Vaccine efficacy probable against COVID-19 variants

Research progress in Fc-effector functions against SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused more than 676 million cases in the global human population with approximately 7 million deaths and vaccination has been proved as the most effective countermeasure in reducing clinical complications and mortality rate of SARS-CoV-2 infection in people. However, the protective elements and correlation of protection induced by vaccination are still not completely understood. Various antibodies with multiple protective mechanisms can be induced simultaneously by vaccination in vivo, thereby complicating the identification and characterization of individual correlate of protection. Recently, an increasing body of observations suggests that antibody-induced Fc-effector functions play a crucial role in combating SARS-CoV-2 infections, including neutralizing antibodies-escaping variants. Here, we review the recent progress in understanding the impact of Fc-effector functions in broadly disarming SARS-CoV-2 infectivity and discuss various efforts in harnessing this conserved antibody function to develop an effective SARS-CoV-2 vaccine that can protect humans against infections by SARS-CoV-2 virus and its variants of concern.

Dynamics of temporal immune responses in nonhuman primates and humans immunized with COVID-19 vaccines

We assessed the humoral immune responses to a COVID-19 vaccine in a well-controlled rhesus macaque model compared to humans immunized with two mRNA vaccines over several months post-second dose. The plasma IgG levels against seven coronaviruses (including SARS-CoV-2) and antibody subtypes (IgG 1-4 and IgM) against SARS-CoV-2 were evaluated using multiplex assays. The neutralization capacity of plasma antibodies against the original SAR-CoV-2 isolate and nine variants was evaluated in vaccinated humans and non-human primates. Immunization of macaques and humans with SARS-CoV-2 vaccines induced a robust neutralizing antibody response. In non-SIV-infected adult macaques immunized with an adenoviral vector expressing S-RBD (n = 7) or N protein (n = 3), elevated levels of IgG and neutralizing antibodies were detected 2 weeks post-second dose. Immune responses to the S-RBD vaccine in SIV-infected adult macaques (n = 2) were similar to the non-SIV-infected animals. Adult humans immunized with Pfizer (n = 35) or Moderna (n = 18) vaccines developed IgG and neutralizing antibodies at 4 weeks post-second dose. In both vaccine groups, IgG 1 was the predominant subtype, followed by IgG 3. The IgG levels, including total and IgG 1,2,3 elicited by the Moderna vaccine, were significantly higher than the corresponding levels elicited by the Pfizer vaccine at 4 weeks post-second dose. A significant correlation was observed between the plasma total IgG antibody levels and neutralization titers in both macaques and humans. Furthermore, broad-spectrum neutralization antibodies against several variants of SARS-CoV-2 were detected in the plasma of both macaques and humans after two vaccinations.

COVID-19 in early 2023: Structure, replication mechanism, variants of SARS-CoV-2, diagnostic tests, and vaccine & drug development studies

Coronavirus Disease-19 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome-coronaviruses-2 (SARS-CoV-2), a highly pathogenic and transmissible coronavirus. Most cases of COVID-19 have mild to moderate symptoms, including cough, fever, myalgias, and headache. On the other hand, this coronavirus can lead to severe complications and death in some cases. Therefore, vaccination is the most effective tool to prevent and eradicate COVID-19 disease. Also, rapid and effective diagnostic tests are critical in identifying cases of COVID-19. The COVID-19 pandemic has a dynamic structure on the agenda and contains up-to-date developments. This article has comprehensively discussed the most up-to-date pandemic situation since it first appeared. For the first time, not only the structure, replication mechanism, and variants of SARS-CoV-2 (Alpha, Beta, Gamma, Omicron, Delta, Epsilon, Kappa, Mu, Eta, Zeta, Theta, lota, Lambda) but also all the details of the pandemic, such as how it came out, how it spread, current cases, what precautions should be taken, prevention strategies, the vaccines produced, the tests developed, and the drugs used are reviewed in every aspect. Herein, the comparison of diagnostic tests for SARS-CoV-2 in terms of procedure, accuracy, cost, and time has been presented. The mechanism, safety, efficacy, and effectiveness of COVID-19 vaccines against SARS-CoV-2 variants have been evaluated. Drug studies, therapeutic targets, various immunomodulators, and antiviral molecules applied to patients with COVID-19 have been reviewed.

Influence of COVID-19 on air travel - A scenario study toward future trusted aviation

This paper develops three scenarios for the aviation industry's recovery from COVID-19 until 2030 by utilizing the scenario methodology. Besides the short- and mid-term pandemic development, the study takes into account the industry's adaptation to changes in the market environment, e.g., toward sustainability and hygiene requirements. The resulting scenarios include the expected point in time of full air traffic recovery to pre-crisis levels. Subsequent implications suggest that most COVID-19-related hygiene measures along the travel chain disappear after the pandemic is contained. Some measures might serve as a differentiator between airline business models, while others are expected to become a new standard. Implications for environmental awareness and resulting operational and technical measures include changes in society's attitude toward traveling post-pandemic, especially in light of varying levels of environmental awareness. The presented scenarios help to identify the range of plausible development paths, thus building the basis for future model-based research.

Continued disruptions in health care services and mental health among health care providers during the COVID-19 pandemic in five sub-Saharan African countries

Background

Continuous monitoring of the pandemic's impact on health service provision and mental health, COVID-19 perceptions, and compliance with prevention measures among health care providers (HCPs) can help with mitigating the pandemic's negative effects.

Methods

A computer-assisted telephone interviewing (CATI) survey was conducted among 1499 HCPs in Burkina Faso (Ouagadougou), Ethiopia (Addis Ababa), Nigeria (Lagos and Ibadan), Tanzania (Dar es Salaam), and Ghana (Kintampo). Self-reported mental health, perceptions of the COVID-19 pandemic, and prevention measures available in the workplace were assessed. HCPs' responses to questions regarding the impact of COVID-19 on nine essential health services were summed into a score; high service disruption was defined as a score higher than the total average score across all sites. Modified Poisson regression was used to identify potential factors related to high service disruption.

Results

Overall, 26.9% of HCPs reported high service disruption, with considerable differences across sites (from 1.6% in Dar es Salaam to 45.0% in Addis Ababa). A considerable proportion of HCPs reported experiencing mild psychological distress (9.4%), anxiety (8.0%), and social avoidance or rejection (13.9%) due to their profession. Participants in Addis Ababa (absolute risk ratio (ARR) = 2.10; 95% confidence interval (CI) = 1.59-2.74), Lagos (ARR = 1.65; 95% CI = 1.24-2.17), and Kintampo (ARR = 2.61; 95% CI = 1.94-3.52) had a higher likelihood of reporting high service disruption compared to those in Ouagadougou. Reporting ever-testing for COVID-19 (ARR = 0.82; 95% CI = 0.69-0.97) and the presence of COVID-19 guidelines in the workplace (ARR = 0.63; 95% CI = 0.53-0.77) were both associated with lower reported health service disruption among HCPs.

Conclusion

The COVID-19 pandemic continues to disrupt essential health services and present a challenge to HCPs' mental health, with important differences across countries and settings; interventions are needed to mitigate these negative effects of the pandemic.

RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis

An important unmet need revealed by the COVID-19 pandemic is the near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available to detect and characterize patterns of natural selection within modestly sized gene-sequence datasets, the computational complexity of these methods and their sensitivity to sequencing errors render them effectively inapplicable in large-scale genomic surveillance contexts. Motivated by the need to analyze new lineage evolution in near-real time using large numbers of genomes, we developed the Rapid Assessment of Selection within CLades (RASCL) pipeline. RASCL applies state of the art phylogenetic comparative methods to evaluate selective processes acting at individual codon sites and across whole genes. RASCL is scalable and produces automatically updated regular lineage-specific selection analysis reports: even for lineages that include tens or hundreds of thousands of sampled genome sequences. Key to this performance is (i) generation of automatically subsampled high quality datasets of gene/ORF sequences drawn from a selected "query" viral lineage; (ii) contextualization of these query sequences in codon alignments that include high-quality "background" sequences representative of global SARS-CoV-2 diversity; and (iii) the extensive parallelization of a suite of computationally intensive selection analysis tests. Within hours of being deployed to analyze a novel rapidly growing lineage of interest, RASCL will begin yielding JavaScript Object Notation (JSON)-formatted reports that can be either imported into third-party analysis software or explored in standard web-browsers using the premade RASCL interactive data visualization dashboard. By enabling the rapid detection of genome sites evolving under different selective regimes, RASCL is well-suited for near-real-time monitoring of the population-level selective processes that will likely underlie the emergence of future variants of concern in measurably evolving pathogens with extensive genomic surveillance.

Fabrication of efficient protein imprinted materials based on pearl necklace-like MOFs bacterial cellulose composites

The acquisition of efficient protein isolation substances is vital for proteomic research, whereas it's still challenging nowadays. Herein, an elaborately designed protein imprinted material based on a bacterial cellulose@ZIF-67 composite carrier (BC@ZIF-67) is proposed for the first time. In particular, due to the ultrafine fiber diameter and abundant hydroxyl functional groups of the bacterial cellulose, BC@ZIF-67 presented a compact arrangement structure similar to a pearl necklace, which greatly promoted template immobilization and mass transfer resistance in protein imprinting technology. Therefore, the protein-imprinted material (BC@ZIF-67@MIPs) fabricated by surface imprinting technology and template immobilization strategy could exhibit ultrahigh adsorption capacity (1017.0 mg g^-1), excellent recognition (IF = 5.98) and rapid adsorption equilibrium time (50 min). In addition, based on the experiment outcomes, our team employed BC@ZIF-67@MIPs to enrich template protein in blended protein solutions and biosamples, identifying them as underlying candidates for isolating and purifying proteins.

Comprehensive Highlights of the Universal Efforts towards the Development of COVID-19 Vaccine

The world has taken proactive measures to combat the pandemic since the coronavirus disease 2019 (COVID-19) outbreak, which was caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). These measures range from increasing the production of personal protective equipment (PPE) and highlighting the value of social distancing to the emergency use authorization (EUA) of therapeutic drugs or antibodies and their appropriate use; nonetheless, the disease is still spreading quickly and is ruining people’s social lives, the economy, and public health. As a result, effective vaccines are critical for bringing the pandemic to an end and restoring normalcy in society. Several potential COVID-19 vaccines are now being researched, developed, tested, and reviewed. Since the end of June 2022, several vaccines have been provisionally approved, whereas others are about to be approved. In the upcoming years, a large number of new medications that are presently undergoing clinical testing are anticipated to hit the market. To illustrate the advantages and disadvantages of their technique, to emphasize the additives and delivery methods used in their creation, and to project potential future growth, this study explores these vaccines and the related research endeavors, including conventional and prospective approaches.

COVID-19 exit strategy during vaccine implementation: a balance between social distancing and herd immunity

Currently, health authorities around the world are struggling to limit the spread of COVID-19. Since the beginning of the pandemic, social distancing has been the most important strategy used by most countries to control disease spread by flattening and elongating the epidemic curve. Another strategy, herd immunity, was also applied by some countries through relaxed control measures that allow the free spread of natural infection to build up solid immunity within the population. In 2021, COVID-19 vaccination was introduced with tremendous effort as a promising strategy for limiting the spread of disease. Therefore, in this review, we present the current knowledge about social distancing, herd immunity strategies, and aspects of their implementation to control the COVID-19 pandemic in the presence of the newly developed vaccines. Finally, we suggest a short-term option for controlling the pandemic during vaccine application.

Perspective Chapter: Tracking Trails of SARS CoV-2 - Variants to Therapy

A virus when replicates itself from one generation to another, tends to change a little bit of its structure. These variations are called mutations. History says that SARS CoV-2 originated from the virus reservoirs of animals, specifically non-human mammals like bats and minks. Since then, there are evolutionary changes in its genome due to recombination in divergent strains of different species. Thus, making the virus more robust and smarter to sustain and evade immune responses in humans. Probably, this has led to the 2019 SARS CoV-2 pandemic. This chapter tracks the evolutionary trails of the virus origin, its pathogenesis in humans, and varying variants with the coming times. Eventually, the chapter overviews the available vaccines and therapies to be followed for SARS CoV-2.

A spatial vaccination strategy to reduce the risk of vaccine-resistant variants

The COVID-19 pandemic demonstrated that the process of global vaccination against a novel virus can be a prolonged one. Social distancing measures, that are initially adopted to control the pandemic, are gradually relaxed as vaccination progresses and population immunity increases. The result is a prolonged period of high disease prevalence combined with a fitness advantage for vaccine-resistant variants, which together lead to a considerably increased probability for vaccine escape. A spatial vaccination strategy is proposed that has the potential to dramatically reduce this risk. Rather than dispersing the vaccination effort evenly throughout a country, distinct geographic regions of the country are sequentially vaccinated, quickly bringing each to effective herd immunity. Regions with high vaccination rates will then have low infection rates and vice versa. Since people primarily interact within their own region, spatial vaccination reduces the number of encounters between infected individuals (the source of mutations) and vaccinated individuals (who facilitate the spread of vaccine-resistant strains). Thus, spatial vaccination may help mitigate the global risk of vaccine-resistant variants.

High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with next generation sequencing

The identification of SARS-CoV-2 variants across the globe and their implications on the outspread of the pandemic, infection potential and resistance to vaccination, requires modification of the current diagnostic methods to map out viral mutations rapidly and reliably. Here, we demonstrate that integrating DNA barcoding technology, sample pooling and Next Generation Sequencing (NGS) provide an applicable solution for large-population viral screening combined with specific variant analysis. Our solution allows high throughput testing by barcoding each sample, followed by pooling of test samples using a multi-step procedure. First, patient-specific barcodes are added to the primers used in a one-step RT-PCR reaction, amplifying three different viral genes and one human housekeeping gene (as internal control). Then, samples are pooled, purified and finally, the generated sequences are read using an Illumina NGS system to identify the positive samples with a sensitivity of 82.5% and a specificity of 97.3%. Using this solution, we were able to identify six known and one unknown SARS-CoV-2 variants in a screen of 960 samples out of which 258 (27%) were positive for the virus. Thus, our diagnostic solution integrates the benefits of large population and epidemiological screening together with sensitive and specific identification of positive samples including variant analysis at a single nucleotide resolution.

The Emergence of SARS-CoV-2 Variants With a Lower Antibody Response: A Genomic and Clinical Perspective

The emergence of several novel SARS-CoV-2 variants regarded as variants of concern (VOCs) has exacerbated pathogenic and immunologic prominences, as well as reduced diagnostic sensitivity due to phenotype modification-capable mutations. Furthermore, latent and more virulent strains that have arisen as a result of unique mutations with increased evolutionary potential represent a threat to vaccine effectiveness in terms of incoming and existing variants. As a result, resisting natural immunity, which leads to higher reinfection rates, and avoiding vaccination-induced immunization, which leads to a lack of vaccine effectiveness, has become a crucial problem for public health around the world. This study attempts to review the genomic variation and pandemic impact of emerging variations of concern based on clinical characteristics management and immunization effectiveness. The goal of this study is to gain a better understanding of the link between genome level polymorphism, clinical symptom manifestation, and current vaccination in the instance of VOCs.

Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor

The SARS-CoV-2 virus, since its appearance in 2019, has caused millions of cases and deaths. To date, there is no effective treatment or a vaccine that is fully protective. Despite the efforts made by governments and health institutions around the globe to control its propagation, the evolution of the virus has accelerated, diverging into hundreds of variants. However, not all of them are variants of concern (VoC’s). VoC’s have appeared in different regions and throughout the two years of the pandemic they have spread around the world. Specifically, in South America, the gamma variant (previously known as P.1) appeared in early 2021, bringing with it a second wave of infections. This variant contains the N501Y, E484K and K417T mutations in the receptor binding domain (RBD) of the spike protein. Although these mutations have been described experimentally, there is still no clarity regarding their role in the stabilization of the complex with the human angiotensin converting enzyme 2 (hACE-2) receptor. In this article we dissect the influence of mutations on the interaction with the hACE-2 receptor using molecular dynamics and estimations of binding affinity through a screened version of the molecular mechanics Poisson Boltzmann surface area (MM-PBSA) and interaction entropy. Our results indicate that mutations E484K and K417T compensate each other in terms of binding affinity, while the mutation N501Y promotes a more convoluted effect. This effect consists in the adoption of a cis configuration in the backbone of residue Y495 within the RBD, which in turn promotes polar interactions with the hACE-2 receptor. These results not only correlate with experimental observations and complement previous knowledge, but also expose new features associated with the specific contribution of concerned mutations. Additionally, we propose a recipe to assess the residue-specific contribution to the interaction entropy.

Design strategies for antiviral coatings and surfaces: A review☆

The routine disinfection and sanitization of surfaces, objects, and textiles has become a time-consuming but necessary task for managing the COVID-19 pandemic. Nonetheless, the excessive use of sanitizers and disinfectants promotes the development of antibiotic-resistant microbes. Moreover, that improper disinfection could lead to more virus transfer, which leads to more viral mutations. Recently developed antiviral surface coatings can reduce the reliance on traditional disinfectants. These surfaces remain actively antimicrobial between periods of active cleaning of the surfaces, allowing a much more limited and optimized use of disinfectants. The novel nature of these surfaces has led, however, to many inconsistencies within the rapidly growing literature. Here we provide tools to guide the design and development of antimicrobial and antiviral surfaces and coatings. We describe how engineers can best choose testing options and propose new avenues for antiviral testing. After defining testing protocols, we summarize potential inorganic and organic materials able to serve as antiviral surfaces and present their antiviral mechanisms. We discuss the main limitations to their application, including issues related to toxicity, antimicrobial resistance, and environmental concerns. We propose solutions to counter these limitations and highlight how the context of specific use of an antiviral surface must guide material selection. Finally, we discuss how the use of coatings that combine multiple antimicrobial mechanisms can avoid the development of antibiotic resistance and improve the antiviral properties of these surfaces.

Communication about vaccine efficacy and COVID-19 vaccine choice: Evidence from a survey experiment in the United States

While mass vaccination campaigns against COVID-19 have inoculated almost 200 million Americans and billions more worldwide, significant pockets of vaccine hesitancy remain. Research has firmly established that vaccine efficacy is an important driver of public vaccine acceptance and choice. However, current vaccines offer widely varying levels of protection against different adverse health outcomes of COVID-19. This study employs an experiment embedded on a survey of 1,194 US adults in June 2021 to examine how communications about vaccine efficacy affect vaccine choice. The experiment manipulated how vaccine efficacy was defined across four treatments: (1) protection against symptomatic infection; (2) protection against severe illness; (3) protection against hospitalization/death; (4) efficacy data on all three metrics. The control group received no efficacy information. Subjects were asked to choose between a pair of vaccines-a one-dose viral vector vaccine or two-dose mRNA vaccine-whose efficacy data varied across the four experimental treatment groups. Efficacy data for each vaccine on each dimension were adapted from clinical trial data on the Johnson & Johnson/Janssen and Pfizer/BioNTech vaccines. Among all respondents, only modest preference gaps between the two vaccines emerged in the control group and when the two vaccines' roughly equivalent efficacy data against hospitalization and death were reported. Strong preferences for a two-dose mRNA vaccine emerged in treatments where its higher efficacy against symptomatic or severe illness was reported, as well as in the treatment where data on all three efficacy criteria were reported. Unvaccinated respondents preferred a one-dose viral vector vaccine when only efficacy data against hospitalization or death was presented. Black and Latino respondents were significantly more likely to choose the one-shot viral vector vaccine in the combined efficacy treatment than were whites. Results speak to the importance of understanding how communications about vaccine efficacy affect public preferences in an era of increasing uncertainty about efficacy against variants.

Comparison of analytical sensitivity and efficiency for SARS-CoV-2 primer sets by TaqMan-based and SYBR Green-based RT-qPCR

The pandemic of coronavirus disease 2019 (COVID-19) continues to threaten public health. For developing countries where vaccines are still in shortage, cheaper alternative molecular methods for SARS-CoV-2 identification can be crucial to prevent the next wave. Therefore, 14 primer sets recommended by the World Health Organization (WHO) was evaluated on testing both clinical patient and environmental samples with the gold standard diagnosis method, TaqMan-based RT-qPCR, and a cheaper alternative method, SYBR Green-based RT-qPCR. Using suitable primer sets, such as ORF1ab, 2019_nCoV_N1 and 2019_nCoV_N3, the performance of the SYBR Green approach was comparable or better than the TaqMan approach, even when considering the newly dominating or emerging variants, including Delta, Eta, Kappa, Lambda, Mu, and Omicron. ORF1ab and 2019_nCoV_N3 were the best combination for sensitive and reliable SARS-CoV-2 molecular diagnostics due to their high sensitivity, specificity, and broad accessibility. KEY POINTS: • With suitable primer sets, the SYBR Green method performs better than the TaqMan one. • With suitable primer sets, both methods should still detect the new variants well. • ORF1ab and 2019_nCoV_N3 were the best combination for SARS-CoV-2 detection.

Evolution of resistance to COVID-19 vaccination with dynamic social distancing

The greatest hope for a return to normalcy following the COVID-19 pandemic is worldwide vaccination. Yet, a relaxation of social distancing that allows increased transmissibility, coupled with selection pressure due to vaccination, will probably lead to the emergence of vaccine resistance. We analyse the evolutionary dynamics of COVID-19 in the presence of dynamic contact reduction and in response to vaccination. We use infection and vaccination data from six different countries. We show that under slow vaccination, resistance is very likely to appear even if social distancing is maintained. Under fast vaccination, the emergence of mutants can be prevented if social distancing is maintained during vaccination. We analyse multiple human factors that affect the evolutionary potential of the virus, including the extent of dynamic social distancing, vaccination campaigns, vaccine design, boosters and vaccine hesitancy. We provide guidelines for policies that aim to minimize the probability of emergence of vaccine-resistant variants.

RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis

An important component of efforts to manage the ongoing COVID19 pandemic is the R apid A ssessment of how natural selection contributes to the emergence and proliferation of potentially dangerous S ARS-CoV-2 lineages and CL ades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations.

AVAILABILITY

RASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl . Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl .

CONTACT

Dr. Sergei L Kosakovsky Pond ( spond@temple.edu ).

SUPPLEMENTARY INFORMATION

N/A.

Diverse vaccine platforms safeguarding against SARS-CoV-2 and its variants

INTRODUCTION

Appearances of SARS-CoV-2 variants have created havoc and additional challenges for the ongoing vaccination drive against pandemic COVID-19. Interestingly, several vaccine platforms are showing great potential to produce successful vaccines against SARS-CoV-2 and its variants. Billions of COVID-19 vaccine doses have been administered worldwide. Mix-and-Match COVID-19 vaccines involving the mixing of the same platform vaccines and also two different vaccine platforms may provide greater protection against SARS-CoV-2 and its variants. COVID-19 vaccines have become one of the most important tools to mitigate the ongoing pandemic COVID-19.

AREAS COVERED

We describe SARS-Cov-2 variants, their impact on the population, COVID-19 vaccines, diverse vaccine platforms, doses of vaccines, the efficacy of vaccines against SARS-CoV-2 and its variants, mitigation of the COVID-19 transmission- alternatives to vaccines.

EXPERT OPINION

Diverse vaccine platforms may safeguard against ongoing, deadly SARS-CoV-2 and its infectious variants. The efficacies of COVID-19 vaccines are significantly high after the administration of the second dose. Further, it protects individuals including vulnerable patients with co-morbidities from SARS-CoV-2 and its variants. The hospitalizations and deaths of the individuals may be prevented by COVID-19 vaccines.

Pathogenesis and treatment of cytokine storm in COVID-19

COVID-19 is a viral infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that killed a large number of patients around the world. A hyperinflammatory state resulting in a cytokine storm and adult respiratory distress syndrome seems to be the major cause of the death. Many mechanisms have been suggested in the pathogenesis of COVID-19 associated cytokine storm (COVID-CS). Insufficient viral clearance and persistence of a strong cytokine response despite inadequate antiviral immunity seem to be the main mechanisms underlying the pathogenesis. The diagnosis of COVID-19 is based on relatively constant clinical symptoms, clinical findings, laboratory tests, and imaging techniques, while the diagnosis of COVID-CS is a rather dynamic process, based on evolving or newly emerging findings during the clinical course. Management of COVID-19 consists of using antiviral agents to inhibit SARS-CoV-2 replication and treating potential complications including the cytokine storm together with general supportive measures. COVID-CS may be treated using appropriate immunosuppressive and immunomodulatory drugs that reduce the level of inappropriate systemic inflammation, which has the potential to cause organ damage. Currently corticosteroids, IL-6 blockers, or IL-1 blockers are most widely used for treating COVID-CS.

Differential Antibody Response to mRNA COVID-19 Vaccines in Healthy Subjects

Knowledge about development and duration of virus-specific antibodies after COVID-19 vaccination is important for understanding how to limit the pandemic via vaccination in different populations and societies. However, the clinical utility of postvaccination testing of antibody response and selection of targeted SARS-CoV-2 antigen(s) has not been established. The results of such testing from clinical teams independent from vaccine manufacturers are also limited. Here, we report the initial results of an ongoing clinical study on evaluation of antibody response to four different SARS-CoV-2 antigens after first and second dose of Pfizer and Moderna mRNA vaccines and at later time points. We revealed a peak of antibody induction after the vaccine boosting dose with a gradual decline of antibody levels at later time. Anti-nucleocapsid antibody was not induced by spike protein-encoding vaccines and this may continue to serve as a marker of previous SARS-CoV-2 infection. No differences between the two vaccines in terms of antibody response were revealed. Age and gender dependencies were determined to be minimal within the healthy adult (but not aged) population. Our results suggest that postvaccination testing of antibody response is an important and feasible tool for following people after vaccination and selecting individuals who might require a third dose of vaccine at an earlier time point or persons who may not need a second dose due to previous SARS-CoV-2 infection. IMPORTANCE Now that authorized vaccines for COVID-19 have been widely used, it is important to understand how they induce antivirus antibodies, which antigens are targeted, how long antibodies circulate, and how personal health conditions and age may affect this humoral immunity. Here, we report induction and time course of multiple anti-SARS-CoV-2 antibody responses in healthy individuals immunized with Pfizer and Moderna mRNA vaccines. We also determined the age and gender dependence of the antibody response and compared antibody levels to responses seen in those who have recovered from COVID-19. Our results suggest the importance of screening for antibody response to multiple antigens after vaccination in order to reveal individuals who require early and late additional boosting and those who may not need second dose due to prior SARS-CoV-2 infection.

Effectiveness of Pulmonary Rehabilitation in Severe and Critically Ill COVID-19 Patients: A Controlled Study

Background: Severe and critically ill COVID-19 patients frequently need pulmonary rehabilitation (PR) after hospitalization. However, little is known about the effectiveness of PR in COVID-19 patients. Methods: We compared the performances in the six-min walk test (6MWT), chronic respiratory questionnaire (CRQ), and Functional Independence Measure (FIM) from inpatient PR between 51 COVID-19 patients and 51 other patients with common pneumonia. We used multivariate linear regression controlled for baseline values at entrance, age, sex, and cumulative illness rating scale. The odds ratios (ORs) of non-improvement/improvement in 6MWT (>30-m) and CRQ (>10-point) at discharge were compared between the two groups (Fisher’s exact test). Results: The two groups had similar improvements in 6MWT and CRQ, but the COVID-19 group achieved a 4-point higher FIM (p-value = 0.004). The OR of non-improvement/improvement in 6MWT was 0.30 (p-value = 0.13) between COVID-19 and controls; however, the odds of non-improvement in CRQ tended to be 3.02 times higher (p-value = 0.075) in COVID-19 patients. Severe and critical COVID-19 patients had similar rehabilitation outcomes. Conclusions: Inpatient PR can effectively improve physical functions and life quality in COVID-19 patients, irrespective of disease severity. Whether the relatively low gains in CRQ is an indicator of chronic disease development in COVID-19 patients needs further studies.

Nebulised Isotonic Hydroxychloroquine Aerosols for Potential Treatment of COVID-19

The coronavirus disease 2019 (COVID-19) is an unprecedented pandemic that has severely impacted global public health and the economy. Hydroxychloroquine administered orally to COVID-19 patients was ineffective, but its antiviral and anti-inflammatory actions were observed in vitro. The lack of efficacy in vivo could be due to the inefficiency of the oral route in attaining high drug concentration in the lungs. Delivering hydroxychloroquine by inhalation may be a promising alternative for direct targeting with minimal systemic exposure. This paper reports on the characterisation of isotonic, pH-neutral hydroxychloroquine sulphate (HCQS) solutions for nebulisation for COVID-19. They can be prepared, sterilised, and nebulised for testing as an investigational new drug for treating this infection. The 20, 50, and 100 mg/mL HCQS solutions were stable for at least 15 days without refrigeration when stored in darkness. They were atomised from Aerogen Solo Ultra vibrating mesh nebulisers (1 mL of each of the three concentrations and, in addition, 1.5 mL of 100 mg/mL) to form droplets having a median volumetric diameter of 4.3-5.2 µm, with about 50-60% of the aerosol by volume < 5 µm. The aerosol droplet size decreased (from 4.95 to 4.34 µm) with increasing drug concentration (from 20 to 100 mg/mL). As the drug concentration and liquid volume increased, the nebulisation duration increased from 3 to 11 min. The emitted doses ranged from 9.1 to 75.9 mg, depending on the concentration and volume nebulised. The HCQS solutions appear suitable for preclinical and clinical studies for potential COVID-19 treatment.

Key Considerations for the Development of Safe and Effective SARS-CoV-2 Subunit Vaccine: A Peptide-Based Vaccine Alternative

COVID-19 is disastrous to global health and the economy. SARS-CoV-2 infection exhibits similar clinical symptoms and immunopathological sequelae to SARS-CoV infection. Therefore, much of the developmental progress on SARS-CoV vaccines can be utilized for the development of SARS-CoV-2 vaccines. Careful antigen selection during development is always of utmost importance for the production of effective vaccines that do not compromise recipient safety. This holds especially true for SARS-CoV vaccines, as several immunopathological disorders are associated with the activity of structural and nonstructural proteins encoded in the virus's genetic material. Whole viral protein and RNA-encoding full-length proteins contain both protective and "dangerous" sequences, unless pathological fragments are deleted. In light of recent advances, peptide vaccines may present a very safe and effective alternative. Peptide vaccines can avoid immunopathological pro-inflammatory sequences, focus immune responses on neutralizing immunogenic epitopes, avoid off-target antigen loss, combine antigens with different protective roles or mechanisms, even from different viral proteins, and avoid mutant escape by employing highly conserved cryptic epitopes. In this review, an attempt is made to exploit the similarities between SARS-CoV and SARS-CoV-2 in vaccine antigen screening, with particular attention to the pathological and immunogenic properties of SARS proteins.

A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses

While the standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered 3 weeks apart, some public health authorities are spacing these doses, raising concerns about efficacy. However, data indicate that a single dose can be up to 90% effective starting 14 days post-administration. To assess the mechanisms contributing to protection, we analyzed humoral and T cell responses three weeks after a single BNT162b2 dose. We observed weak neutralizing activity elicited in SARS-CoV-2 naive individuals but strong anti-receptor binding domain and spike antibodies with Fc-mediated effector functions and cellular CD4+ T cell responses. In previously infected individuals, a single dose boosted all humoral and T cell responses, with strong correlations between T helper and antibody immunity. Our results highlight the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support for spacing doses to vaccinate more individuals in conditions of vaccine scarcity.

The variants question: What is the problem?

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China in early December 2019 has rapidly widespread worldwide. Over the course of the pandemic, due to the advance of whole-genome sequencing technologies, an unprecedented number of genomes have been generated, providing both invaluable insights into the ongoing evolution and epidemiology of the virus and allowing the identification of hundreds of circulating genetic variants during the pandemic. In recent months variants of SARS-CoV-2 that have an increased number of mutations on the Spike protein have brought concern all over the world. These have been called "variants of concerns" (VOCs), and/or "variants of interests" (VOIs) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. Tracking the spread of emerging SARS-CoV-2 variants is crucial to inform public health efforts and control the ongoing pandemic. In this review, a concise characterization of the SARS-CoV-2 mutational patterns of the main VOCs and VOIs circulating and cocirculating worldwide has been presented to determine the magnitude of the SARS-CoV-2 threat to better understand the virus genetic diversity and its potential impact on vaccination strategy.

Influence of 25-hydroxy-cholecalciferol levels on SARS-CoV-2 infection and COVID-19 severity: A systematic review and meta-analysis

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease 19 (COVID-19), a respiratory infection that, starting from December 2019, has spread around the world in a few months, becoming a pandemic. The lack of initial knowledge on its management has led to a great effort in developing vaccines and in finding therapeutic weapons capable of improving the clinical outcome of the affected patients. In particular, the possible role of vitamin D status in the management of COVID-19 has been widely analysed, resulting in a great amount of data. This systematic review and meta-analysis aimed to assess whether hypovitaminosis D is a risk factor for developing SARS-CoV-2 infection and whether it affects the worsening of the clinical course of COVID-19.

METHODS

Data were extracted through extensive searches in the Pubmed, MEDLINE, Cochrane, Academic One Files, Google Scholar, and Scopus databases from December 2019 to January 2021, using the keywords: "Vitamin D", "25 hydroxy Vitamin D", "25 hydroxycholecalciferol", "cholecalciferol", "COVID 19″, "SARS-CoV-2″. We included observational cohort, cross-sectional, and case-control studies that evaluated differences in serum levels of 25‑hydroxy-cholecalciferol [25(OH)D] in patients who were positive or negative for SARS-CoV-2, in patients with mild or severe forms of COVID-19, and in patients who died or were discharged from the hospital. Finally, studies that evaluated the risk of developing severe illness or death in patients with vitamin D deficiency (VDD), defined as levels of 25(OH)D <20 ng/ml, were also included. We calculated the mean difference (MD) and the 95% confidence intervals (CI) for quantitative variables such as 25(OH)D levels in patients with or without SARS-CoV-2 infection, in those with mild vs. severe COVID-19, or those who have died vs. those who have been discharged. Instead, we calculated odds ratios and 95% CI for qualitative ones, such as the number of patients with severe illness/death in the presence of VDD vs. those with normal serum 25(OH)D levels. A p-value lower than 0.05 was considered statistically significant. The study was registered on PROSPERO (CRD42021241473).

FINDINGS

Out of 662 records, 30 articles met inclusion criteria and, therefore, were included in the meta-analysis. We found that the serum levels of 25(OH)D were significantly lower in patients with SARS-CoV-2 infection than in negative ones [MD -3.99 (-5.34, -2.64); p <0.00001; I2= 95%]. Furthermore, its levels were significantly lower in patients with severe disease [MD -6.88 (-9.74, -4.03); p <0.00001; I2=98%] and in those who died of COVID-19 [MD -8.01 (-12.50, -3.51); p = 0.0005; I2=86%]. Finally, patients with VDD had an increased risk of developing severe disease [OR 4.58 (2.24, 9.35); p <0.0001; I2=84%] but not a fatal outcome [OR 4.92 (0.83, 29.31); p = 0.08; I2=94%].

INTERPRETATION

This meta-analysis revealed a large heterogeneity of the studies included due to the different enrolment criteria of patient samples (age, body mass index, ethnicity, comorbidities), the country where they live, all factors influencing serum 25(OH)D levels, and the different criteria used to define the severity of COVID-19. Furthermore, the observational nature of these studies does not allow to establish a cause-effect relationship, even taking into account that 25(OH)D represents a marker of acute inflammation. Treatment with vitamin D might be considered for the primary prevention of SARS-CoV-2 infection and the management of patients with COVID-19. However, further intervention studies are needed to prove this hypothesis.

Discovery and in-vitro evaluation of potent SARS-CoV-2 entry inhibitors

SARS-CoV-2 infection initiates with the attachment of spike protein to the ACE2 receptor. While vaccines have been developed, no SARS-CoV-2 specific small molecule inhibitors have been approved. Herein, utilizing the crystal structure of the ACE2/Spike receptor binding domain (S-RBD) complex in computer-aided drug design (CADD) approach, we docked ∼8 million compounds within the pockets residing at S-RBD/ACE2 interface. Five best hits depending on the docking score, were selected and tested for their in vitro efficacy to block SARS-CoV-2 replication. Of these, two compounds (MU-UNMC-1 and MU-UNMC-2) blocked SARS-CoV-2 replication at sub-micromolar IC ₅₀ in human bronchial epithelial cells (UNCN1T) and Vero cells. Furthermore, MU-UNMC-2 was highly potent in blocking the virus entry by using pseudoviral particles expressing SARS-CoV-2 spike. Finally, we found that MU-UNMC-2 is highly synergistic with remdesivir (RDV), suggesting that minimal amounts are needed when used in combination with RDV, and has the potential to develop as a potential entry inhibitor for COVID-19.

A single BNT162b2 mRNA dose elicits antibodies with Fc-mediated effector functions and boost pre-existing humoral and T cell responses

The standard dosing of the Pfizer/BioNTech BNT162b2 mRNA vaccine validated in clinical trials includes two doses administered three weeks apart. While the decision by some public health authorities to space the doses because of limiting supply has raised concerns about vaccine efficacy, data indicate that a single dose is up to 90% effective starting 14 days after its administration. We analyzed humoral and T cells responses three weeks after a single dose of this mRNA vaccine. Despite the proven efficacy of the vaccine at this time point, no neutralizing activity were elicited in SARS-CoV-2 naïve individuals. However, we detected strong anti-receptor binding domain (RBD) and Spike antibodies with Fc-mediated effector functions and cellular responses dominated by the CD4 ⁺ T cell component. A single dose of this mRNA vaccine to individuals previously infected by SARS-CoV-2 boosted all humoral and T cell responses measured, with strong correlations between T helper and antibody immunity. Neutralizing responses were increased in both potency and breadth, with distinctive capacity to neutralize emerging variant strains. Our results highlight the importance of vaccinating uninfected and previously-infected individuals and shed new light into the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support to spacing the doses of two-vaccine regimens to vaccinate a larger pool of the population in the context of vaccine scarcity against SARS-CoV-2.