infecting and beginning deaths in thousands to millions, creating of the global economic crisis. Biosurfactants (BSs) can carry the prevention, control and management of pandemic out through diverse approaches, such as pharmaceutical, therapeutic, hygienic and environmental. The microbiotas having virulent intrinsic properties towards starting as easily as spreading of diseases (huge morbidity and mortality) could be inhibited via BSs. Such elements could be recognised for their antimicrobial activity, capability to interact with the immune system via micelles formation and in nanoparticulate synthesis. However, they can be used for developing novel and more effective therapeutics, pharmaceuticals, non-toxic formulations, vaccines, and effective cleaning agents. Such approaches can be utilized for product development and implemented for managing and combating the pandemic conditions. This review emphasized on the potentiality of BSs as key components with several ways for protecting against unknown and known pathogens, including COVID-19.

Phytovid19: a compilation of phytochemicals research in coronavirus

The COVID-19 pandemic has immensely impacted global health causing colossal damage. The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has increased the quest to explore phytochemicals as treatment options. We summarize phytochemicals with activity against various coronaviruses including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). We compiled 705 phytochemical compounds through text mining of 893 PubMed articles. The physicochemical properties including molecular weight, lipophilicity, and the number of hydrogen bond donors and acceptors were determined from the structures of these compounds. A structure-based evaluation of these properties with respect to drug likeness showed that most compounds have a positive score of drug likeness. QSAR analysis showed that 5 descriptors, namely polar surface area, relative polar surface area, number of hydrogen bond donors, solubility, and lipophilicity, are significantly related to IC50. We envisage that these phytochemicals could be further explored for developing new potential therapeutic molecules for COVID-19.

Therapeutic and anti-inflammatory effects of baricitinib on mortality, ICU transfer, clinical improvement, and CRS-related laboratory parameters of hospitalized patients with moderate to severe COVID-19 pneumonia: a systematic review and meta-analysis

BACKGROUND

Due to the high incidence and mortality of the worldwide COVID-19 pandemic, beneficial effects of effective antiviral and anti-inflammatory drugs used in other diseases, especially rheumatic diseases, were observed in the treatment of COVID-19.

METHODS

Clinical and laboratory parameters of eight included cohort studies and five Randomized Control Trials between the baricitinib group and the control group were analyzed on the first day of admission and days 7, 14, and 28 during hospitalization.

RESULTS

According to the meta-analysis result of eight included cohort studies with 2088 patients, the Pooled Risk Ratios were 0.46 (P<0.001) for mortality, 6.14 (P< 0.001) for hospital discharge, and the mean differences of 76.78 (P< 0.001) for PaO₂/FiO₂ ratio was -47.32 (P= 0.02) for CRP, in the baricitinib group vs. control group on the seventh or fourteenth day of the treatment compared to the first day. Based on the meta-analysis of five RCT studies with 11825 patients, the pooled RR was 0.84 (P= 0.001) for mortality and 1.07 (P= 0.014) for patients' recovery. The mean differences were -0.80 (P<0.001) for hospitalization days, -0.51(P= 0.33) for time to recovery in the baricitinib group vs. control group.

CONCLUSIONS

Baricitinib prescription is strongly recommended in moderate to severe COVID-19.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration number: CRD42021254541.

Construction and Immunogenicity of a Recombinant Pseudorabies Virus Expressing SARS-CoV-2-S and SARS-CoV-2-N

Coronavirus (CoV) is an important pathogen of humans and animals, which can infect humans or animals through the respiratory mucosal route. Syndrome coronavirus 2 (SARS-CoV-2) is quite similar to syndrome coronavirus (SARS-CoV) with the same receptor, angiotensin-converting enzyme 2 (ACE2). The S and N proteins are the most important protective antigens of the SARS-CoV-2. The S protein on the viral membrane mediates the virus attachment with the host cells, and the N protein is the most abundant expression during infection. In this study, the recombinant viruses expressing the S and N proteins of SARS-CoV-2 were successfully constructed by Red/ET recombinant technology using Pseudorabies virus (PRV) strain Bartha-K61 as a vector. Genetic stability and growth kinetics analysis showed that the recombinant viruses rPRV-SARS-CoV-2-S and rPRV-SARS-CoV-2-N had similar genetic stability and proliferation characteristics to the parental PRV. The immunoassay results showed that mice immunized with recombinant viruses could produce total IgG antibodies. Therefore, PRV is feasible and promising as a viral vector to express SARS-CoV-2-S and SARS-CoV-2-N genes. This study can provide a reference for future research on live vector vaccines for domestic animals, pets, and wild animals.

Revealing the toxicity of lopinavir- and ritonavir-containing water and wastewater treated by photo-induced processes to Danio rerio and Allivibrio fischeri

In coronavirus disease 2019 (COVID-19), among many protocols, lopinavir and ritonavir in individual or combined forms with other drugs have been used, causing an increase in the concentration of antiviral drugs in the wastewater and hospital effluents. In conventional wastewater treatment plants, the removal efficiency of various antiviral drugs is estimated to be low (<20%). The high values of predicted no-effect concentration (PNEC) for lopinavir and ritonavir (in ng∙L^-1) reveal their high chronic toxicity to aquatic organisms. This indicates that lopinavir and ritonavir are current priority antiviral drugs that need to be thoroughly monitored and effectively removed from any water and wastewater samples. In this study, we attempt to explore the impacts of two photo-induced processes (photolysis and photocatalysis) on the toxicity of treated water and wastewater samples containing lopinavir and ritonavir to zebrafish (Danio rerio) and marine bacteria (Allivibrio fischeri). The obtained results reveal that traces of lopinavir in water under photo-induced processes may cause severe problems for Danio rerio, including pericardial edema and shortening of the tail, affecting its behavior, and for Allivibrio fischeri as a result of the oxygen-depleted environment, inflammation, and oxidative stress. Hence, lopinavir must be removed from water and wastewater before being in contact with light. In contrast, the photo-induced processes of ritonavir-containing water and wastewater reduce the toxicity significantly. This shows that even if the physicochemical parameters of water and wastewater are within the standard requirements/limits, the presence of traces of antiviral drugs and their intermediates can affect the survival and behavior of Danio rerio and Allivibrio fischeri. Therefore, the photo-induced processes and additional treatment of water and wastewater containing ritonavir can minimize its toxic effect.

Macroalgae Bioactive Compounds for the Potential Antiviral of SARS-CoV-2: An In Silico Study

Coronavirus disease (COVID-19), which was due to novel coronavirus was detected in December 2019 in Wuhan, China for the first time and spread rapidly became a global pandemic. This study aimed to predict the potential of macroalgae compounds as SARS-CoV-2 antiviral by inhibiting of ACE2 receptor through in silico approach. Twenty-seven macroalgae compounds were obtained from PubChem (NCBI, USA), while target protein ACE2 receptor was collected from Protein Data Bank (PDB). Then the initial screening study drug-likeness conducted by Lipinski rule of five web server and prediction of bioactive probability carried out by PASS (Prediction of activity spectra for biologically active substances) Online web server. After those compounds were approved by Lipinski’s rule of five and PASS online prediction web server, the blind docking simulation was performed using PyRx 0.8 software to show binding energy value. Molecular interaction analysis was done using BIOVIA Discovery Studio 2016 v16.1.0 and PyMOL v2.4.1 software. There are six macroalgae compounds approved by Lipinski’s rule of five and PASS Online Analysis. The result is that macroalgae compound siphonaxanthin among 27 macroalgae compound showed strong binding energy to bind ACE2 receptor with -8.8 kcal/mol. This study also used the SARS-CoV-2 drugs as positive control: remdesivir, molnupiravir, baricitinib, lopinavir, oseltamivir, and favipiravir. The result shows that siphonaxanthin has lowest binding energy than the common SARS-CoV-2 drug. Macroalgae compounds are predicted to have potential as SARS-CoV-2 antiviral. Thus, extension studies need to investigate by in vitro and in vivo analysis for confirmation the siphonaxanthin’s inhibitory activity in combat SARS-CoV-2.

Detoxifying SARS-CoV-2 antiviral drugs from model and real wastewaters by industrial waste-derived multiphase photocatalysts

The use of antiviral drugs has surged as a result of the COVID-19 pandemic, resulting in higher concentrations of these pharmaceuticals in wastewater. The degradation efficiency of antiviral drugs in wastewater treatment plants has been reported to be too low due to their hydrophilic nature, and an additional procedure is usually necessary to degrade them completely. Photocatalysis is regarded as one of the most effective processes to degrade antiviral drugs. The present study aims at synthesizing multiphase photocatalysts by a simple calcination of industrial waste from ammonium molybdate production (WU photocatalysts) and its combination with WO₃ (WW photocatalysts). The X-ray diffraction (XRD) results confirm that the presence of multiple crystalline phases in the synthesized photocatalysts. UV-Vis diffuse reflectance spectra reveal that the synthesized multiphase photocatalysts absorb visible light up to 620 nm. Effects of calcination temperature of industrial waste (550-950 °C) and WO₃ content (0-100%) on photocatalytic activity of multiphase photocatalysts (WU and WW) for efficient removal of SARS-CoV-2 antiviral drugs (lopinavir and ritonavir) in model and real wastewaters are studied. The highest k₁ value is observed for the photocatalytic removal of ritonavir from model wastewater using WW4 (35.64 ×10^-2 min^-1). The multiphase photocatalysts exhibit 95% efficiency in the photocatalytic removal of ritonavir within 15 of visible light irradiation. In contrast, 60 min of visible light irradiation is necessary to achieve 95% efficiency in the photocatalytic removal of lopinavir. The ecotoxicity test using zebrafish (Danio rerio) embryos shows no toxicity for photocatalytically treated ritonavir-containing wastewater, and the contrary trend is observed for photocatalytically treated lopinavir-containing wastewater. The synthesized multiphase photocatalysts can be tested and applied for efficient degradation of other SARS-CoV-2 antiviral drugs in wastewater in the future.

Do Diet and Dietary Supplements Mitigate Clinical Outcomes in COVID-19?

The coronavirus disease 2019 (COVID-19) has caused a pandemic and upheaval that health authorities and citizens around the globe are still grappling with to this day. While public health measures, vaccine development, and new therapeutics have made great strides in understanding and managing the pandemic, there has been an increasing focus on the potential roles of diet and supplementation in disease prevention and adjuvant treatment. In the literature, the impact of nutrition on other respiratory illnesses, including the common cold, pneumonia, and influenza, has been widely demonstrated in both animal and human models. However, there is much less research on the impact related to COVID-19. The present study discusses the potential uses of diets, vitamins, and supplements, including the Mediterranean diet, glutathione, zinc, and traditional Chinese medicine, in the prevention of infection and severe illness. The evidence demonstrating the efficacy of diet supplementation on infection risk, disease duration, severity, and recovery is mixed and inconsistent. More clinical trials are necessary in order to clearly demonstrate the contribution of nutrition and to guide potential therapeutic protocols.

Exploring New Characteristics: Using Deep Learning and 3D Reconstruction to Compare the Original COVID-19 and Its Delta Variant Based on Chest CT

Purpose: Computer-aided diagnostic methods were used to compare the characteristics of the Original COVID-19 and its Delta Variant.

Methods: This was a retrospective study. A deep learning segmentation model was applied to segment lungs and infections in CT. Three-dimensional (3D) reconstruction was used to create 3D models of the patient’s lungs and infections. A stereoscopic segmentation method was proposed, which can subdivide the 3D lung into five lobes and 18 segments. An expert-based CT scoring system was improved and artificial intelligence was used to automatically score instead of visual score. Non-linear regression and quantitative analysis were used to analyze the dynamic changes in the percentages of infection (POI).

Results: The POI in the five lung lobes of all patients were calculated and converted into CT scores. The CT scores of Original COVID-19 patients and Delta Variant patients since the onset of initial symptoms were fitted over time, respectively. The peak was found to occur on day 11 in Original COVID-19 patients and on day 15 in Delta Variant patients. The time course of lung changes in CT of Delta Variant patients was redetermined as early stage (0–3 days), progressive and peak stage (4–16 days), and absorption stage (17–42 days). The first RT-PCR negative time in Original COVID-19 patients appeared earlier than in Delta Variant patients (22 [17–30] vs. 39 [31–44], p < 0.001). Delta Variant patients had more re-detectable positive RT-PCR test results than Original COVID-19 patients after the first negative RT-PCR time (30.5% vs. 17.1%). In the early stage, CT scores in the right lower lobe were significantly different (Delta Variant vs. Original COVID-19, 0.8 ± 0.6 vs. 1.3 ± 0.6, p = 0.039). In the absorption stage, CT scores of the right middle lobes were significantly different (Delta Variant vs. Original COVID-19, 0.6 ± 0.7 vs. 0.3 ± 0.4, p = 0.012). The left and the right lower lobes contributed most to lung involvement at any given time.

Conclusion: Compared with the Original COVID-19, the Delta Variant has a longer lung change duration, more re-detectable positive RT-PCR test results, different locations of pneumonia, and more lesions in the early stage, and the peak of infection occurred later.

Nanotechnology and COVID-19: quo vadis?

The pandemic COVID-19 has worried everyone due to the high mortality rate and the high number of people hospitalized with severe acute respiratory syndrome caused by SARS-CoV-2. Given the seriousness of this disease, several companies and research institutions have sought alternative treatment and/or prevention methods for COVID-19. Due to its versatility, nanotechnology has allowed the development of protective equipment and vaccines to prevent the disease and reduce the number of severe COVID-19 cases. Thus, this article combined the main works and products developed in a nanotechnological field for COVID-19. We performed a literature search using the keywords "COVID-19," "SARS-CoV-2," "nanoparticles," "nanotechnology," and "liposomes" in the SciELO, Scifinder, PubMed, Sciencedirect, ClinicalTrials, and Nanotechnology Products databases Database. The data survey indicated 48 articles, 62 products, and 32 patents. The use of nanotechnology against COVID-19 has brought benefits in several parameters of this disease, helping develop rapid diagnostic tests that release the result in 10 min, as well as developing vaccines containing genetic material from SARS-CoV-2 (DNA, mRNA, and protein subunits). Nanotechnology is an exceptional ally against COVID-19, contributing to the most diverse areas, helping both prevent, diagnose, and treat COVID-19.

Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations

(1) Background: Main Protease (Mpro) is an attractive therapeutic target that acts in the replication and transcription of the SARS-CoV-2 coronavirus. Mpro is rich in residues exposed to protonation/deprotonation changes which could affect its enzymatic function. This work aimed to explore the effect of the protonation/deprotonation states of Mpro at different pHs using computational techniques. (2) Methods: The different distribution charges were obtained in all the evaluated pHs by the Semi-Grand Canonical Monte Carlo (SGCMC) method. A set of Molecular Dynamics (MD) simulations was performed to consider the different protonation/deprotonation during 250 ns, verifying the structural stability of Mpro at different pHs. (3) Results: The present findings demonstrate that active site residues and residues that allow Mpro dimerisation was not affected by pH changes. However, Mpro substrate-binding residues were altered at low pHs, allowing the increased pocket volume. Additionally, the results of the solvent distribution around Sγ, Hγ, Nδ1 and Hδ1 atoms of the catalytic residues Cys145 and His41 showed a low and high-water affinity at acidic pH, respectively. It which could be crucial in the catalytic mechanism of SARS-CoV-2 Mpro at low pHs. Moreover, we analysed the docking interactions of PF-00835231 from Pfizer in the preclinical phase, which shows excellent affinity with the Mpro at different pHs. (4) Conclusion: Overall, these findings indicate that SARS-CoV-2 Mpro is highly stable at acidic pH conditions, and this inhibitor could have a desirable function at this condition.

Antibodies against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) in individuals with and without COVID-19 vaccination: A method comparison of two different commercially available serological assays from the same manufacturer

Background

We compared two serological assays from Roche Diagnostics in individuals with and without COVID-19 vaccination, namely the Elecsys Anti-SARS-CoV-2 assay (detecting antibodies against the nucleocapsid protein of SARS-CoV-2) and the Elecsys Anti-SARS-CoV-2 S assay (detecting antibodies against the spike protein of SARS-CoV-2).

Methods

With both assays, we analyzed 3033 serum samples collected from 2496 patients without COVID-19 vaccination. In addition, we studied 34 healthcare-workers who received two injections of the BNT162b2 COVID-19 vaccine from BioNTech/Pfizer three weeks apart and who had repeatedly determined their antibody response by both assays.

Results

In our cohort of patients without COVID-19 vaccination, 62.9% of all determinations were negative with both Roche assays and 31.5% were positive with both assays. In 5.6% of our cohort, however, there were discordant results with both assays (partly because initially discordant results of the two assays became concordantly positive over time). In the healthcare-workers with the COVID-19 vaccination, the results of the Roche anti-nucleocapsid assay remained negative throughout the observation period of 5 weeks after vaccination. The initially negative antibodies against the spike protein became positive with the Roche assay in all samples two weeks after the initial injection, and the serum concentrations of anti-spike antibodies increased constantly until 4–5 weeks after the initial injection.

Conclusions

Here, we provide information on serological testing with the two Roche assays, which may be important for the application of the two assays in clinical routine. There are differences in the pattern of antibodies in individuals with and without COVID-19 vaccination.