The British variant of the new coronavirus-19 (Sars-Cov-2) should not create a vaccine problem

How anxiety attributed to COVID-19, disease knowledge, and intention to vaccinate against SARS-CoV-2 viral infection prevail in general public of Saudi Arabia?

Aim

The study aimed to document the anxiety attributed to COVID-19, disease knowledge, and intention to vaccinate against the disease in general public. Moreover, the interplay among these three outcomes was also investigated.

Methods

A cross-sectional study was conducted for 2 months in three cities of Dammam Region of Saudi Arabia. The target segment was the adult population of Saudi Arabia. Convenience sampling was used and all adults aged ≥18 were invited to participate. The questionnaire used in the study was available in both Arabic and English languages. It included a demographic section, a section dedicated to vaccination intention and, a section containing coronavirus anxiety scale (CAS). The data analysis was carried out using IBM SPSS version 23. The study was approved by an ethics committee (IRB-2021-05-297).

Results

A total of 542 responses were analyzed. Most respondents had no anxiety attributed to COVID-19 (92.1%), self-reported good knowledge of COVID-19 (79.7%) and intended to administer a vaccine (57.4%). Age groups 18-29 years and 30-45 years, and having a chronic medical condition, were found to be determinants of having COVID-19 anxiety (p < 0.05). The variables of self-rated good knowledge of disease, never contracted COVID-19, and incomes of SAR 5,000 (i.e., USD 1333), and SAR 7,500-10,000 (i.e., USD 1999.5-2666), were found to be determinants of having positive intention toward vaccination (p < 0.05).

Conclusion

The anxiety due to COVID-19 was present in a few participants. Besides, self-reported knowledge about COVID-19 and intention to administer a vaccine, were positively linked to each other. However, both variables had no effect on COVID-19 anxiety. It is important to review and address the determinants of positive intention to further increase vaccine acceptance rate.

A model simulation on the SARS-CoV-2 Omicron variant containment in Beijing, China

Objective

The Omicron variant of SARS-COV-2 is replacing previously circulating variants around the world in 2022. Sporadic outbreaks of the Omicron variant into China have posed a concern how to properly response to battle against evolving coronavirus disease 2019 (COVID-19).

Methods

Based on the epidemic data from website announced by Beijing Center for Disease Control and Prevention for the recent outbreak in Beijing from April 22nd to June 8th in 2022, we developed a modified SEPIR model to mathematically simulate the customized dynamic COVID-zero strategy and project transmissions of the Omicron epidemic. To demonstrate the effectiveness of dynamic-changing policies deployment during this outbreak control, we modified the transmission rate into four parts according to policy-changing dates as April 22nd to May 2nd, May 3rd to 11st, May 12th to 21st, May 22nd to June 8th, and we adopted Markov chain Monte Carlo (MCMC) to estimate different transmission rate. Then we altered the timing and scaling of these measures used to understand the effectiveness of these policies on the Omicron variant.

Results

The estimated effective reproduction number of four parts were 1.75 (95% CI 1.66-1.85), 0.89 (95% CI 0.79-0.99), 1.15 (95% CI 1.05-1.26) and 0.53 (95% CI 0.48 -0.60), respectively.  In the experiment, we found that till June 8th the cumulative cases would rise to 132,609 (95% CI 59,667-250,639), 73.39 times of observed cumulative cases number 1,807 if no policy were implemented on May 3rd, and would be 3,235 (95% CI 1,909 - 4,954), increased by 79.03% if no policy were implemented on May 22nd. A 3-day delay of the implementation of policies would led to increase of cumulative cases by 58.28% and a 7-day delay would led to increase of cumulative cases by 187.00%. On the other hand, taking control measures 3 or 7 days in advance would result in merely 38.63% or 68.62% reduction of real cumulative cases. And if lockdown implemented 3 days before May 3rd, the cumulative cases would be 289 (95% CI 211-378), reduced by 84%, and the cumulative cases would be 853 (95% CI 578-1,183), reduced by 52.79% if lockdown implemented 3 days after May 3rd.

Conclusion

The dynamic COVID-zero strategy might be able to effectively minimize the scale of the transmission, shorten the epidemic period and reduce the total number of infections.

Advanced Plasmonic Nanoparticle-Based Techniques for the Prevention, Detection, and Treatment of Current COVID-19

Coronavirus is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2. Coronavirus disease 2019 known as COVID-19 is the worst pandemic since World War II. The outbreak of COVID-19 had a significant repercussion on the health, economy, politics, and environment, making coronavirus-related issues more complicated and becoming one of the most challenging pandemics of the last century with deadly outcomes and a high rate of the reproduction number. There are thousands of different types - or variants - of COVID circulating across the world. Viruses mutate all the time; it emphasizes the critical need for the designing of efficient vaccines to prevent virus infection, early and fast diagnosis, and effective antiviral and protective therapeutics. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis, and treatment of COVID-19. This review presents an outline of the platforms developed using plasmonic nanoparticles in the detection, treatment, and prevention of SARS-CoV-2. We select the best strategies in each of these approaches. The properties of metallic plasmon NPs and their relevance in the development of novel point-of-care diagnosis approaches for COVID-19 are highlighted. Also, we discuss the current challenges and the future perspectives looking towards the clinical translation and the commercial aspects of nanotechnology and plasmonic NP-based diagnostic tools and therapy to fight COVID-19 pandemic. The article could be of significance for researchers dedicated to developing suitable plasmonic detection tools and therapy approaches for COVID-19 viruses and future pandemics.

Forecasting the Post-Pandemic Effects of the SARS-CoV-2 Virus Using the Bullwhip Phenomenon Alongside Use of Nanosensors for Disease Containment and Cure

The COVID-19 pandemic has the tendency to affect various organizational paradigm alterations, which civilization hasyet to fully comprehend. Personal to professional, individual to corporate, and across most industries, the spectrum of transformations is vast. Economically, the globe has never been more intertwined, and it has never been subjected to such widespread disruption. While many people have felt and acknowledged the pandemic’s short-term repercussions, the resultant paradigm alterations will certainly have long-term consequences with an unknown range and severity. This review paper aims at acknowledging various approaches for the prevention, detection, and diagnosis of the SARS-CoV-2 virus using nanomaterials as a base material. A nanostructure is a material classification based on dimensionality, in proportion to the characteristic diameter and surface area. Nanoparticles, quantum dots, nanowires (NW), carbon nanotubes (CNT), thin films, and nanocomposites are some examples of various dimensions, each acting as a single unit, in terms of transport capacities. Top-down and bottom-up techniques are used to fabricate nanomaterials. The large surface-to-volume ratio of nanomaterials allows one to create extremely sensitive charge or field sensors (electrical sensors, chemical sensors, explosives detection, optical sensors, and gas sensing applications). Nanowires have potential applications in information and communication technologies, low-energy lightning, and medical sensors. Carbon nanotubes have the best environmental stability, electrical characteristics, and surface-to-volume ratio of any nanomaterial, making them ideal for bio-sensing applications. Traditional commercially available techniques have focused on clinical manifestations, as well as molecular and serological detection equipment that can identify the SARS-CoV-2 virus. Scientists are expressing a lot of interest in developing a portable and easy-to-use COVID-19 detection tool. Several unique methodologies and approaches are being investigated as feasible advanced systems capable of meeting the demands. This review article attempts to emphasize the pandemic’s aftereffects, utilising the notion of the bullwhip phenomenon’s short-term and long-term effects, and it specifies the use of nanomaterials and nanosensors for detection, prevention, diagnosis, and therapy in connection to the SARS-CoV-2.

Cross-Reactivity of IgG Antibodies and Virus Neutralization in mRNA-Vaccinated People Against Wild-Type SARS-CoV-2 and the Five Most Common SARS-CoV-2 Variants of Concern

The rapid development, approval, and production of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in less than 1 year after the first reports of a new infectious disease was a real game changer, providing 80%–90% efficacy in preventing severe etiopathologies of the coronavirus disease 2019 (COVID-19). These vaccines induce an immune response against the SARS-CoV-2 spike (S) protein located on the surface of the virus particle. Antibodies (Abs) recognizing the S-protein can inhibit binding of the virus via the S-protein to the angiotensin-converting enzyme-2 (ACE-2) receptor expressed on different human cells, especially when these Abs bind to the interaction site, the so-called receptor-binding domain (RBD). We have expressed the RBDs of wild-type SARS-CoV-2 and five variants of concern (VOCs) to test the immune response in people before vaccination with mRNA vaccines BNT162b2 and mRNA-1273 and after up to three vaccinations using in-house ELISA and inhibition assays. The methods of both assays are provided. Both vaccines initiated similarly high IgG titers after two vaccinations against the wild-type and even two VOC-RBDs (alpha and delta) and strongly inhibited the corresponding RBD-ACE-2 binding. The IgG titers and inhibition of ACE-2 binding were lower for beta and gamma RBDs and much lower for omicron RBD. The third vaccination after 6 months strongly increased both the IgG titers and the neutralizing effect against all variants, especially for omicron, leading to 63% ± 13% neutralization potential. Importantly, neutralization linearly increased with the IgG titers.

Assessment of COVID-19 Vaccine Acceptance and Reluctance Among Staff Working in Public Healthcare Settings of Saudi Arabia: A Multicenter Study

Objective

The study aimed to evaluate the novel coronavirus disease 2019 (COVID-19) vaccination acceptance and reluctance among staff working in Saudi healthcare facilities.

Methods

A cross-sectional study was conducted during April - May 2021, among healthcare workers in five public hospitals under the National Guards Health Association located in Alahsa, Dammam, Jeddah, Madinah, and Riyadh. The study used a questionnaire in English language, which was distributed through official email communication among healthcare staff currently working at study venues. The data was analyzed using IBM SPSS v23. An ethical approval was obtained.

Results

A total of 1,031 responses were recorded. Most of the staff had both doses of COVID-19 vaccine (89%). The mean score for vaccine acceptance on a scale of 1 (strongly disagree) to 5 (strongly agree) was 3.55 ± 1.6. The mean score for vaccine reluctance on the same scale was 2.71 ± 1.05. Most participants mentioned safety (76.9%) and efficacy (56.3%) as vaccine concerns and believed that COVID-19 vaccine may not be effective because of changes in virus strain (55.5%). The variables of gender and nationality significantly affected vaccine acceptance, while age, gender, nationality, and profession significantly affected vaccine reluctance (p < 0.05).

Conclusion

Most healthcare staff were vaccinated, and a high acceptance for COVID-19 vaccination was reported. Several demographic factors affected the vaccine acceptance and reluctance.

A review on drug repurposing in COVID-19: from antiviral drugs to herbal alternatives

Background

COVID-19 is an illness caused by severe acute respiratory syndrome coronavirus 2. Due to its rapid spread, in March 2020 the World Health Organization (WHO) declared pandemic. Since the outbreak of pandemic many governments, scientists, and institutions started to work on new vaccines and finding of new and repurposing drugs.

Main body of the abstract

Drug repurposing is an excellent option for discovery of already used drugs, effective against COVID-19, lowering the cost of production, and shortening the period of delivery, especially when preclinical safety studies have already been performed. There are many approved drugs that showed significant results against COVID-19, like ivermectin and hydrochloroquine, including alternative treatment options against COVID-19, utilizing herbal medicine.

Short conclusion

This article summarized 11 repurposing drugs, their positive and negative health implications, along with traditional herbal alternatives, that harvest strong potential in efficient treatments options against COVID-19, with small or no significant side effects. Out of 11 repurposing drugs, four drugs are in status of emergency approval, most of them being in phase IV clinical trials. The first repurposing drug approved for clinical usage is remdesivir, whereas chloroquine and hydrochloroquine approval for emergency use was revoked by FDA for COVID-19 treatment in June 2020.

Sinovac vaccination and the course of COVID-19 disease in hospitalized patients in Turkey

BACKGROUND

The Alpha variant of SARS-CoV-2 has a higher transmission rate than the first variant identified. The efficacy of vaccines is affected by the characteristics of SARS-CoV-2 variants.

OBJECTIVE

Investigate the relationship of vaccination and virus variant on the course of the disease in patients who were hospitalized with a diagnosis of COVID-19.

DESIGN

Retrospective, cohort study SETTING: Tertiary health institution PATIENTS AND METHODS: The study included patients older than the age of 18 years who were hospitalized in a COVID-19 service or the intensive care unit with a diagnosis of COVID-19 between 1 January 2021 and 30 April 2021. Demographic characteristics, vaccination and the Alpha virus variant status, comorbidities, and information about hospitalization were obtained from the hospital automation system and patient files.

MAIN OUTCOME MEASURES

Vaccination rate and relationship with course of disease.

SAMPLE SIZE

608 RESULTS: Most of the patients (n=482, 79.3%) were admitted to the COVID-19 service. More of the COVID-19 service patients had the Alpha variant than the patients admitted to ICU (P<.009). The Alpha variant was also more common in younger patients (P<.001). There was no relationship between the Alpha virus and comorbid diseases such as diabetes mellitus and hypertension. Mortality was lower in the patients who had received a second dose of the Sinovac vaccine (P=.004) compared with unvaccinated patients.

CONCLUSION

Although the Alpha variant spreads faster, it has a milder course. If only the Sinovac vaccine is available, we recommend that the two doses of the Sinovac vaccine be administered.

LIMITATIONS

Our study is single-center and did not include pregnant and pediatric patients.

CONFLICT OF INTEREST

None.

Role of the Microbiome in the Pathogenesis of COVID-19

The ongoing pandemic coronavirus disease COVID-19 is caused by the highly contagious single-stranded RNA virus, SARS-coronavirus 2 (SARS-CoV-2), which has a high rate of evolution like other RNA viruses. The first genome sequences of SARS-CoV-2 were available in early 2020. Subsequent whole-genome sequencing revealed that the virus had accumulated several mutations in genes associated with viral replication and pathogenesis. These variants showed enhanced transmissibility and infectivity. Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide. Thereafter, several variants emerged, which were found to harbor mutations in essential viral genes encoding proteins that could act as drug and vaccine targets. Numerous vaccines have been successfully developed to assuage the burden of COVID-19. These have different rates of efficacy, including, although rarely, a number of vaccinated individuals exhibiting side effects like thrombosis. However, the recent emergence of the Britain strain with 70% more transmissibility and South African variants with higher resistance to vaccines at a time when several countries have approved these for mass immunization has raised tremendous concern regarding the long-lasting impact of currently available prophylaxis. Apart from studies addressing the pathophysiology, pathogenesis, and therapeutic targets of SARS-CoV-2, analysis of the gut, oral, nasopharyngeal, and lung microbiome dysbiosis has also been undertaken to find a link between the microbiome and the pathogenesis of COVID-19. Therefore, in the current scenario of skepticism regarding vaccine efficacy and challenges over the direct effects of currently available drugs looming large, investigation of alternative therapeutic avenues based on the microbiome can be a rewarding finding. This review presents the currently available understanding of microbiome dysbiosis and its association with cause and consequence of COVID-19. Taking cues from other inflammatory diseases, we propose a hypothesis of how the microbiome may be influencing homeostasis, pro-inflammatory condition, and the onset of inflammation. This accentuates the importance of a healthy microbiome as a protective element to prevent the onset of COVID-19. Finally, the review attempts to identify areas where the application of microbiome research can help in reducing the burden of the disease.

SARS-COV-2 Variants: Differences and Potential of Immune Evasion

The structural spike (S) glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) plays an essential role in infection and is an important target for neutralizing antibody recognition. Mutations in the S gene can generate variants of concern (VOCs), which improve “viral fitness” through selective or survival advantages, such as increased ACE-2 receptor affinity, infectivity, viral replication, higher transmissibility, resistance to neutralizing antibodies and immune escape, increasing disease severity and reinfection risk. Five VOCs have been recognized and include B.1.1.7 (U.K.), B.1.351 (South Africa), P.1 (Brazil), B.1.617.2 (India), and B.1.1.529 (multiple countries). In this review, we addressed the following critical points concerning VOCs: a) characteristics of the SARS-CoV-2 VOCs with mutations in the S gene; b) possible evasion of variants from neutralizing antibodies generated through vaccination, previous infection, or immune therapies; c) potential risk of new pandemic waves induced by the variants worldwide; and d) perspectives for further studies and actions aimed at preventing or reducing the impact of new variants during the current COVID-19 pandemic.

Do COVID19 infection rates change over time and space? Population density and socio-economic measures as regressors

The COVID19 pandemic motivated an interesting debate, which is related directly to core issues in urban economics, namely, the advantages and disadvantages of dense cities. On the one hand, compact areas facilitate more intensive human interaction and could lead to higher exposure to the infection, which make them the potential epicenter of the pandemic crisis. On the other hand, dense areas tend to provide superior health and educational systems, which are better prepared to handle pandemics, leading to higher recovery rates and lower mortality rates. The objective of the current study is to test the relationship between COVID19 infection rates (cases÷population) as the dependent variable, and two explanatory variables, population density and socio-economic measures, within two timeframes: May 11, 2020 and January 19, 2021. We use a different methodology to address the relationship between COVID19 spread and population density by fitting a parabolic, instead of a linear, model, while controlling socio-economic indices. We thus apply a better examination of the factors that shape the COVID19 spread across time and space by permitting a non-monotonic relationship. Israel provides an interesting case study based on a highly non-uniform distribution of urban population, and diversified populations. Results of the analyses demonstrate two patterns of change: 1) a significant rise in the median and average infection-population ratio for each level of population density; and 2) a moderate (a steep) rise in infection rates with increased population density on May 11, 2020 (January 19, 2021) for population densities of 4000 to 20,000 persons per square kilometer. The significant rise in the average and median infection-population ratios might be as attributed to the outcome of new COVID19 variants (i.e., the British and the South African mutants), which, in turn, intensify the virus spread. The steeper slope of infection rates and the rise in the standard deviation of the infection-population ratio may be explained by non-uniform spatial distribution of: dissemination of information in a variety of language; different levels of medical infrastructure in different parts of the country; varying levels of compliance to social distancing rules; and strict (limited) compliance to social distancing rules. The last factor of limited compliance might be the outcome of premature optimism due to extensive scope of the vaccination campaign in Israel, which is located in first place globally.

Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617

COVID-19 pathogen SARS-CoV-2 has infected hundreds of millions and caused over 5 million deaths to date. Although multiple vaccines are available, breakthrough infections occur especially by emerging variants. Effective therapeutic options such as monoclonal antibodies (mAbs) are still critical. Here, we report the development, cryo-EM structures, and functional analyses of mAbs that potently neutralize SARS-CoV-2 variants of concern. By high-throughput single cell sequencing of B cells from spike receptor binding domain (RBD) immunized animals, we identified two highly potent SARS-CoV-2 neutralizing mAb clones that have single-digit nanomolar affinity and low-picomolar avidity, and generated a bispecific antibody. Lead antibodies showed strong inhibitory activity against historical SARS-CoV-2 and several emerging variants of concern. We solved several cryo-EM structures at ∼3 Å resolution of these neutralizing antibodies in complex with prefusion spike trimer ectodomain, and revealed distinct epitopes, binding patterns, and conformations. The lead clones also showed potent efficacy in vivo against authentic SARS-CoV-2 in both prophylactic and therapeutic settings. We also generated and characterized a humanized antibody to facilitate translation and drug development. The humanized clone also has strong potency against both the original virus and the B.1.617.2 Delta variant. These mAbs expand the repertoire of therapeutics against SARS-CoV-2 and emerging variants.

Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach

Background: An immunoinformatic approach may be useful to investigate the conserved region in the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Indonesia isolates. The aim of this study was to investigate Indonesian SARS-CoV-2 isolates based on B cell epitopes by targeting the conserved regions in the spike glycoprotein to trigger increased multi-variant virus neutralization and memory response for the development of vaccine seed candidates. Methods: SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesia were compared with Wuhan (China), the United Kingdom, South Africa, India, the United States, and Brazil isolates obtained from the NCBI and GISAID databases. The recognition of antigens was carried out directly using B cells through the B cell receptor (BCR). An indirect B cell activation by Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) based on IC ₅₀ value. In addition, vaccine allergenicity and toxicity were investigated. During the molecular complex examination, the 3D peptide structure was investigated and the lowest amount of energy formed when the vaccine candidate peptide bound to BCR and MHC-II was calculated. Results: As a result, the spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates had conserved regions which were very similar to reference countries such as China, the United Kingdom, South Africa, India, the United States, and Brazil. Conclusion: It was predicted that the conserved regions could be identified as the epitope of B and T CD4+ cells that produced the peptides for vaccine candidate with antigenic, non-allergen, and non-toxic properties.

A Comparative Study between Spanish and British SARS-CoV-2 Variants

The study of the interaction between the SARS-CoV-2 spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor is key to understanding binding affinity and stability. In the present report, we sought to investigate the differences between two already sequenced genome variants (Spanish and British) of SARS-CoV-2. Methods: In silico model evaluating the homology, identity and similarity in the genome sequence and the structure and alignment of the predictive spike by computational docking methods. Results: The identity results between the Spanish and British variants of the Spike protein were 28.67%. This close correspondence in the results between the Spanish and British SARS-CoV-2 variants shows that they are very similar (99.99%). The alignment obtained results in four deletions. There were 23 nucleotide substitutions also predicted which could affect the functionality of the proteins produced from this sequence. The interaction between the binding receptor domain from the spike protein and the ACE2 receptor produces some of the mutations found and, therefore, the energy of this ligand varies. However, the estimated antigenicity of the British variant is higher than its Spanish counterpart. Conclusions: Our results indicate that minimal mutations could interfere in the infectivity of the virus due to changes in the fitness between host cell recognition and interaction proteins. In particular, the N501Y substitution, situated in the RBD of the spike of the British variant, might be the reason for its extraordinary infective potential.

Differences in Sources of Information, Risk Perception, and Cognitive Appraisals between People with Various Latent Classes of Motivation to Get Vaccinated against COVID-19 and Previous Seasonal Influenza Vaccination: Facebook Survey Study with Latent Profile Analysis in Taiwan

The present study aimed (1) to identify distinct latent classes of motivation to get vaccinated against coronavirus disease 2019 (COVID-19) and previous seasonal influenza vaccination among people in Taiwan and (2) to examine the roles of sources of information, risk perception, and cognitive appraisals of vaccination against COVID-19 in these classes. We recruited 1047 participants through a Facebook advertisement. The participants' motivation to get vaccinated against COVID-19, previous seasonal influenza vaccination, sources of information about COVID-19 vaccination, risk perception of COVID-19, and cognitive appraisals of vaccination against COVID-19 were determined. We examined the participants' motivation for COVID-19 vaccination and previous seasonal influenza vaccination through latent profile analysis. Four latent classes of motivation were identified: participants with high motivation for COVID-19 vaccination and high seasonal influenza vaccination, those with high motivation for COVID-19 vaccination but low seasonal influenza vaccination, those with low motivation for COVID-19 vaccination but high seasonal influenza vaccination, and those with low motivation for COVID-19 vaccination and low seasonal influenza vaccination. Compared with participants in the latent class of high motivation for COVID-19 vaccination and high seasonal influenza vaccination, those in the other three latent classes had lower levels of positive appraisals of COVID-19 vaccination; participants in the latent class of low motivation for COVID-19 vaccination and low seasonal influenza vaccination had lower risk perception of COVID-19 and were also less likely to obtain information about COVID-19 vaccination from the internet, friends, and family members. The various motivations and behaviors for vaccination, sources of information, risk perception, and cognitive appraisals of vaccination against COVID-19 should be considered in intervention programs aiming to increase people's motivation to get vaccinated against COVID-19.

Molecular modeling of the interaction of ligands with ACE2-SARS-CoV-2 spike protein complex

COVID-19 is a new communicable disease with a widespread outbreak that affects all populations worldwide triggering a rush of scientific interest in coronavirus research globally. In silico molecular docking experiment was utilized to determine interactions of available compounds with SARS-CoV-2 and angiotensin-converting enzyme 2 (ACE2) complex. Chimera and AutoDock Vina were used for protein-ligand interaction structural analysis. Ligands were chosen based on the known characteristics and indications of the drugs as ACE inhibitors (captopril, enalapril, quinapril, moexipril, benazepril, ramipril, perindopril, zofenopril, fosinopril), as ACE2 blockers (losartan, olmesartan), as blood thinning agent (clopidogrel), as cholesterol-lowering prescriptions (simvastatin, atorvastatin), repurposed medications (dexamethasone, hydroxychloroquine, chloroquine), and as investigational drug (remdesivir). Experimental ACE/ACE2 inhibitors are also included: Sigma ACEI, N-(2-aminoethyl)-1-aziridine-ethanamine (NAAE), nicotianamine (NAM), and MLN-4760 (ACE2 inhibitor). The best docked conformations were all located in the ACE2 protein, 50% docked at the interface with lower scores and only clopidogrel and hydroxychloroquine docked at the spike protein. Captopril, moexipril, benazepril, fosinopril, losartan, remdesivir, Sigma ACEI, NAA, and NAM interacted and docked at the interface of ACE2 and SARS-CoV-2 spike protein complex. This may have significant implication in enhancing our understanding of the mechanism to hinder viral entry into the host organism during infection.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40203-021-00114-w.

Anti-SARS-CoV-2 Strategies and the Potential Role of miRNA in the Assessment of COVID-19 Morbidity, Recurrence, and Therapy

Recently, we have experienced a serious pandemic. Despite significant technological advances in molecular technologies, it is very challenging to slow down the infection spread. It appeared that due to globalization, SARS-CoV-2 spread easily and adapted to new environments or geographical or weather zones. Additionally, new variants are emerging that show different infection potential and clinical outcomes. On the other hand, we have some experience with other pandemics and some solutions in virus elimination that could be adapted. This is of high importance since, as the latest reports demonstrate, vaccine technology might not follow the new, mutated virus outbreaks. Thus, identification of novel strategies and markers or diagnostic methods is highly necessary. For this reason, we present some of the latest views on SARS-CoV-2/COVID-19 therapeutic strategies and raise a solution based on miRNA. We believe that in the face of the rapidly increasing global situation and based on analogical studies of other viruses, the possibility of using the biological potential of miRNA technology is very promising. It could be used as a promising diagnostic and prognostic factor, as well as a therapeutic target and tool.

Clinical laboratory evaluation of COVID-19

COVID-19, caused by SARS-CoV-2, is a highly infectious disease, and clinical laboratory detection has played important roles in its diagnosis and in evaluating progression of the disease. Nucleic acid amplification testing or gene sequencing can serve as pathogenic evidence of COVID-19 diagnosing for clinically suspected cases, and dynamic monitoring of specific antibodies (IgM, IgA, and IgG) is an effective complement for false-negative detection of SARS-CoV-2 nucleic acid. Antigen tests to identify SARS-CoV-2 are recommended in the first week of infection, which is associated with high viral loads. Additionally, many clinical laboratory indicators are abnormal as the disease evolves. For example, from moderate to severe and critical cases, leukocytes, neutrophils, and the neutrophil-lymphocyte ratio increase; conversely, lymphocytes decrease progressively but are over activated. LDH, AST, ALT, CK, high-sensitivity troponin I, and urea also increase progressively, and increased D-dimer is an indicator of severe disease and an independent risk factor for death. Severe infection leads to aggravation of inflammation. Inflammatory biomarkers and cytokines, such as CRP, SAA, ferritin, IL-6, and TNF-α, increase gradually. High-risk COVID-19 patients with severe disease, such as the elderly and those with underlying diseases (cardiovascular disease, diabetes, chronic respiratory disease, hypertension, obesity, and cancer), should be monitored dynamically, which will be helpful as an early warning of serious diseases.

Measures for Ensuring Sustainability during the Current Spreading of Coronaviruses in the Czech Republic

This manuscript focuses on the SARS-CoV-2 outbreak in the Czech Republic and its impact on economic and social sustainability in this country. The topic of this manuscript is the topical issue of how to manage the outbreak of this infectious disease and thereby reduce any disruption to economic and social sustainability. The aim of the authors was to identify serious risks and to propose priority measures that can lead to their significant mitigation. A modified semi-quantitative three-component probability method Pj, consequences Cj and opinion of evaluators OEj were used to assess active risks. The manuscript also presents risk analysis and risk management and the construction of developmental regression models. The manuscript presents a proposal for preventive measures to mitigate risks in the period of the third wave of the occurrence and spread of the coronavirus. Most of the proposed preventive measures were based on brainstorming of the views and experience of the implementation team. Consultation with and materials by experts in the field of developmental biology, parasitology, epidemiology and virology were also used. As such, this survey provides lessons for other cities and regions involved in coping with COVID-19 infection and implementing the policy of a positive and timely return to work.

SARS-CoV-2 Genetic Variability and Non-Specific Immunity Associated with the Use of Different BCG Strains-A Molecular and Clinical Approach

The effect of BCG vaccination against tuberculosis on the reduction in COVID-19 infection is related to the effect of the BCG vaccine on the immunomodulation of non-specific immunity. In the early stages of the pandemic, countries with universal BCG vaccination programs registered a low number of new cases of COVID-19, with the situation now reversed, as exemplified by India. The high genetic variability of SARS-CoV-2, a known characteristic of RNA viruses, causing the occurrence of SARS-CoV-2 variants may have led to the virus adapting to overcome the initial immune protection. The strains from the United Kingdom (B1.1.7), Brazil (B1.1.28 and B1.1.33), South Africa (B.1.351), and India (B.1.617) are characterized by a greater ability to spread in the environment, in comparison with the original infectious agent of SARS-CoV-2. It should be remembered that the large variation in the genetic makeup of SARS-CoV-2 may result in future changes in its pathogenicity, immunogenicity and antigenicity, and therefore it is necessary to carefully study the mutations occurring within the virus to determine whether the current vaccines will remain effective. However, most studies show that monoclonal antibodies produced after vaccination against COVID-19 are effective against the newly developed variants.

Brief review of the mRNA vaccines COVID-19

The global COVID-19 pandemic continues to claim victims worldwide, representing a health and socioeconomic challenge with few precedents in human history. The therapeutic agents used to treat COVID-19 infection are mostly aimed at avoiding the most serious complications and organ damage that in a percentage of cases can be fatal. Recently, the first COVID-19 vaccines have been authorised, starting a massive vaccination campaign worldwide. The COVID-19 vaccines authorized or under testing use different methods of action such as mRNA, DNA vaccine, viral vector, protein subunit, and virus inactivated immunization strategies. The mRNA vaccines are the first authorised vaccines with this new method of action, initiating a new era of preventive medicine. To date, data indicate that they may be effective against the newly identified SARS-CoV-2 variants. Short-term studies indicated an acceptable safety profile but long-term immunity as well as safety is not yet available. In this article, we briefly describe mRNA vaccines and highlight some aspects yet to be fully defined.

Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein

New SARS-CoV-2 mutations are constantly emerging, raising concerns of increased transmissibility, virulence or escape from host immune response. We describe a nested RT-PCR assay (~1500 bps) to detect multiple nucleotide changes resulting in key spike protein mutations distinctive of the major known circulating SARS-CoV-2 variants, including the three Variants of Concern (VOCs) 20I/501Y.V1 (United Kingdom), 20H/501Y.V2 (South Africa), and 20 J/501Y.V3 (Brazil), as well as the 20E.EU1 variant (Spain), the CAL.20C recently identified in California, and the mink-associated variant (GR, lineage B.1.1.298). Prior to application to field samples, the discriminatory potential of this PCR assay was explored using GISAID and Nextclade. To extend variant detection to challenging matrices such as sewage, where the amplification of long fragments is problematic, two short nested RT-PCR assays (~300 bps) were also designed, targeting portions of the region spanned by the long nested assay. The three newly-designed assays were then tested on field samples, including 31 clinical samples (7 fully-sequenced swab samples, and 24 uncharacterized ones) and 34 urban wastewater samples, some of which collected in areas where circulation of VOCs had been reported. The long assay successfully amplified 29 of the 31 swabs (93%), allowing the correct identification of variants 20I/501Y.V1 and 20E.EU1 present in the panel of previously characterized samples. The Spanish variant was detected in 14/24 of the uncharacterized samples as well. The sequences obtained using the short assays were consistent with those obtained with the long assay. Mutations characteristic of VOCs (UK and Brazilian variant) and of other variant (Spanish) were detected in sewage samples. To our knowledge, this is the first evidence of the presence of sequences harboring key mutations of 20I/501Y.V1 and 20 J/501Y.V3 in urban wastewaters, highlighting the potential contribution of wastewater surveillance to explore SARS-CoV-2 diversity. The developed nested RT-PCR assays can be used as an initial rapid screening test to select clinical samples containing mutations of interest. This can speed up diagnosis and optimize resources since it allows full genome sequencing to be done only on clinically relevant specimens. The assays can be also employed for a rapid and cost-effective detection of VOCs or other variants in sewage for the purposes of wastewater-based epidemiology. The approach proposed here can be used to better understand SARS-CoV-2 variant diversity, geographic distribution and impact worldwide.

Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of the coronavirus disease 2019 (COVID-19), has been identified in China in late December 2019. SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA betacoronavirus of the Coronaviridae family. Coronaviruses have genetic proofreading mechanism that corrects copying mistakes and thus SARS-CoV-2 genetic diversity is extremely low. Despite lower mutation rate of the virus, researchers have detected a total of 12,706 mutations in the SARS-CoV-2 genome, the majority of which were single nucleotide polymorphisms. Sequencing data revealed that the SARS-CoV-2 accumulates two-single nucleotide mutations per month in its genome. Recently, an amino acid aspartate (D) to glycine (G) (D614G) mutation due to an adenine to guanine nucleotide change at position 23,403 at the 614th amino-acid position of the spike protein in the original reference genotype has been identified. The SARS-CoV-2 viruses that carry the spike protein D614G mutation have become dominant variant around the world. The D614G mutation has been found to be associated with 3 other mutations in the spike protein. Clinical and pseudovirus experimental studies have demonstrated that the spike protein D614G mutation alters the virus phenotype. However, the impact of the mutation on the rate of transmission between people, disease severity and the vaccine and therapeutic development remains unclear. Three variants of SARS-CoV-2 have recently been identified. They are B.1.1.7 (UK) variant, B.1.351 (N501Y.V2, South African) variant and B.1.1.28 (Brazilian) variant. Epidemiological data suggest that they have a higher transmissibility than the original variant. There are reports that some vaccines are less efficacious against the B.1.351 variant. This review article discusses the effects of novel mutations in the SARS-CoV-2 genome on transmission, clinical outcomes and vaccine development.

Impact of Ribosome Activity on SARS-CoV-2 LNP - Based mRNA Vaccines

Coronavirus-related Severe Acute Respiratory Syndrome-2 (SARS-CoV-2) initially was detected in Wuhan, Hubei, China. Since early 2021, World Health Organization (WHO) has declared Coronavirus Disease 2019 (COVID-19) a pandemic due to rapidly transformed to a globally massive catastrophic viral infection. In order to confront this emergency situation, many pharmaceutical companies focused on the design and development of efficient vaccines that are considered necessary for providing a level of normalization in totally affected human social-economical activity worldwide. A variety of vaccine types are under development, validation or even some of them have already completed these stages, initially approved as conditional marketing authorisation by Food and Drug Administration (FDA), European Medicines Agency (EMA), and other national health authorities for commercial purposes (in vivo use in general population), accelerating their production and distribution process. Innovative nucleoside-modified viral messenger RNA (v-mRNA)-based vaccines encapsulated within nanoparticles-specifically lipid ones (LNPs)-are now well recognized. Although this is a promising genetic engineering topic in the field of nanopharmacogenomics or targeted nucleic vaccines, there are limited but continuously enriched in vivo data in depth of time regarding their safety, efficacy, and immune response. In the current paper we expand the limited published data in the field of ribosome machinery and SARS-CoV-2 mRNA fragment vaccines interaction by describing their functional specialization and modifications. Additionally, alterations in post-transcriptional/translational molecules and mechanisms that could potentially affect the interaction between target cells and vaccines are also presented. Understanding these mechanisms is a crucial step for the next generation v-mRNA vaccines development.

Decision support for the quickest detection of critical COVID-19 phases

During the course of an epidemic, one of the most challenging tasks for authorities is to decide what kind of restrictive measures to introduce and when these should be enforced. In order to take informed decisions in a fully rational manner, the onset of a critical regime, characterized by an exponential growth of the contagion, must be identified as quickly as possible. Providing rigorous quantitative tools to detect such an onset represents an important contribution from the scientific community to proactively support the political decision makers. In this paper, leveraging the quickest detection theory, we propose a mathematical model of the COVID-19 pandemic evolution and develop decision tools to rapidly detect the passage from a controlled regime to a critical one. A new sequential test-referred to as MAST (mean-agnostic sequential test)-is presented, and demonstrated on publicly available COVID-19 infection data from different countries. Then, the performance of MAST is investigated for the second pandemic wave, showing an effective trade-off between average decision delay [Formula: see text] and risk [Formula: see text], where [Formula: see text] is inversely proportional to the time required to declare the need to take unnecessary restrictive measures. To quantify risk, in this paper we adopt as its proxy the average occurrence rate of false alarms, in that a false alarm risks unnecessary social and economic disruption. Ideally, the decision mechanism should react as quick as possible for a given level of risk. We find that all the countries share the same behaviour in terms of quickest detection, specifically the risk scales exponentially with the delay, [Formula: see text], where [Formula: see text] depends on the specific nation. For a reasonably small risk level, say, one possibility in ten thousand (i.e., unmotivated implementation of countermeasures every 27 years, on the average), the proposed algorithm detects the onset of the critical regime with delay between a few days to 3 weeks, much earlier than when the exponential growth becomes evident. Strictly from the quickest-detection perspective adopted in this paper, it turns out that countermeasures against the second epidemic wave have not always been taken in a timely manner. The developed tool can be used to support decisions at different geographic scales (regions, cities, local areas, etc.), levels of risk, instantiations of controlled/critical regime, and is general enough to be applied to different pandemic time-series. Additional analysis and applications of MAST are made available on a dedicated website.

Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes

The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands unprecedented attention. We report four X-ray crystal structures of three synthetic nanobodies (sybodies) (Sb16, Sb45 and Sb68) bind to the receptor-binding domain (RBD) of SARS-CoV-2: binary complexes of Sb16-RBD and Sb45-RBD; a ternary complex of Sb45-RBD-Sb68; and Sb16 unliganded. Sb16 and Sb45 bind the RBD at the ACE2 interface, positioning their CDR2 and CDR3 loops diametrically. Sb16 reveals a large CDR2 shift when binding the RBD. Sb68 interacts peripherally at the ACE2 interface; steric clashes with glycans explain its mechanism of viral neutralization. Superposing these structures onto trimeric spike (S) protein models indicates these sybodies bind conformations of the mature S protein differently, which may aid therapeutic design.

ONE SENTENCE SUMMARY

X-ray structures of synthetic nanobodies complexed with the receptor-binding domain of the spike protein of SARS-CoV-2 reveal details of CDR loop interactions in recognition of distinct epitopic sites.

COVID-19 in Children With Liver Disease

Background: The global pandemic caused by novel Coronavirus SARS-CoV-2 disease (COVID-19) is a major threat to the general population and for patients with pre-existing chronic conditions. We report data concerning SARS-CoV-2 infection in children with chronic liver disease (CLD). Methods: A literature review using the online database PubMed was performed to summarize available findings on the association between pre-existing liver disease and COVID-19 infection in children. Results: Children with COVID-19 have preserved effector and immunosuppressive components resulting in a milder disease compared to adults. The most common hepatic manifestation is an elevation of hepatic transaminases. Liver damage may be directly caused by viral infection of liver cells, by medications or by the chronic hypoxia seen in COVID-19 patients. A multicenter study reported that the majority of children with a CLD remained healthy during the outbreak. Similarly, studies reported that children on immunosuppressive treatment, including patients with autoimmune liver disease (AILD) and liver transplantation (LT), maintained good health during the outbreak without experiencing major complications even if infected with COVID-19. Conclusion: COVID-19-related liver injury presents with a mild elevation of transaminases, although its clinical significance is unclear. Children with CLD, including those with AILD and post-LT, do not have an increased risk for severe disease course of SARS-CoV-2 infection with little or no liver dysfunction. These data highlight the necessity to ensure normal standards of care while adhering to national Covid-19 guidelines, and particularly to maintain immunosuppressive medication to prevent relapse or rejection. Further research is required to evaluate the differences in clinical course between immunosuppressed adults and children and in particular whether asymptomatic infection is a concern.