SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Investigation of SARS-CoV-2 IgG Binding Capability to Variants of the SARS-CoV-2 Virus

The SARS-CoV-2 pandemic has confirmed that the ability to rapidly mutate may be extremely beneficial for a virus. Not long after the first wave, new variants emerged with altered infectivity, disease severity, and mortality. These new strains most notably had numerous mutations of the spike (S) protein, a surface protein responsible for binding to and entering the host cell. The Delta and Omicron strains demonstrated increased immune evasion and improved binding affinity to the host cell receptor, angiotensin-converting enzyme 2 (ACE2). This study examines the ability of wild-type SARS-CoV-2 IgG to bind Delta and Omicron antigens, as well as their functional binding capabilities to two different S-ACE2 complexes. Twenty SARS-CoV-2 positive samples from patients who had recovered from infection with ancestral SARS-CoV-2 in the first wave of COVID-19 and 10 pre-pandemic control samples were studied. SARS-CoV-2 exposed patients showed significantly higher levels of IgG to SARS-CoV-2 S1/RBD (p < 0.001), N protein (p < 0.001), and Omicron spike variant (p = 0.01), but not to Delta spike variant (p = 0.966) when compared with controls. Furthermore, patient samples showed significantly greater inhibition of SARS-CoV-2 S1/RBD and E484K spike to ACE2 binding (p < 0.001 and p = 0.015, respectively). Conversely, there was no correlation between the binding inhibition of S1/RBD and E484K spike to ACE2 receptor. This study shows there is considerable cross-reactivity of IgG generated by wild-type SARS-CoV-2 infection to the Delta and Omicron variants.

Sequential Immunization with Vaccines Based on SARS-CoV-2 Virus-like Particles Induces Broadly Neutralizing Antibodies

Although many people have been vaccinated against COVID-19, infections with SARS-CoV-2 seem hard to avoid. There is a need to develop more effective vaccines and immunization strategies against emerging variants of infectious diseases. To understand whether different immunization strategies using variants sequence-based virus-like particles (VLPs) vaccines could offer superior immunity against future SARS-CoV-2 variants, our team constructed VLPs for the original Wuhan-Hu-1 strain (prototype), Delta (δ) variant, and Omicron (ο) variant of SARS-CoV-2, using baculovirus-insect expression system. Then we used these VLPs to assess the immune responses induced by homologous prime-boost, heterologous prime-boost, and sequential immunizations strategies in a mouse model. Our results showed that the pro+δ+ο sequential strategies elicited better neutralizing antibody responses. These sequential strategies also take advantage of inducing CD4+ T and CD8+ T lymphocytes proliferation and tendency to cytokine of Th1. Currently, our data suggest that sequential immunization with VLPs of encoding spike protein derived from SARS-CoV-2 variants of concern may be a potential vaccine strategy against emerging diseases, such as "Disease X".

A live attenuated influenza B virus vaccine expressing RBD elicits protective immunity against SARS-CoV-2 in mice

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to human health globally. It is crucial to develop a vaccine to reduce the effect of the virus on public health, economy, and society and regulate the transmission of SARS-CoV-2. Influenza B virus (IBV) can be used as a vector that does not rely on the current circulating influenza A strains. In this study, we constructed an IBV-based vector vaccine by inserting a receptor-binding domain (RBD) into a non-structural protein 1 (NS1)-truncated gene (rIBV-NS110-RBD). Subsequently, we assessed its safety, immunogenicity, and protective efficacy against SARS-CoV-2 in mice, and observed that it was safe in a mouse model. Intranasal administration of a recombinant rIBV-NS110-RBD vaccine induced high levels of SARS-CoV-2-specific IgA and IgG antibodies and T cell-mediated immunity in mice. Administering two doses of the intranasal rIBV-NS110-RBD vaccine significantly reduced the viral load and lung damage in mice. This novel IBV-based vaccine offers a novel approach for controlling the SARS-CoV-2 pandemic.

Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements

The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.

Understanding the time-driven shifts of vaccine effectiveness against any and severe COVID-19 before and after the surge of Omicron variants within 2.5 years of vaccination: A meta-regression

OBJECTIVES

The COVID-19 pandemic required rapid development of vaccines within a short period of time which did not allow to assess vaccine effectiveness (VE) in the long-term.

METHODS

A computerized literature search was undertaken to identify eligible studies, with no language restrictions, published between 1 December 2020 and 30 June 2023.

RESULTS

Out of a total of 27,597 publications, 761 studies were included. Early VE of 87.2% decreased to 55.1% after 9 months among populations fully immunized not only with mRNA (proxy mRNA) vaccines, and 66.3% decreased to 23.5% in populations immunized exclusively with non-mRNA vaccines. Protection against severe COVID-19 declined to 80.9% for proxy mRNA vaccines and 67.2% for non-mRNA vaccines. Omicron variants significantly diminished VE. Within 6-8 months of receiving a single booster of an mRNA vaccine, VE declined to 14.0% and 67.7% for any and severe COVID-19, respectively. Multiple mRNA booster doses restored protection that declined to 29.5% and 70.6% for any and severe COVID-19, respectively, within 5-7 months.

CONCLUSION

Outcomes of this meta-regression underscore the evolving nature of COVID-19 in response to vaccination, dosing schedules, and emerging variants, and provide crucial insights for public health interventions and vaccination strategies.

Effectiveness of BBV152 vaccine and ChAdOx1-S vaccine in preventing severe disease among vaccinated patients admitted to a designated COVID-19 hospital in India

Purpose

Coronavirus disease 2019 (COVID-19) is a highly formidable disease. Globally, multiple vaccines have been developed to prevent and manage this disease. However, the periodic mutations of severe acute respiratory syndrome coronavirus 2 variants cast doubt on the effectiveness of commonly used vaccines in mitigating severe disease in the Indian population. This study aimed to assess the effectiveness of the BBV152 vaccine and ChAdOx1-S vaccine in preventing severe forms of the disease.

Materials and Methods

This retrospective study, based on hospital records, was conducted on 204 vaccinated COVID-19 patients using a consecutive sampling approach. Data on their vaccination status, comorbidities, and high-resolution computed tomography lung reports' computed tomography severity scores were extracted from their medical records. Fisher's exact test and binomial logistic regression analysis were employed to assess the independent associations of various factors with the dependent variables.

Results

Of the 204 records, 57.9% represented males, with a mean age of 61.5±9.8 years. Both vaccines demonstrated effective protection against severe illness (90.2%), with BBV152 offering slightly better protection compared to ChAdOx1-S. Male gender, partial vaccination, comorbid conditions, and the type of vaccine were identified as independent predictors of severe lung involvement.

Conclusion

This study indicates that both vaccines were highly effective (90%) in preventing severe forms of the disease in fully vaccinated individuals. When comparing the two vaccines, BBV152 was slightly more effective than ChAdOx1-S in preventing severe COVID-19.

The Worrying Phenomenon of COVID-19 Vaccine Hesitancy and Its Negative Impact on Pandemic Control Efforts: Common Themes that Emerged in the Middle East and North Africa (MENA) Region

Since the declaration of coronavirus disease 2019 (COVID-19) as a pandemic, intensive measures were taken to mitigate its negative health, psychological, social, and economic impact. COVID-19 continues to pose serious threats globally, with vaccination as the central safe strategy to control the pandemic. However, COVID-19 vaccine hesitancy is a major concern, especially in the Middle East and North Africa (MENA). Concerns regarding vaccine safety, efficacy, and misinformation contribute to vaccine hesitancy. Addressing these concerns and providing accurate information is crucial for increasing COVID-19 vaccine acceptance and uptake in this region, where the coverage is low. Variable rates of COVID-19 vaccine hesitancy were found in the numerous studies conducted in the region. Complex factors contributed to vaccination hesitancy in the region including concerns about COVID-19 vaccine safety and efficacy, low trust in healthcare systems, complacency toward the risks of COVID-19, constraints hindering access to COVID-19 vaccination services, as well as the circulation of misinformation and conspiracy beliefs about COVID-19 and its vaccination. Effective approaches to address COVID-19 vaccine hesitancy in the MENA region rely on developing evidence-based communication strategies that are recommended to build trust in vaccination, highlight the disease risks, and counter COVID-19 vaccine-related misinformation. Ensuring COVID-19 vaccine affordability is also necessary besides the cautious consideration of implementing COVID-19 vaccine mandates. Based on the preceding discussion, this chapter aims to identify the common themes of COVID-19 vaccine hesitancy in the MENA region. In addition, the chapter highlights the importance of understanding the root causes of COVID-19 vaccination hesitancy and its associated determinants to develop effective strategies for promoting COVID-19 vaccine acceptance and uptake in the MENA region. To build community trust, promote community education and awareness, and counter misinformation for better COVID-19 vaccine coverage in the region, it is recommended to involve healthcare professionals and policymakers.

Changing epidemiology of COVID-19: potential future impact on vaccines and vaccination strategies

INTRODUCTION

COVID-19 was an unprecedented challenge worldwide; however, disease epidemiology has evolved, and COVID-19 no longer constitutes a public health emergency of international concern. Nonetheless, COVID-19 remains a global threat and uncertainties remain, including definition of the end of the pandemic and transition to endemicity, and understanding true rates of SARS-CoV-2 infection/transmission.

AREAS COVERED

Six international experts convened (April 2023) to interpret changing COVID-19 epidemiology and public health challenges. We report the panel's recommendations and knowledge gaps in COVID-19 epidemiology, SARS-CoV-2 evolution, and future vaccination strategies, informed by peer-reviewed publications, surveillance data, health authority assessments, and clinical experience.

EXPERT OPINION

High population SARS-CoV-2 immunity indicates the likely end to the pandemic's acute phase. Continued emergence of variants/sublineages that can evade the vaccine-induced antibody response are likely, but widespread immunity reduces the risk of disease severity. Continued surveillance is required to capture transition to endemicity, seasonality, and emergence of novel variants/sublineages, to inform future vaccination strategies. COVID-19 vaccination should be integrated into routine vaccination programs throughout life. Co-circulation with other respiratory viruses should be monitored to avoid a combined peak, which could overrun healthcare systems. Effective, combined vaccines and improved education may help overcome vaccine hesitancy/booster fatigue and increase vaccination uptake.

From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics

The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the detection, monitoring, and treatment of the disease. Robust surveillance systems have been established to understand the clinical characteristics of new variants, although the unpredictable nature of these variants presents significant challenges. Some variants have shown resistance to current treatments, but innovative technologies like computational protein design (CPD) offer promising solutions and versatile therapeutics against SARS-CoV-2. Advances in computing power, coupled with open-source platforms like AlphaFold and RFdiffusion (employing deep neural network and diffusion generative models), among many others, have accelerated the design of protein therapeutics with precise structures and intended functions. CPD has played a pivotal role in developing peptide inhibitors, mini proteins, protein mimics, decoy receptors, nanobodies, monoclonal antibodies, identifying drug-resistance mutations, and even redesigning native SARS-CoV-2 proteins. Pending regulatory approval, these designed therapies hold the potential for a lasting impact on human health and sustainability. As SARS-CoV-2 continues to evolve, use of such technologies enables the ongoing development of alternative strategies, thus equipping us for the "New Normal".

Preclinical evaluation of PHH-1V vaccine candidate against SARS-CoV-2 in non-human primates

SARS-CoV-2 emerged in December 2019 and quickly spread worldwide, continuously striking with an unpredictable evolution. Despite the success in vaccine production and mass vaccination programs, the situation is not still completely controlled, and therefore accessible second-generation vaccines are required to mitigate the pandemic. We previously developed an adjuvanted vaccine candidate coded PHH-1V, based on a heterodimer fusion protein comprising the RBD domain of two SARS-CoV-2 variants. Here, we report data on the efficacy, safety, and immunogenicity of PHH-1V in cynomolgus macaques. PHH-1V prime-boost vaccination induces high levels of RBD-specific IgG binding and neutralizing antibodies against several SARS-CoV-2 variants, as well as a balanced Th1/Th2 cellular immune response. Remarkably, PHH-1V vaccination prevents SARS-CoV-2 replication in the lower respiratory tract and significantly reduces viral load in the upper respiratory tract after an experimental infection. These results highlight the potential use of the PHH-1V vaccine in humans, currently undergoing Phase III clinical trials.

A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G

Introduction

A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection.

Materials and Methods

We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy).

Results

HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 - 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3'UTR polymorphism (rs371194629) shows that the HLA-G 3'UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X² = 7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X² = 11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as β-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3'UTR Del/Del genotype was independent from the other significant variables [OR_M = 0.4 (95% CI 0.2 - 0.7), P_M = 6.5 x 10^-4].

Conclusion

Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients.

Preclinical safety evaluation of intradermal SARS-CoV-2 inactivated vaccine (Vero cells) administration in macaques

Coronavirus disease 2019 (COVID-19) is an acute and highly pathogenic infectious disease in humans caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Six months after immunization with the SARS-CoV-2 vaccine, however, antibodies are almost depleted. Intradermal immunization could be a new way to solve the problem of nondurable antibody responses against SARS-CoV-2 or the poor immune protection against variant strains. We evaluated the preclinical safety of a SARS-CoV-2 vaccine for intradermal immunization in rhesus monkeys. The results showed that there were no obvious abnormalities in the general clinical condition, food intake, body weight or ophthalmologic examination except for a reaction at the local vaccination site. In the hematology examination, bone marrow imaging, serum biochemistry, and routine urine testing, the related indexes of each group fluctuated to different degrees after administration, but there was no dose-response or time-response correlation. The neutralization antibody and ELISpot results also showed that strong humoral and cellular immunity could be induced after vaccination, and the levels of neutralizing antibodies increased with certain dose- and time-response trends. The results of a repeated-administration toxicity test in rhesus monkeys intradermally inoculated with a SARS-CoV-2 inactivated vaccine showed good safety and immunogenicity.

Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease

SARS-CoV-2 is the causative agent of COVID-19. The main viral protease (Mpro) is an attractive target for antivirals. The clinically approved drug nirmatrelvir and the clinical candidate ensitrelvir have so far showed great potential for treatment of viral infection. However, the broad use of antivirals is often associated with resistance generation. Herein, we enzymatically characterized 14 naturally occurring Mpro polymorphisms that are close to the binding site of these antivirals. Nirmatrelvir retained its potency against most polymorphisms tested, while mutants G143S and Q189K were associated with diminished inhibition constants. For ensitrelvir, diminished inhibition constants were observed for polymorphisms M49I, G143S, and R188S, but not for Q189K, suggesting a distinct resistance profile between inhibitors. In addition, the crystal structures of selected polymorphisms revealed interactions that were critical for loss of potency. In conclusion, our data will assist the monitoring of potential resistant strains, support the design of combined therapy, as well as assist the development of the next generation of Mpro inhibitors.

Evaluation the efficacy and safety of N-acetylcysteine inhalation spray in controlling the symptoms of patients with COVID-19: An open-label randomized controlled clinical trial

The aim of this study was to evaluate the effect and safety of N-acetylcysteine (NAC) inhalation spray in the treatment of patients with coronavirus disease 2019 (COVID-19). This randomized controlled clinical trial study was conducted on patients with COVID-19. Eligible patients (n = 250) were randomly allocated into the intervention group (routine treatment + NAC inhaler spray one puff per 12 h, for 7 days) or the control group who received routine treatment alone. Clinical features, hemodynamic, hematological, biochemical parameters and patient outcomes were assessed and compared before and after treatment. The mortality rate was significantly higher in the control group than in the intervention group (39.2% vs. 3.2%, p < 0.001). Significant differences were found between the two groups (intervention and control, respectively) for white blood cell count (6.2 vs. 7.8, p < 0.001), hemoglobin (12.3 vs. 13.3, p = 0.002), C-reactive protein (CRP: 6 vs. 11.5, p < 0.0001) and aspartate aminotransferase (AST: 32 vs. 25.5, p < 0.0001). No differences were seen for hospital length of stay (11.98 ± 3.61 vs. 11.81 ± 3.52, p = 0.814) or the requirement for intensive care unit (ICU) admission (7.2% vs. 11.2%, p = 0.274). NAC was beneficial in reducing the mortality rate in patients with COVID-19 and inflammatory parameters, and a reduction in the development of severe respiratory failure; however, it did not affect the length of hospital stay or the need for ICU admission. Data on the effectiveness of NAC for Severe Acute Respiratory Syndrome Coronavirus-2 is limited and further research is required.

Risk factors affecting COVID-19 vaccine effectiveness identified from 290 cross-country observational studies until February 2022: a meta-analysis and meta-regression

BACKGROUND

Observational studies made it possible to assess the impact of risk factors on the long-term effectiveness of mRNA and adenoviral vector (AdV) vaccines against COVID-19.

METHODS

A computerized literature search was undertaken using the MEDLINE, EMBASE, and MedRxiv databases to identify eligible studies, with no language restrictions, published up to 28 February 2022. Eligible were observational studies assessing vaccine effectiveness (VE) by disease severity with reference groups of unvaccinated participants or participants immunized with one, two, or three vaccine doses. Our study was carried out in compliance with the PRISMA and MOOSE guidelines. The risk of study bias was identified using the Newcastle-Ottawa Quality Assessment Scale. The GRADE guidelines were applied to assess the strength of evidence for the primary outcome. The synthesis was conducted using a meta-analysis and meta-regression.

RESULTS

Out of a total of 14,155 publications, 290 studies were included. Early VE of full vaccination against COVID-19 of any symptomatology and severity decreased from 96% (95% CI, 95-96%) for mRNA and from 86% (95% CI, 83-89%) for AdV vaccines to 67% for both vaccine types in the last 2 months of 2021. A similar 1-year decline from 98 to 86% was found for severe COVID-19 after full immunization with mRNA, but not with AdV vaccines providing persistent 82-87% effectiveness. Variant-reduced VE was only associated with Omicron regardless of disease severity, vaccine type, or vaccination completeness. The level of protection was reduced in participants aged >65 years, with a comorbidity or those in long-term care or residential homes independently of the number of doses received. The booster effect of the third mRNA dose was unclear because incompletely restored effectiveness, regardless of disease severity, declined within a short-term interval of 4 months.

CONCLUSIONS

Full vaccination provided an early high, yet waning level of protection against COVID-19 of any severity with a strong impact on the high-risk population. Moreover, the potential risk of new antigenically distinct variants should not be underestimated, and any future immunization strategy should include variant-updated vaccines.

Approaching Challenges Posed by SARS-CoV-2 Genetic Variants

In this new collection of the most viewed and cited papers, one of the Editor's chosen articles, published in Pathogens in 2021, addressed the impact and the concerns relating to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants [...].

A systematic review of current status and challenges of vaccinating children against SARS-CoV-2

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has inflicted immense damage to countries, economies and societies worldwide. Authorized COVID-19 vaccines based on different platforms have been widely inoculated in adults, showing up to 100% immunogenicity with significant efficacy in preventing SARS-CoV-2 infections and the occurrence of severe COVID-19. It has also greatly slowed the evolution of SARS-CoV-2 variants, as shown in clinical trials and real-world evidence. However, the total dosage of COVID-19 vaccines for children is much smaller than that for adults due to limitations from parental concern of vaccine safety, presenting a potential obstacle in ending the COVID-19 pandemic. SARS-CoV-2 not only increases the risk of severe multisystem inflammatory syndrome (MIS-C) in children, but also negatively affects children's psychology and academics, indirectly hindering the maintenance and progress of normal social order. Therefore, this article examines the clinical manifestations of children infected with SARS-CoV-2, the status of vaccination against COVID-19 in children, vaccination-related adverse events, and the unique immune mechanisms of children. In particular, the necessity and challenges of vaccinating children against SARS-CoV-2 were highlighted from the perspectives of society and family. In summary, parental hesitancy is unnecessary as adverse events after COVID-19 vaccination have been proven to be infrequent, comprise of mild symptoms, and have a good prognosis.

The Deltacron conundrum: Its origin and potential health risks

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since its outbreak in December 2019, has been capable of continuing the pandemic by mutating itself into different variants. Mass vaccinations, antibiotic treatment therapy, herd immunity, and preventive measures have reduced the disease's severity from the emerging variants. However, the virus is undergoing recombination among the current two variants: Delta and Omicron, resulting in a new variant, informally known as "Deltacron," which was controversial as it might be a product of lab contamination between Omicron and Delta samples. However, the proclamation was proved wrong, and the experts are putting more effort into better understanding the variant's epidemiological characteristics to control potential outbreaks. This review has discussed the potential mutations in the novel variant and prospective risk factors and therapeutic options in the context of this new variant. This study could be used as a guide for implementing appropriate controls in a sudden outbreak of this new variant.

Randomized clinical trial of BCG vaccine in patients with convalescent COVID-19: Clinical evolution, adverse events, and humoral immune response

BACKGROUND

The Bacillus Calmette-Guérin (BCG) vaccine may confer cross-protection against viral diseases in adults. This study evaluated BCG vaccine cross-protection in adults with convalescent coronavirus disease 2019 (COVID-19).

METHOD

This was a multicenter, prospective, randomized, placebo-controlled, double-blind phase III study (ClinicalTrials.gov: NCT04369794).

SETTING

University Community Health Center and Municipal Outpatient Center in South America.

PATIENTS

a total of 378 adult patients with convalescent COVID-19 were included.

INTERVENTION

single intradermal BCG vaccine (n = 183) and placebo (n = 195).

MEASUREMENTS

the primary outcome was clinical evolution. Other outcomes included adverse events and humoral immune responses for up to 6 months.

RESULTS

A significantly higher proportion of BCG patients with anosmia and ageusia recovered at the 6-week follow-up visit than placebo (anosmia: 83.1% vs. 68.7% healed, p = 0.043, number needed to treat [NNT] = 6.9; ageusia: 81.2% vs. 63.4% healed, p = 0.032, NNT = 5.6). BCG also prevented the appearance of ageusia in the following weeks: seven in 113 (6.2%) BCG recipients versus 19 in 126 (15.1%) placebos, p = 0.036, NNT = 11.2. BCG did not induce any severe or systemic adverse effects. The most common and expected adverse effects were local vaccine lesions, erythema (n = 152; 86.4%), and papules (n = 111; 63.1%). Anti-severe acute respiratory syndrome coronavirus 2 humoral response measured by N protein immunoglobulin G titer and seroneutralization by interacting with the angiotensin-converting enzyme 2 receptor suggest that the serum of BCG-injected patients may neutralize the virus at lower specificity; however, the results were not statistically significant.

CONCLUSION

BCG vaccine is safe and offers cross-protection against COVID-19 with potential humoral response modulation.

LIMITATIONS

No severely ill patients were included.

SARS-CoV-2 Mutation Mechanism, Features, and Future Perspective

Over two years, the SARS-CoV-2 virus has evolved by producing several variants by RNA polymerase mutation. This mutation created many virus variants that five of them are designated by WHO. These are Alpha, Beta, Gamma, Delta, and Omicron, among them Alpha, Delta, and Omicron spread faster. Coronaviruses (CoVs) are enveloped in positive-sense RNA viruses and contain huge RNA virus genomes. RNA polymerase controls the replication in which the genomic material is copied, and it often makes errors that lead to create a new mutation. Most mutations create a virus that cannot replicate and spread among people. However, some mutations lead to a virus that can replicate and create a variant. This chapter will discuss the mechanism of the mutations during the last two years and the future of these mutations in SARS-CoV-2.

A bibliometric analysis of the 100 most cited articles describing SARS-CoV-2 variants

Background

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with mutations in the spike protein has risen concerns about the efficacy of infection- or vaccine-induced antibodies and has posed a serious threat to global public health, education, travel and economy. Few studies have described the detailed characterizations of highly cited articles on SARS-CoV-2 variants.

Objective

To identify and characterize the 100 most-cited articles in SARS-CoV-2 variants research.

Design and methods

Articles published recently were extracted from the web of science core collection database using a query based on MeSH terms and topics of SARS-CoV-2 and variants. Characteristics of the 100 most-cited articles were analyzed via the following parameters: publication number over year, number of citations, type of articles, authors, journal, journal impact factor, country, and topics covered in articles. In addition, clinical trials in these articles were also analyzed.

Results

The majority of articles (66%) were published in 2021. Number of citations of the 100 most cited articles ranged from 1720 to 75 (median: 178.5). Mutations in the S protein such as D614G mutation and the B.1.1.7 (UK) and B.1.351 (South Africa) were the dominant variants in the 100 most cited articles. The United States, the United Kingdom, and South Africa had the strongest collaboration in the contribution of publication. Science, Cell, Nature and New England Journal of Medicine were mostly cited and the main direction in these top journals were vaccine neutralizing tests and efficacy evaluation studies. Response of antibody neutralization tests against variants was always weakened due to the presence of variants but the results of clinical trials were encouraging. Genomics information, spike protein structure confirmation and neutralization studies evaluating antibody resistance were highly represented in the 100 most cited articles in SARS-CoV-2 variants literature.

Conclusions and relevance

Altogether, genomic information, epidemiology, immune neutralization, and vaccine efficacy studies of COVID-19 variants are the main research orientations in these articles and relevant results have been published in influential journals. Given the continuous evolution of the SARS-CoV-2 and the constant development in our understanding of the impact of variants, current working strategies and measures may be periodically adjusted.

Costs for a hospital stay: another lesson learned from the COVID-19 pandemic

Background and aim: After two years of pandemic, planning and budgeting for use of healthcare resources and services is very important. Inpatient COVID-19 hospitalizations costs, regardless of ICD-10 procedure codes, in a Covid-19 support military hospital were analyzed. Methods: The national protocol for the treatment of Covid-19 infection was applied. The costs for laboratory tests, drugs, protection equipment and radiological investigations (imaging techniques such as computed-tomography or radiography), hospitalization days and food were assessed. Results: In our hospital, from August 2020 through June 2021, 241 patients were hospitalized with COVID-19: mean age 59.92±7.8 years, 46% men, 26% military personnel, 11.57±3 days of hospitalization; two third of patients had moderate and severe forms of COVID-19. The main manifestations were: 69% respiratory (18% with severe pneumonia), 3.3% cardiac (2.9% with pulmonary embolism, diagnosed by computed tomography angiography), 28% digestive and 33% psychiatric (most commonly anxiety). The average estimated costs were about 3000€/patient, without significant differences based on disease severity. Equipment costs were 2 times higher than for drugs and 3 times than for laboratory tests. Conclusions: In a Covid-19 support military hospital that cared for patients with predominantly moderate forms of COVID-19, the costs for equipment were much higher than those for treatment. New criteria for hospitalization of these forms of COVID-19 deserve to be analyzed in order to avoid useless costs

COVID-19 and Adult Acute Leukemia: Our Knowledge in Progress

The majority of publications regarding SARS-CoV-2 infections in adult patients with acute leukemia (AL) refer to hematological patients in general and are not focused on acute myeloid leukemia (AML) or acute lymphoblastic leukemia (ALL). We herein report a review of the current literature on adult AL patients infected with SARS-CoV-2. Overall, SARS-CoV-2-associated mortality ranges from 20-52% in patients with adult AL. AML patients have a particularly high COVID-19-related mortality. Of note, most of the available data relate to the pre-vaccination era and to variants before Omicron. The impact of COVID-19 infections on AL treatment is rarely reported. Based on the few studies available, treatment delay does not appear to be associated with an increased risk of relapse, whereas therapy discontinuation was associated with worse outcomes in AML patients. Therefore, the current recommendations suggest delaying systemic AL treatment in SARS-CoV-2-positive patients until SARS-CoV-2 negativity, if immediate AL treatment is not required. It is recommended to offer vaccination to all AL patients; the reported antibody responses are around 80-96%. Seronegative patients should additionally receive prophylactic administration of anti-SARS-CoV-2 monoclonal antibodies. Patients with AL infected with SARS-CoV-2 should be treated early with antiviral therapy to prevent disease progression and enable the rapid elimination of the virus.

Non-structure protein ORF1ab (NSP8) in SARS-CoV-2 contains potential γδT cell epitopes

Upon activation by the pathogen through T-cell receptors (TCRs), γδT cells suppress the pathogenic replication and thus play important roles against viral infections. Targeting SARS-CoV-2 via γδT cells provides alternative therapeutic strategies. However, little is known about the recognition of SARS-CoV-2 antigens by γδT cells. We discovered a specific Vγ9/δ2 CDR3 by analyzing γδT cells derived from the patients infected by SARS-CoV-2. Using a cell model exogenously expressing γδ-TCR established, we further screened the structural motifs within the CDR3 responsible for binding to γδ-TCR. Importantly, these sequences were mapped to NSP8, a non-structural protein in SARS-CoV-2. Our results suggest that NSP8 mediates the recognition by γδT cells and thus could serve as a potential target for vaccines.

Inhibitors of Activin Receptor-like Kinase 5 Interfere with SARS-CoV-2 S-Protein Processing and Spike-Mediated Cell Fusion via Attenuation of Furin Expression

Screening of a protein kinase inhibitor library identified SB431542, targeting activin receptor-like kinase 5 (ALK5), as a compound interfering with SARS-CoV-2 replication. Since ALK5 is implicated in transforming growth factor β (TGF-β) signaling and regulation of the cellular endoprotease furin, we pursued this research to clarify the role of this protein kinase for SARS-CoV-2 infection. We show that TGF-β1 induces the expression of furin in a broad spectrum of cells including Huh-7 and Calu-3 that are permissive for SARS-CoV-2. The inhibition of ALK5 by incubation with SB431542 revealed a dose-dependent downregulation of both basal and TGF-β1 induced furin expression. Furthermore, we demonstrate that the ALK5 inhibitors SB431542 and Vactosertib negatively affect the proteolytic processing of the SARS-CoV-2 Spike protein and significantly reduce spike-mediated cell-cell fusion. This correlated with an inhibitory effect of ALK5 inhibition on the production of infectious SARS-CoV-2. Altogether, our study shows that interference with ALK5 signaling attenuates SARS-CoV-2 infectivity and cell-cell spread via downregulation of furin which is most pronounced upon TGF-β stimulation. Since a TGF-β dominated cytokine storm is a hallmark of severe COVID-19, ALK5 inhibitors undergoing clinical trials might represent a potential therapy option for COVID-19.

Antiviral phytocompounds “ellagic acid” and “(+)-sesamin” of Bridelia retusa identified as potential inhibitors of SARS-CoV-2 3CL pro using extensive molecular docking, molecular dynamics simulation studies, binding free energy calculations, and bioactivity prediction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected billions and has killed millions to date. Studies are being carried out to find therapeutic molecules that can potentially inhibit the replication of SARS-CoV-2. 3-chymotrypsin-like protease (3CL pro) involved in the polyprotein cleavage process is believed to be the key target for viral replication, and hence is an attractive target for the discovery of antiviral molecules. In the present study, we aimed to identify natural phytocompounds from Bridelia retusa as potential inhibitors of SARS-CoV-2 3CL pro (PDB ID: 6M2N) using in silico techniques. Molecular docking studies conducted with three different tools in triplicates revealed that ellagic acid (BR6) and (+)-sesamin (BR13) has better binding affinity than the co-crystal inhibitor “3WL” of 6M2N. BR6 and BR13 were found to have a high LD₅₀ value with good bioavailability. 3WL, BR6, and BR13 bind to the same active binding site and interacted with the HIS41-CYS145 catalytic dyad including other crucial amino acids. Molecular dynamics simulation studies revealed stability of protein–ligand complexes as evidenced from root-mean-square deviations, root-mean-square fluctuations (RMSF), protein secondary structure elements, ligand-RMSF, protein–ligand contacts, ligand torsions, and ligand properties. BR6 (−22.3064 kcal/mol) and BR13 (−19.1274 kcal/mol) showed a low binding free energy value. The Bayesian statistical model revealed BR6 and BR13 as better protease inhibitors than 3WL. Moreover, BR6 and BR13 had already been reported to elicit antiviral activities. Therefore, we conclude that ellagic acid and (+)-sesamin as natural antiviral phytocompounds with inhibitory potential against SARS-CoV-2 3CL pro.

Outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 B.1.620 Lineage in the General Hospital of Jeju Island, Republic of Korea

The number of coronavirus disease (COVID-19)-positive cases has increased in Jeju Island, Republic of Korea. Identification and monitoring of new mutations in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are extremely important to fighting the global pandemic. We report a breakout of the B.1.620 lineage, harboring the E484 mutation in the virus spike protein in a general hospital on Jeju Island. A cluster of cases was detected between August 4 and September 10, 2021, involving 20 patients positive for COVID-19 of 286 individuals exposed to the virus, comprising hospital patients, staff, and caregivers. We analyzed the epidemiological characteristics and spike proteins mutation sites using Sanger sequencing and phylogenetic analysis on these 20 patients. By analyzing genomic variance, it was confirmed that 12 of the confirmed patients harbored the SARS-CoV-2 B.1.620 lineage. The breakthrough rate of infection was 2% in fully vaccinated individuals among these patients. Next clade analysis revealed that these SARS-CoV-2 genomes belong to clade 20A. This is the first reported case of SARS-CoV-2 sub-lineage B.1.620, although the B.1.617.2 lineage has prevailed in August and September in Jeju, which has a geographical advantage of being an island. We reaffirm that monitoring the spread of SARS-CoV-2 variants with characteristic features is indispensable for controlling COVID-19 outbreaks.

Is hypoimmunogenic stem cell therapy safe in times of pandemics?

The manipulation of human leukocyte antigens (HLAs) and immune modulatory factors in “universal” human pluripotent stem cells (PSCs) holds promise for immunological tolerance without HLA matching. This paradigm raises concerns should "universal" grafts become virally infected. Furthermore, immunological manipulation might functionally impair certain progeny, such as hematopoietic stem cells. We discuss the risks and benefits of hypoimmunogenic PSCs, and the need to further advance HLA matching and autologous strategies.

SARS-CoV-2: Recent Variants and Clinical Efficacy of Antibody-Based Therapy

Multiple variants of SARS-CoV-2 have emerged and are now prevalent at the global level. Currently designated variants of concern (VOCs) are B.1.1.7, B1.351, P.1, B.1.617.2 variants and B.1.1.529. Possible options for VOC are urgently required as they carry mutations in the virus spike protein that allow them to spread more easily and cause more serious illness. The primary targets for most therapeutic methods against SARS-CoV-2 are the S (Spike) protein and RBD (Receptor-Binding Domain), which alter the binding to ACE2 (Angiotensin-Converting Enzyme 2). The most popular of these strategies involves the use of drug development targeting the RBD and the NTD (N-terminal domain) of the spike protein and multiple epitopes of the S protein. Various types of mutations have been observed in the RBDs of B.1.1.7, B1.351, P. and B.1.620. The incidence of RBD mutations increases the binding affinity to the ACE2 receptor. The high binding affinity of RBD and ACE2 has provided a structural basis for future evaluation of antibodies and drug development. Here we discuss the variants of SARS-CoV-2 and recent updates on the clinical evaluation of antibody-based treatment options. Presently, most of the antibody-based treatments have been effective in patients with SARS-CoV-2. However, there are still significant challenges in verifying independence, and the need for further clinical evaluation.

Echinacea as a Potential Force against Coronavirus Infections? A Mini-Review of Randomized Controlled Trials in Adults and Children

Echinacea purpurea has been shown to broadly inhibit coronaviruses and SARS-CoV-2 in vitro. This review discusses the available clinical evidence from randomized, blinded and controlled human studies. Two RCTs capturing incidence of viral respiratory tract infections during Echinacea preventative treatment were identified including coronavirus infections. Incidence and/or viral loads were measured by RT-PCR and symptom severity was recorded. In a first study, Jawad et al. collected nasopharyngeal swabs from adults (N = 755) over 4 months of continuous prevention. Overall, 24 and 47 enveloped virus infections occurred, including 21 and 33 coronavirus detections (229E; HKU1; OC43) with Echinaforce® extract (2400 mg daily) and placebo, respectively (p = 0.0114). In a separate study, Ogal et al. administered the same extract (1200 mg) or control for 4 months to children (4-12 years) (N = 203). Echinacea reduced the incidence of enveloped virus infections from 47 to 29 (p = 0.0038) whereas 11 and 13 coronavirus detections (229E, OC43, NL63) were counted (p > 0.05). Respiratory symptoms during coronavirus infections were significantly lower with area-under-curve AUC = 75.8 (+/-50.24) versus 27.1 (+/-21.27) score points (p = 0.0036). Importantly, viral loads in nasal secretions were significantly reduced by 98.5% in the Echinacea group, with Ct-values 31.1 [95% CI 26.3; 35.9] versus 25.0 [95% CI 20.5; 29.5] in the control group (p = 0.0479). Results from clinical studies confirm the antiviral activity found for Echinacea in vitro, embracing enveloped respiratory pathogens and therefore coronaviruses as well. Substantiating results from a new, completed study seem to extrapolate these effects to the prevention of SARS-CoV-2 infections. As hypothesized, the established broad antiviral activity of Echinacea extract appears to be inclusive for SARS-CoV-2.