Immune Evasive Effects of SARS-CoV-2 Variants to COVID-19 Emergency Used Vaccines

A Meta-Analysis on the Immunogenicity of Homologous versus Heterologous Immunization Regimens against SARS-CoV-2 Beta, Delta, and Omicron BA.1 VoCs in Healthy Adults

Since the outbreak of the COVID-19 pandemic, SARS-CoV-2 has not stopped evolving, leading to the emergence of variants of concern (VoCs) involved in significant immune escape. Here, we compared the immunogenicity of different prime-boost vaccination regimens against SARS-CoV-2 wildtype (WT) and its Beta, Delta, and Omicron BA.1 VoCs. We used 5 databases to retrieve publications and random-effect models to estimate pooled neutralization titers. We included 11 randomized controlled trials (RCTs) and 16 non-RCTs, 10 prime-boost vaccination regimens, and 4598 subjects. We found neutralization activity against SARS-CoV-2 decreased with virus evolution. The heterologous immunization was more effective. The increase in neutralization titers against SARS-CoV-2 WT and Beta, Delta, and Omicron BA.1 VoCs after heterologous immunization was 1.41(95%CI:0.82-2.01), 0.90(95%CI:0.39-1.41), 1.23 (95%CI: 0.81-1.65), and 1.32 (95%CI: 0.99-1.65), respectively. Furthermore, the booster dose of viral vector vaccine did not show a higher increase in neutralization titers against SARS-CoV-2 WT(MD=0.48; 95%CI:-1.12-1.09), Beta (MD=0.20; 95%CI:-0.26-0.67), Delta (MD=0.35; 95%CI:-0.09-0.79), and Omicron BA.1 (MD=0.38; 95%CI:-0.14-0.89) VoCs. The combination of inactivated-recombinant protein vaccines showed a higher increase in neutralization titers (Beta: MD=1.88 and Delta: MD=1.70) than other combinations of vaccines. However, only a combination of mRNA-viral vector vaccines showed a higher increase in neutralization titers (MD:1.52; 95%CI:0.34-2.70) against Omicron BA.1 VoC. Interestingly, the viral vector-mRNA immunization regimen appears better compared to mRNA-viral vector regimen, especially against Beta and Delta VoCs. Overall, the type of combination followed by the order of administration of COVID-19 vaccines could be a potential vaccine strategy against the occurrence of SARS-CoV-2 variants.

Genomic Analysis and Tracking of SARS-CoV-2 Variants in Gwangju, South Korea, From 2020 to 2022

BACKGROUND

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, in December 2019, it has spread rapidly, and many coronavirus disease (COVID-19) cases have occurred in Gwangju, South Korea. Viral mutations following the COVID-19 epidemic have increased interest in the characteristics of epidemics in this region, and pathogen genetic analysis is required for infection control and prevention.

METHODS

In this study, SARS-CoV-2 whole-genome analysis was performed on samples from patients with COVID-19 in Gwangju from 2020 to 2022 to identify the trends in COVID-19 prevalence and to analyze the phylogenetic relationships of dominant variants. B.41 and B.1.497 prevailed in 2020, the early stage of the COVID-19 outbreak; then, B.1.619.1 mainly occurred until June 2021. B.1.617.2, classified as sublineages AY.69 and AY.122, occurred continuously from July to December 2021. Since strict measures to strengthen national quarantine management had been implemented in South Korea until this time, the analysis of mutations was also able to infer the epidemiological relationship between infection transmission routes. Since the first identification of the Omicron variant in late December 2021, the spread of infection has been very rapid, and weekly whole-genome analysis of specimens has enabled us to monitor new Omicron sublineages occurring in Gwangju.

CONCLUSIONS

Our study suggests that conducting regional surveillance in addition to nation-level genomic surveillance will enable more rapid and detailed variant surveillance, which will be helpful in the overall prevention and management of infectious diseases.

Nanobody engineering for SARS-CoV-2 neutralization and detection

In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases.

IMPORTANCE

Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.

A T cell-targeted multi-antigen vaccine generates robust cellular and humoral immunity against SARS-CoV-2 infection

SARS-CoV-2, the etiological agent behind the coronavirus disease 2019 (COVID-19) pandemic, has continued to mutate and create new variants with increased resistance against the WHO-approved spike-based vaccines. With a significant portion of the worldwide population still unvaccinated and with waning immunity against newly emerging variants, there is a pressing need to develop novel vaccines that provide broader and longer-lasting protection. To generate broader protective immunity against COVID-19, we developed our second-generation vaccinia virus-based COVID-19 vaccine, TOH-VAC-2, encoded with modified versions of the spike (S) and nucleocapsid (N) proteins as well as a unique poly-epitope antigen that contains immunodominant T cell epitopes from seven different SARS-CoV-2 proteins. We show that the poly-epitope antigen restimulates T cells from the PBMCs of individuals formerly infected with SARS-CoV-2. In mice, TOH-VAC-2 vaccination produces high titers of S- and N-specific antibodies and generates robust T cell immunity against S, N, and poly-epitope antigens. The immunity generated from TOH-VAC-2 is also capable of protecting mice from heterologous challenge with recombinant VSV viruses that express the same SARS-CoV-2 antigens. Altogether, these findings demonstrate the effectiveness of our versatile vaccine platform as an alternative or complementary approach to current vaccines.

Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies

The application of B-cell epitope identification to develop therapeutic antibodies and vaccine candidates is well established. However, the validation of epitopes is time-consuming and resource-intensive. To alleviate this, in recent years, multiple computational predictors have been developed in the immunoinformatics community. Brewpitopes is a pipeline that curates bioinformatic B-cell epitope predictions obtained by integrating different state-of-the-art tools. We used additional computational predictors to account for subcellular location, glycosylation status, and surface accessibility of the predicted epitopes. The implementation of these sets of rational filters optimizes in vivo antibody recognition properties of the candidate epitopes. To validate Brewpitopes, we performed a proteome-wide analysis of SARS-CoV-2 with a particular focus on S protein and its variants of concern. In the S protein, we obtained a fivefold enrichment in terms of predicted neutralization versus the epitopes identified by individual tools. We analyzed epitope landscape changes caused by mutations in the S protein of new viral variants that were linked to observed immune escape evidence in specific strains. In addition, we identified a set of epitopes with neutralizing potential in four SARS-CoV-2 proteins (R1AB, R1A, AP3A, and ORF9C). These epitopes and antigenic proteins are conserved targets for viral neutralization studies. In summary, Brewpitopes is a powerful pipeline that refines B-cell epitope bioinformatic predictions during public health emergencies in a high-throughput capacity to facilitate the optimization of experimental validation of therapeutic antibodies and candidate vaccines.

Analysis of the COVID-19 pandemic using a compartmental model with time-varying parameters fitted by a genetic algorithm

Analyzing the COVID-19 pandemic is a critical factor in developing effective policies to deal with similar challenges in the future. However, many parameters (e.g., the actual number of infected people, the effectiveness of vaccination) are still subject to considerable debate because they are unobservable. To model a pandemic and estimate unobserved parameters, researchers use compartmental models. Most often, in such models, the transition rates are considered as constants, which allows simulating only one epidemiological wave. However, multiple waves have been reported for COVID-19 caused by different strains of the virus. This paper presents an approach based on the reconstruction of real distributions of transition rates using genetic algorithms, which makes it possible to create a model that describes several pandemic peaks. The model is fitted on registered COVID-19 cases in four countries with different pandemic control strategies (Germany, Sweden, UK, and US). Mean absolute percentage error (MAPE) was chosen as the objective function, the MAPE values of 2.168%, 2.096%, 1.208% and 1.703% were achieved for the listed countries, respectively. Simulation results are consistent with the empirical statistics of medical studies, which confirms the quality of the model. In addition to observables such as registered infected, the output of the model contains variables that cannot be measured directly. Among them are the proportion of the population protected by vaccines, the size of the exposed compartment, and the number of unregistered cases of COVID-19. According to the results, at the peak of the pandemic, between 14% (Sweden) and 25% (the UK) of the population were infected. At the same time, the number of unregistered cases exceeds the number of registered cases by 17 and 3.4 times, respectively. The average duration of the vaccine induced immune period is shorter than claimed by vaccine manufacturers, and the effectiveness of vaccination has declined sharply since the appearance of the Delta and Omicron strains. However, on average, vaccination reduces the risk of infection by about 65-70%.

An assessment of the strategy and status of COVID-19 vaccination in India

The COVID-19 disease continues to cause devastation for almost 3 years of its identification. India is one of the leading countries to set clinical trials, production, and administration of COVID-19 vaccination. Recent COVID-19 vaccine tracker record suggests that 12 vaccines are approved in India, including protein subunit, RNA/DNA, non-replicating viral vector, and inactivated vaccine. Along with that 16 more vaccines are undergoing clinical trials to counter COVID-19. The availability of different vaccines gives alternate and broad perspectives to fight against viral immune resistance and, thus, viruses escaping the immune system by mutations. Using the recently published literature on the Indian vaccine and clinical trial sites, we have reviewed the development, clinical evaluation, and registration of vaccines trial used in India against COVID-19. Moreover, we have also summarized the status of all approved vaccines in India, their associated registered clinical trials, manufacturing, efficacy, and their related safety and immunogenicity profile.

Remdesivir for Hospitalized COVID-19 Patients in the United States: Optimization of Health Care Resources

INTRODUCTION

In addition to significant morbidity and mortality, the coronavirus disease (COVID-19) has strained health care systems globally. This study investigated the cost-effectiveness of remdesivir + standard of care (SOC) for hospitalized COVID-19 patients in the USA.

METHODS

This cost-effectiveness analysis considered direct and indirect costs of remdesivir + SOC versus SOC alone among hospitalized COVID-19 patients in the US. Patients entered the model stratified according to their baseline ordinal score. At day 15, patients could transition to another health state, and on day 29, they were assumed to have either died or been discharged. Patients were then followed over a 1-year time horizon, where they could transition to death or be rehospitalized.

RESULTS

Treatment with remdesivir + SOC avoided, per patient, a total of 4 hospitalization days: two general ward days and a day for both the intensive care unit and the intensive care unit plus invasive mechanical ventilation compared to SOC alone. Treatment with remdesivir + SOC presented net cost savings due to lower hospitalization and lost productivity costs compared to SOC alone. In increased and decreased hospital capacity scenarios, remdesivir + SOC resulted in more beds and ventilators being available versus SOC alone.

CONCLUSIONS

Remdesivir + SOC alone represents a cost-effective treatment for hospitalized patients with COVID-19. This analysis can aid in future decisions on the allocation of healthcare resources.

Physician stress in the era of COVID-19 vaccine disparity: a multi-institutional survey

CONTEXT

Healthcare workers are at a high risk of infection during infectious disease outbreaks, such as the COVID-19 pandemic. Despite the availability of several vaccines against COVID-19, the absence of vaccination in patients and colleagues remains a continuous source of stress in healthcare workers. We conducted a survey of physician preceptors, both MDs and DOs, to explore the impact of differences in the patients' and colleagues' vaccination status on their well-being, stress, and burnout.

OBJECTIVES

The objective of this study is to determine whether exposure to unvaccinated patients and/or colleagues increases stress and burnout in physician preceptors by utilizing a self-reported survey.

METHODS

This multi-institutional study was carried out in the United States in 2022. An online survey questionnaire was utilized to collect data from physicians working as preceptors for multiple academic institutions. The anonymous Qualtrics^® survey utilized a modified version of the questionnaire from the expanded Physician Well-being Index (ePWBI) designed by MedEd Web Solutions (MEWS). Statistical analysis on both descriptive and qualitative data were performed. Utilizing a threshold of p≤0.05, data analysis revealed many statistically significant relationships between the variables.

RESULTS

A total of 218 physician preceptors completed the survey. The survey results showed that physicians overwhelmingly (p < 0.001) felt that all patients (and healthcare workers) should be vaccinated. The results also indicated that physicians experienced more stress when working with unvaccinated patients (p<0.001), and these stressors were often associated with the physician's gender and age. Furthermore, physicians stated that both their assessment and treatment plans were significantly different for vaccinated vs unvaccinated patients (p=0.039 and p=0.0167, respectively). Most importantly, stress levels (p<0.001) and burnout characteristics (p=0.024) were noted by physicians, both in themselves and in their colleagues.

CONCLUSIONS

Findings suggest that physician stress and burnout is a common theme due to the differences in vaccination status of patients admitted to COVID-19 clinics. Due to a more rapid progression of COVID-19 in unvaccinated patients, treatment plans for vaccinated vs unvaccinated patients were also considerably different.

Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform

Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a readout for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in numerous cell culture models, independently of cytopathogenic effect formation. Compared to other models, the Caco-2 subline Caco-2-F03 displayed superior performance. It possesses a stable SARS-CoV-2 susceptibility phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (HK2) inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2-F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false-positive hits.

Humoral and cellular immunity of two-dose inactivated COVID-19 vaccination in Chinese children: A prospective cohort study

Children are the high-risk group for COVID-19, and in need of vaccination. However, humoral and cellular immune responses of COVID-19 vaccine remain unclear in vaccinated children. To establish the rational immunization strategy of inactivated COVID-19 vaccine for children, the immunogenicity of either one dose or two doses of the vaccine in children was evaluated. A prospective cohort study of 322 children receiving inactivated COVID-19 vaccine was established in China. The baseline was conducted after 28 days of the first dose, and the follow-up was conducted after 28 days of the second dose. The median titers of receptor binding domain (RBD)-IgG, and neutralizing antibody (NAb) against prototype strain and Omicron variant after the second dose increased significantly compared to those after the first dose (first dose: 70.0, [interquartile range, 30.0-151.0] vs. second dose: 1261.0 [636.0-2060.0] for RBD-IgG; 2.5 [2.5-18.6] vs. 252.0 [138.6-462.1] for NAb against prototype strain; 2.5 [2.5-2.5] vs. 15.0 [7.8-26.5] for NAb against Omicron variant, all p < 0.05). The flow cytometry results showed that the first dose elicited SARS-CoV-2 specific cellular immunity, while the second dose strengthened SARS-CoV-2 specific IL-2⁺ or TNF-α⁺  monofunctional, IFN-γ⁺ TNF-α⁺  bifunctional, and IFN-γ^- IL-2⁺ TNF-α⁺ multifunctional CD4⁺ T cell responses (p < 0.05). Moreover, SARS-CoV-2 specific memory T cells were generated after the first vaccination, including the central memory T cells and effector memory T cells. The present findings provide scientific evidence for the vaccination strategy of the inactive vaccines among children against COVID-19 pandemic.

SARS-CoV-2 evolves to reduce but not abolish neutralizing action

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have prolonged coronavirus disease 2019 (COVID-19) pandemic by escaping pre-existing immunity acquired by natural infection or vaccination. Elucidation of VOCs' mutation trends and evasion of neutralization is required to update current control measures. Mutations and the prevalence of VOCs were analyzed in the global immunization coverage rate context. Lentivirus-based pseudovirus neutralization analysis platforms for SARS-CoV-2 prototype strain (PS) and VOCs, containing Alpha, Beta, Gamma, Delta, and Omicron, were constructed based on the spike protein of each variant and HEK 293T cell line expressing the human angiotensin-converting enzyme 2 (hACE2) receptor on the surface, and an enhanced green fluorescent protein reporter. Serum samples from 65 convalescent individuals and 20 WIBP-CorV vaccine recipients and four therapeutic monoclonal antibodies (mAbs) namely imdevimab, casirivimab, bamlanivimab, and etesevimab were used to evaluate the neutralization potency against the variants. Pseudovirus-based neutralization assay platforms for PS and VOCs were established, and multiplicity of infection (MOI) was the key factor influencing the assay result. Compared to PS, VOCs may enhance the infectivity of hACE2-293T cells. Except for Alpha, other VOCs escaped neutralization to varying degrees. Attributed to favorable and emerging mutations, the current pandemic Omicron variant of all VOCs demonstrated the most significant neutralization-escaping ability to the sera and mAbs. Compared with the PS pseudovirus, Omicron had 15.7- and 3.71-fold decreases in the NT50 value (the highest serum dilution corresponding to a neutralization rate of 50%); and correspondingly, 90% and 43% of immunization or convalescent serum samples lost their neutralizing activity against the Omicron variant, respectively. Therefore, SARS-CoV-2 has evolved persistently with a strong ability to escape neutralization and prevailing against the established immune barrier. Our findings provide important clues to controlling the COVID-19 pandemic caused by new variants.

SARS-CoV-2: An Analysis of the Vaccine Candidates Tested in Combatting and Eliminating the COVID-19 Virus

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), better known as COVID-19, is a highly contagious virus, transferable via air droplets from close human-human contact. The pandemic has led to over 6.5 million deaths worldwide, making it the largest global health crisis since the influenza pandemic in 1918. SARS-CoV-2 rapidly spread around the world, forcing the World Health Organization (WHO) to deem it a global health pandemic after three months of its initiation. The virus has wreaked havoc on many countries worldwide, overwhelming healthcare systems, hence damaging many economies. Even though research has progressed the understanding of the SARS-CoV-2 virus, the information gathered about the vaccine trials and their findings have been scarcely distributed to the public in a single study. The information available to scientists has therefore given researchers a pathway to building an efficacious vehicle to substantially decrease the spread of the virus. The vaccines formulated had many challenges due to multiple factors such as viral mutations and clinical trial delays. This paper will aim to educate readers on the processes that the vaccine candidates took, and better understand the procedures; additionally, we'll look at all candidates' findings that went into clinical trials, assessing, analyzing, and evaluating the 27 vaccine candidates that went into phase III trials and the 13 candidates that went into either phase I/II trials.

Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged continuously, challenging the effectiveness of vaccines, diagnostics, and treatments. Moreover, the possibility of the appearance of a new betacoronavirus with high transmissibility and high fatality is reason for concern. In this study, we used a natively paired yeast display technology, combined with next-generation sequencing (NGS) and massive bioinformatic analysis to perform a comprehensive study of subdomain specificity of natural human antibodies from two convalescent donors. Using this screening technology, we mapped the cross-reactive responses of antibodies generated by the two donors against SARS-CoV-2 variants and other betacoronaviruses. We tested the neutralization potency of a set of the cross-reactive antibodies generated in this study and observed that most of the antibodies produced by these patients were non-neutralizing. We performed a comparison of the specific and non-specific antibodies by somatic hypermutation in a repertoire-scale for the two individuals and observed that the degree of somatic hypermutation was unique for each patient. The data from this study provide functional insights into cross-reactive antibodies that can assist in the development of strategies against emerging SARS-CoV-2 variants and divergent betacoronaviruses.

The Tragedy of Liberal Democratic Governance in the Face of Global Threats

In hindsight, the early response of liberal governments to the SARS-CoV-2 pandemic was chaotic and generally inefficient. Though one might be tempted to attribute these failures to the incompetence of certain political decision-makers, we propose another explanation. Global threats require a coordinated international response, which is only possible if the threat is perceived in the same way by all, and if government priorities are similar. The effectiveness of the response also relies on massive adhesion of citizens to the measures imposed, which in turn requires trust in government. Our hypothesis is that certain fundamental features of liberalism complicate such global and collective responses: neutrality of the state and primacy of the individual over collective society. Liberalism considers that institutions and public policy must not be designed to favor any specific conception of the common good. That which is best for all is usually determined by a "competition of opinions," which frequently leads to scientific expertise being considered as only one opinion among many. Liberalism also imposes strict respect for individual freedoms and private interests and tends to reject any form of collectivism or dictate imposed by the common good. In order to solve these structural problems and improve society's management of global threats, we make several proposals, such as the introduction of a minimal and consensual definition of the common good and the promotion of a health policy guided by One Health-like concepts. Overall, our analysis suggests that because political ideologies provide their own definitions of the common good and the place of scientific knowledge in the governance process and can thus affect the response to global threats, they should be urgently taken into consideration by public health experts.