The challenges of COVID-19 Delta variant: Prevention and vaccine development

Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies

The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.

Recent advances in chemometric modelling of inhibitors against SARS-CoV-2

The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.

Rational prediction of immunogenicity clustering through cross-reactivity analysis of thirteen SARS-CoV-2 variants

SARS-CoV-2 breakthrough infections in vaccinated individuals underscore the threat posed by continuous mutating variants, such as Omicron, to vaccine-induced immunity. This necessitates the search for broad-spectrum immunogens capable of countering infections from such variants. This study evaluates the immunogenicity relationship among SARS-CoV-2 variants, from D614G to XBB, through Guinea pig vaccination, covering D614G, Alpha, Beta, Gamma, Delta, BA.1, BA.2, BA.2.75, BA.2.75.2, BA.5, BF.7, BQ.1.1, and XBB, employing three immunization strategies: three-dose monovalent immunogens, three-dose bivalent immunogens, and a two-dose vaccination with D614G followed by a booster immunization with a variant strain immunogen. Three distinct immunogenicity clusters were identified: D614G, Alpha, Beta, Gamma, and Delta as cluster 1, BA.1, BA.2, and BA.2.75 as cluster 2, BA.2.75.2, BA.5, BF.7, BQ.1.1, and XBB as cluster 3. Broad-spectrum protection could be achieved through a combined immunization strategy using bivalent immunogens or D614G and XBB, or two initial D614G vaccinations followed by two XBB boosters. A comparison of neutralizing antibody levels induced by XBB boosting and equivalent dosing of D614G and XBB revealed that the XBB booster produced higher antibody levels. The study suggests that vaccine antigen selection should focus on the antigenic alterations among variants, eliminating the need for updating vaccine components for each variant.

Research progress in spike mutations of SARS-CoV-2 variants and vaccine development

The coronavirus disease 2019 (COVID-19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID-19 convalescent or vaccinated individuals is decreased against SARS-CoV-2 variants. Moreover, the vaccine effectiveness of current COVID-19 vaccines against SARS-CoV-2 VOCs is not as high as that against wild-type SARS-CoV-2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS-CoV-2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS-CoV-2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.

A Heterologous Challenge Rescues the Attenuated Immunogenicity of SARS-CoV-2 Omicron BA.1 Variant in Syrian Hamster Model

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is becoming a dominant circulator and has several mutations in the spike glycoprotein, which may cause shifts of immunogenicity, so as to result in immune escape and breakthrough infection among the already infected or vaccinated populations. It is unclear whether infection with Omicron could generate adequate cross-variant protection. To investigate this possibility, we used Syrian hamsters as an animal model for infection of SARS-CoV-2. The serum from Omicron BA.1 variant-infected hamsters showed a significantly lower neutralization effect against infection of the same or different SARS-CoV-2 variants than the serum from Beta variant-infected hamsters. Furthermore, the serum from Omicron BA.1 variant-infected hamsters were insufficient to protect against rechallenge of SARS-CoV-2 Prototype, Beta and Delta variants and itself. Importantly, we found that rechallenge with different SARS-CoV-2 lineages elevated cross-variant serum neutralization titers. Overall, our findings indicate a weakened immunogenicity feature of Omicron BA.1 variant that can be overcome by rechallenge of a different SARS-CoV-2 lineages. Our results may lead to a new guideline in generation and use of the vaccinations to combat the pandemic of SARS-CoV-2 Omicron variant and possible new variants. IMPORTANCE The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant causes breakthrough infections among convalescent patients and vaccinated populations. However, Omicron does not generate robust cross-protective responses. Here, we investigate whether heterologous SARS-CoV-2 challenge is able to enhance antibody response in a sensitive animal model, namely, Syrian hamster. Of note, a heterologous challenge of Beta and Omicron BA.1 variant significantly broadens the breadth of SARS-CoV-2 neutralizing responses against the prototype, Beta, Delta, and Omicron BA.1 variants. Our findings confirm that vaccination strategy with heterologous antigens might be a good option to protect against the evolving SARS-CoV-2.

A vaccine delivery system promotes strong immune responses against SARS-CoV-2 variants

Global coronavirus disease 2019 (COVID-19) pandemics highlight the need of developing vaccines with universal and durable protection against emerging SARS-CoV-2 variants. Here we developed an extended-release vaccine delivery system (GP-diABZI-RBD), consisting the original SARS-CoV-2 WA1 strain receptor-binding domain (RBD) as the antigen and diABZI stimulator of interferon genes (STING) agonist in conjunction with yeast β-glucan particles (GP-diABZI) as the platform. GP-diABZI-RBD could activate STING pathway and inhibit SARS-CoV-2 replication. Compared to diABZI-RBD, intraperitoneal injection of GP-diABZI-RBD elicited robust cellular and humoral immune responses in mice. Using SARS-CoV-2 GFP/ΔN transcription and replication-competent virus-like particle system (trVLP), we demonstrated that GP-diABZI-RBD-prototype vaccine exhibited the strongest and durable humoral immune responses and antiviral protection; whereas GP-diABZI-RBD-Omicron displayed minimum neutralization responses against trVLP. By using pseudotype virus (PsVs) neutralization assay, we found that GP-diABZI-RBD-Prototype, GP-diABZI-RBD-Delta, and GP-diABZI-RBD-Gamma immunized mice sera could efficiently neutralize Delta and Gamma PsVs, but had weak protection against Omicron PsVs. In contrast, GP-diABZI-RBD-Omicron immunized mice sera displayed the strongest neutralization response to Omicron PsVs. Taken together, the results suggest that GP-diABZI can serve as a promising vaccine delivery system for enhancing durable humoral and cellular immunity against broad SARS-CoV-2 variants. Our study provides important scientific basis for developing SARS-CoV-2 VOC-specific vaccines.

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.

Knowledge, practice and attitude associated with SARS-CoV-2 Delta Variant among adults in Jordan

COVID-19 infection is a global pandemic health emergency. This contagious disease was caused by the Severe Acute Respiratory Syndrome Coronavirus‑2 (SARS‑CoV-2) which is mutating over time. In 2021, the Delta variant became the most dominant transmissible form. During the crisis, human practice and knowledge were critical in the overall efforts to encompass the outbreak. A cross-sectional, web-based approach was conducted among adults in Jordan to quantify knowledge, attitude, and practices towards SARS-CoV-2 (Delta variant). This research was carried out between 15th April and 15th of May 2021. The study questionnaire consisted of four sections including the participant's demographics, knowledge, practices and attitude. Comparative evaluation of responses was accomplished using a scoring system. Respondents who scored above the mean score (60%) on the item measured were categorized as knowledgeable, having a positive attitude, and good practices. Participants were allocated to one of the three groups; medical, non-medical and others (unemployed and housewives). Data collected was analyzed using Statistical Package for Social Sciences (SPSS) version 23.0 software. A variance test to assess the statistical difference between groups was used. Pearson's chi-squared test was applied to compare the variables and identify significant predictors. Of the participants, 308 (66%) were in the age group of 18-25yrs, 392 (84.1%) females, 120 (25.8%) employed and 346 (74.2%) unemployed. The principle source of knowledge was social media (291, 62.4%). Interestingly, participants had adequate overall knowledge. The mean knowledge score was 22.6 (± 0.19), 20.6 (± 0.19), and 21.3 (± 0.18) for the medical, the non-medical and the others group, respectively. Also, participants showed a positive attitude and good practices towards SARS-CoV-2 (Delta variant). The mean practice score for medical, the non-medical and the others groups was 7.35 (± 0.25), 7.38 (± 0.24), 7.35 (± 0.24) and the mean attitude score was 10.8 (± 0.16), 9.4 (± 0.21), 9.5 (± 0.22), respectively. The studied groups generally had good knowledge, positive attitudes and good practices about SARS-CoV-2 (Delta variant). This was expected due to the authorities' successful management of the pandemic and the high educational level of the Jordanian society, bearing in mind the economic and social impact of COVID-19 disease.

A new strategy: identification of specific antibodies for neutralizing epitope on SARS-CoV-2 S protein by LC-MS/MS combined with immune repertoire

Although the SARS-CoV-2 vaccine has been widely used worldwide, not all individuals can produce neutralization antibodies, so it is still urgent to find and prepare neutralization antibodies for COVID-19 prevention or treatment. In this study, we created a new strategy to effectively obtain neutralizing antibodies or complementary determining region 3 (CDR3) of neutralizing antibodies against SARS-CoV-2. We first predicted and synthesized several B cell epitopes on RBD and adjacent RBD of S protein, then the B cell epitopes were used to prepare affinity chromatography columns respectively and purify the binding IgG from serum samples of convalescent COVID-19 patients. After these IgGs were identified to have neutralizing activity, the peptide sequences of the antigen-binding regions (variable region) of neutralizing antibodies were analyzed by protein mass spectrometry. Subsequently, the B cells from the same individual were sorted and used to obtain their full BCR repertoire by 5′ RACE combined with high-throughput of PacBio sequencing method. Then, the peptide sequence of neutralizing antibody variable region by protein mass spectrometry was mapped to the full BCR repertoire and found the full variable region sequence of neutralizing antibodies. Finally, we obtained and synthesized numerous CDR3 peptides of neutralizing antibodies to confirm the neutralizing activity for SARS-CoV-2 infection. Our results indicate that the novel scheme will be suitable for rapid screening of neutralizing antibodies, including screening neutralizing antibodies against SARS-CoV-2 and other pathogenic microorganisms.

Impact of the COVID-19 Pandemic on Gyne-Oncological Treatment-A Retrospective Single-Center Analysis of a German University Hospital with 30,525 Patients

The study pursues the objective of drawing a comparison between the data of gyne-oncology, gynecology, and obstetrics patient collectives of a German university hospital regarding the progression of patient number and corresponding treatment data during the five-year period of 2017-2021 to assess the impact of the COVID-19 pandemic on gyne-oncological treatment. Descriptive assessment is based on data extracted from the database of the hospital controlling system QlikView^® for patients hospitalized at the Department of Gynecology and Obstetrics of Marburg University Hospital. Gynecology and gyne-oncology experience a maintained decline in patient number (n_Gynecology: -6% 2019 to 2020, -5% 2019 to 2021; n_{Gyne-Oncology}: -6% 2019 to 2020, -2% 2019 to 2021) with varying effects on the specific gyne-oncological main diagnoses. Treatment parameters remain unchanged in relative assessment, but as gyne-oncology constitutes the dominating revenue contributor in gynecology (35.1% of patients, 52.9% of revenue, 2021), the extent of the decrease in total revenue (-18%, 2019 to 2020, -14%, 2019 to 2021) surpasses the decline in patient number. The study displays a negative impact on the gynecology care situation of a German university hospital for the entire pandemic, with an even greater extent on gyne-oncology. This development not only endangers the quality of medical service provision but collaterally pressurizes gynecology service providers.

The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far

The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.

Gesundheitsökonomischer Vergleich von onkologischen und COVID-19-Patienten

Zielsetzung Ziel der Studie ist es die Auswirkungen der COVID-19 Pandemie auf die stationär behandelten Patienten eines universitären Maximalversorgers mit einer Krebs- und/oder COVID-19-Erkrankung zu untersuchen. Unterscheiden sich die Patientenkollektive gesundheitsökonomisch und ergeben sich aus den Resultaten administrative Konsequenzen für eine proaktive Steuerung der regionalen Krebsversorgung.

Methodik Es wurde eine retrospektive, deskriptive Datenanalyse klinischer und gesundheitsökonomischer Parameter aller am Universitätsklinikum Marburg stationär aufgenommenen onkologischen und COVID-19-postiven Patienten sowie der Kombination von onkologischen Patienten mit einer COVID-19-Erkrankung innerhalb des Beobachtungszeitraums von 2017 bis 2021 durchgeführt.

Ergebnisse Es wurde ein Rückgang onkologisch behandelter Patienten über den gesamten Zeitraum der COVID-19-Pandemie beobachtet. Onkologische Patienten mit einer COVID-19-Erkrankung stellen das Patientenkollektiv mit dem höchsten Schweregrad der Erkrankung dar, gefolgt von der COVID-19- und rein onkologischen Patienten. Dies spiegelt sich gleichsam in den ökonomischen Leistungskennzahlen wider. Die chronologischen Verläufe des DRG-Erlöses und Case Mix Index pro COVID-19-Patienten weisen Unterschiede für Zeitabschnitte des Pandemiegeschehens in Deutschland auf.

Schlussfolgerung Der Vergleich der Patientenkollektive bestätigt das hohes Gefährdungspotential von onkologischen Patienten, welches sich in einer gesundheitsökonomisch aufwendigen Behandlung widerspiegelt. Nationale Maßnahmen, Kontaktbeschränkungen oder pandemische Ereignisse lassen sich am chronologischen Verlauf der klinischen und wirtschaftlichen Parameter nachvollziehen. Trotz des internationalen Rückgangs an ambulanten und stationären onkologischen Patienten ist die „state-of-the-art“ Krebsversorgung in pandemischen Zeiten realisierbar. Aufgrund dessen besteht die Handlungsnotwendigkeit für einen stationären Maximalversorger durch Kommunikation und Versorgungsmodellierung die onkologische Versorgung proaktiver zu steuern.

Lactoferrin for COVID-19 prevention, treatment, and recovery

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), a unique beta-coronavirus, has caused the most serious outbreak of the last century at the global level. SARS-CoV-2 infections were firstly reported in the city of Wuhan in China in 2019 and this new disease was named COVID-19 by World Health Organization (WHO). As this novel disease can easily be transmitted from one individual to another via respiratory droplets, many nations around the world have taken several precautions regarding the reduction in social activities and quarantine for the limitation of the COVID-19 transmission. SARS-CoV-2 is known to cause complications that may include pneumonia, acute respiratory distress syndrome (ARDS), multi-organ failure, septic shock, and death. To prevent and treat COVID-19, some significant studies have been conducted since the outbreak. One of the most noticeable therapeutic approaches is related to a multifunctional protein, lactoferrin. Lactoferrin (Lf) is an 80 kDa cationic glycoprotein that has a great range of benefits from improving the immunity to antiviral effects due to its unique characteristics such as the iron-binding ability. This review summarizes the characteristics of SARS-CoV-2 and the potential applications of Lf for the prevention, treatment, and recovery of COVID-19.

Potential of conserved antigenic sites in development of universal SARS-like coronavirus vaccines

Given pandemic risks of zoonotic SARS-CoV-2 variants and other SARS-like coronaviruses in the future, it is valuable to perform studies on conserved antigenic sites to design universal SARS-like coronavirus vaccines. By using antibodies obtained from convalescent COVID-19 patients, we succeeded in functional comparison of conserved antigenic sites at multiple aspects with each other, and even with SARS-CoV-2 unique antigenic sites, which promotes the cognition of process of humoral immune response to the conserved antigenic sites. The conserved antigenic sites between SARS-CoV-2 and SARS-CoV can effectively induce affinity maturation of cross-binding antibodies, finally resulting in broadly neutralizing antibodies against multiple variants of concern, which provides an important basis for universal vaccine design, however they are subdominant, putatively due to their lower accessibility relative to SARS-CoV-2 unique antigenic sites. Furthermore, we preliminarily design RBDs to improve the immunogenicity of these conserved antigenic sites. Our study focusing on conserved antigenic sites provides insights for promoting the development of universal SARS-like coronavirus vaccines, thereby enhancing our pandemic preparedness.

SARS-CoV-2 Seroprevalence Study in Pediatric Patients and Health Care Workers Using Multiplex Antibody Immunoassays

SARS-CoV-2 infection has become a global health problem specially exacerbated with the continuous appearance of new variants. Healthcare workers (HCW) have been one of the most affected sectors. Children have also been affected, and although infection generally presents as a mild disease, some have developed the Pediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS). We recruited 190 adults (HCW and cohabitants, April to June 2020) and 57 children (April 2020 to September 2021), of whom 12 developed PIMS-TS, in a hospital-based study in Spain. Using an in-house Luminex assay previously validated, antibody levels were measured against different spike and nucleocapsid SARS-CoV-2 proteins, including the receptor-binding domain (RBD) of the Alpha, Beta, Gamma, and Delta variants of concern (VoC). Seropositivity rates obtained from children and adults, respectively, were: 49.1% and 11% for IgG, 45.6% and 5.8% for IgA, and 35.1% and 7.3% for IgM. Higher antibody levels were detected in children who developed PIMS-TS compared to those who did not. Using the COVID-19 IgM/IgA ELISA (Vircell, S.L.) kit, widely implemented in Spanish hospitals, a high number of false positives and lower seroprevalences compared with the Luminex estimates were found, indicating a significantly lower specificity and sensitivity. Comparison of antibody levels against RBD-Wuhan versus RBD-VoCs indicated that the strongest positive correlations for all three isotypes were with RBD-Alpha, while the lowest correlations were with RBD-Delta for IgG, RBD-Gamma for IgM, and RBD-Beta for IgA. This study highlights the differences in antibody levels between groups with different demographic and clinical characteristics, as well as reporting the IgG, IgM, and IgA response to RBD VoC circulating at the study period.

SARS-CoV-2 infection in pediatric population before and during the Delta (B.1.617.2) and Omicron (B.1.1.529) variants era

BACKGROUND

COVID-19, the coronavirus disease that emerged in December 2019, caused drastic damage worldwide. At the beginning of the pandemic, available data suggested that the infection occurs more frequently in adults than in infants. In this review, we aim to provide an overview of SARS-CoV-2 infection in children before and after B.1.617.2 Delta and B.1.1.529 Omicron variants emergence in terms of prevalence, transmission dynamics, clinical manifestations, complications and risk factors.

METHODS

Our method is based on the literature search on PubMed, Science Direct and Google Scholar. From January 2020 to July 2022, a total of 229 references, relevant for the purpose of this review, were considered.

RESULTS

The incidence of SARS-CoV-2 infection in infants was underestimated. Up to the first half of May, most of the infected children presented asymptomatic or mild manifestations. The prevalence of COVID-19 varied from country to another: the highest was reported in the United States (22.5%). COVID-19 can progress and become more severe, especially with the presence of underlying health conditions. It can also progress into Kawasaki or Multisystem Inflammatory Syndrome (MIS) manifestations, as a consequence of exacerbating immune response. With the emergence of the B.1.617.2 Delta and B.1.1.529 Omicron variants, it seems that these variants affect a large proportion of the younger population with the appearance of clinical manifestations similar to those presented by adults with important hospitalization rates.

CONCLUSION

The pediatric population constitutes a vulnerable group that requires particular attention, especially with the emergence of more virulent variants. The increase of symptomatic SARS-CoV-2 infection and hospitalization rate among children highlights the need to extend vaccination to the pediatric population.

Rational identification of small molecules derived from 9,10-dihydrophenanthrene as potential inhibitors of 3CLpro enzyme for COVID-19 therapy: a computer-aided drug design approach

Small molecules such as 9,10-dihydrophenanthrene derivatives have remarkable activity toward inhibition of SARS-CoV-2 3CL^pro and COVID-19 proliferation, which show a strong correlation between their structures and bioactivity. Therefore, these small compounds could be suitable for clinical pharmaceutical use against COVID-19. The objective of this study was to remodel the structures of 9,10-dihydrophenanthrene derivatives to achieve a powerful biological activity against 3CL^pro and favorable pharmacokinetic properties for drug design and discovery. Therefore, by the use of bioinformatics techniques, we developed robust 3D-QSAR models that are capable of describing the structure–activity relationship for 46 molecules based on 9,10-dihydrophenanthrene derivatives using CoMFA/SE (R² = 0.97, Q² = 0.81, R²_pred = 0.95, ^cR²_p = 0.71) and CoMSIA/SEHDA (R² = 0.94, Q² = 0.76, R²_pred = 0.91, ^cR²_p = 0.65) techniques. Accordingly, 96 lead compounds were generated based on a template molecule that showed the highest observed activity in vitro (T40, pIC₅₀ = 5.81) and predicted their activities and bioavailability in silico. The rational screening outputs of 3D-QSAR, Molecular docking, ADMET, and MM-GBSA led to the identification of 9 novel modeled molecules as potent noncovalent drugs against SARS-CoV-2-3CL^pro. Finally, by molecular dynamics simulations, the stability and structural dynamics of 3CL^pro free and complex (PDB code: 6LU7) were discussed in the presence of samples of 9,10-dihydrophenanthrene derivative in an aqueous environment. Overall, the retrosynthesis of the proposed drug compounds in this study and the evaluation of their bioactivity in vitro and in vivo may be interesting for designing and discovering a new drug effective against COVID-19.

Chronological development of in-patient oncology in times of COVID-19: a retrospective analysis of hospitalized oncology and COVID-19 patients of a German University Hospital

Purpose

The goal of this study is to examine the chronological development of hospitalized oncology and COVID-19 patients, and compare effects on oncology sub-disciplines for pre-pandemic (2017–19) and pandemic (2020–21) years in the setting of a German university maximum care provider.

Methods

Data were retrospectively retrieved from the hospital performance controlling system for patient collectives with oncological main (n_Onco) and COVID-19 secondary diagnosis (n_COVID-19). Data analysis is based on descriptive statistical assessment.

Results

The oncology patient collective (n_Onco = 27,919) shows a decrease of hospitalized patients for the whole pandemic (− 4% for 2020 and − 2,5% for 2021 to 2019). The number of hospitalized COVID-19 patients increases from first to second pandemic year by + 106.71% (n_COVID-19 = 868). Maximum decline in monthly hospitalized oncology patients amounts to − 19% (May 2020) during the first and − 21% (December 2020) during the second lockdown. Relative monthly hospitalization levels of oncology patients reverted to pre-pandemic levels from February 2021 onwards.

Conclusion

The results confirm a decline in hospitalized oncology patients for the entire pandemic in the setting of a maximum care provider. Imposed lockdown and contact restrictions, rising COVID-19 case numbers, as well as discovery of new virus variants have a negative impact on hospitalized treated oncological patients.

Exploring the risk factors of COVID-19 Delta variant in the USA based on Bayesian spatio-temporal analysis

The transmission of coronavirus disease‐2019 (COVID‐19) epidemic is a global emergency, which is worsened by the genetic mutations of SARS‐CoV‐2. However, till date, few statistical studies have researched the COVID‐19 spread patterns in terms of the variant cases. Hence, this paper aims to explore the associated risk factors of Delta variant, the most contagious strain of COVID‐19. The study collected the state‐level COVID‐19 Delta variant cases in the United States during a 12‐week period and included potential environmental, socioeconomic, and public prevention factors as independent variables. Instead of regarding the covariate effects as constant, this paper proposes a flexible Bayesian hierarchical model with spatio‐temporally varying coefficients to account for data heterogeneity. The method enables us to cluster the states into distinctive groups based on the temporal trends of the coefficients and simultaneously identify significant risk factors for each cluster. The findings contribute novel insight into the dynamics of covariate effects on the COVID‐19 Delta variant over space and time, which could help the government develop targeted prevention measures for vulnerable regions based on the selected risk factors.

SARS-CoV-2: phenotype, genotype, and characterization of different variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), a major international public health concern. Because of very similar amino acid sequences of the seven domain names, SARS-CoV-2 belongs to the Coronavirinae subfamily of the family Coronaviridae, order Nidovirales, and realm Riboviria, placed in exceptional clusters, but categorized as a SARS-like species. As the RNA virus family with the longest genome, the Coronaviridae genome consists of a single strand of positive RNA (25–32 kb in length). Four major structural proteins of this genome include the spike (S), membrane (M), envelope (E), and the nucleocapsid (N) protein, all of which are encoded within the 3′ end of the genome. By engaging with its receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 infects host cells. According to the most recent epidemiological data, as the illness spread globally, several genetic variations of SARS-CoV-2 appeared quickly, with the World Health Organization (WHO) naming 11 of them. Among these, seven SARS-CoV-2 subtypes have received the most attention. Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.617.2) are now designated as variations of concern (VOC) (B.1.1.529). Lambda (C.37) and Mu are variations of interest (VOI) (B.1.621). The remaining six are either being monitored or are no longer considered a threat. On the basis of studies done so far, antiviral drugs, antibiotics, glucocorticoids, recombinant intravenous immunoglobulin, plasma therapy, and IFN-α2b have been used to treat patients. Moreover, full vaccination is associated with lower infection and helps prevent transmission, but the risk of infection cannot be eliminated completely in vaccinated people.

Therapeutics to tackle Omicron outbreak

In this commentary, the authors have focused on the mutational impact of the Omicron variant on the current therapeutics to manage #COVID19.

Omicron (B.1.1.529) variant of SARS-CoV-2: Concerns, challenges, and recent updates

Omicron has shown immune escape from neutralizing antibodies generated through previous infection or vaccination. It could evade the protection provided by mAbs being used in clinics for treating coronavirus disease 2019 (COVID‐19) patients. Booster dose is recommended to elevate the protective levels of antibodies in COVID‐19 vaccinated individuals. The development of powerful oral antiviral drugs such as Molnupiravir and Paxlovid have shown promising clinical results and raised new hopes of COVID‐19 treatment. High efforts are being made to develop highly efficacious vaccines, and by implementing appropriate prevention and control strategies to counter Omicron.

Perceived Vulnerability to Disease and the Relationship with Teacher Satisfaction in South Africa during COVID-19: The Serial Role of Burnout, Role Conflict, and Ambiguity

Teachers’ work roles and responsibilities have changed dramatically because of the COVID-19 pandemic. These unprecedented changes have the potential to generate role stress and burnout and reduce teachers’ job satisfaction. This study investigated the serial relationship between perceived vulnerability to disease, role stress, burnout, and teaching satisfaction. It was hypothesised that individuals who perceive themselves to be at high risk of contracting COVID-19 would report high role conflict and ambiguity in the workplace, which would in turn lead to high levels of burnout and low satisfaction with teaching. Participants were schoolteachers (N = 355) who completed the Perceived Vulnerability to Disease Questionnaire, the Role Orientation Questionnaire, the Maslach Burnout Inventory, and the Teaching Satisfaction Scale. Path analysis confirmed that perceived vulnerability to disease was associated with role conflict and ambiguity, which was in turn associated with emotional exhaustion, depersonalisation, and low teaching satisfaction. Teachers who appraised themselves as being more vulnerable to contracting COVID-19 experienced greater role stress, which was associated with high levels of burnout and low teaching satisfaction. This study highlights that threat appraisals related to contracting COVID-19 represent an additional job demand and this needs to be matched by job resources that can facilitate coping.

Heterologous immunization with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant

The recent emergence of the Omicron variant has raised concerns on vaccine efficacy and the urgent need to study more efficient vaccination strategies. Here we observed that an mRNA vaccine booster in individuals vaccinated with two doses of inactivated vaccine significantly increased the plasma level of specific antibodies that bind to the receptor-binding domain (RBD) or the spike (S) ectodomain (S1 + S2) of both the G614 and the Omicron variants, compared to two doses of homologous inactivated vaccine. The level of RBD- and S-specific IgG antibodies and virus neutralization titers against variants of concern in the heterologous vaccination group were similar to that in individuals receiving three doses of homologous mRNA-vaccine or a boost of mRNA vaccine after infection, but markedly higher than that in individuals receiving three doses of a homologous inactivated vaccine. This heterologous vaccination regime furthermore significantly enhanced the RBD-specific memory B cell response and S1-specific T cell response, compared to two or three doses of homologous inactivated vaccine. Our study demonstrates that mRNA vaccine booster in individuals vaccinated with inactivated vaccines can be highly beneficial, as it markedly increases the humoral and cellular immune responses against the virus, including the Omicron variant.

COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development

In the two years since the SARS-CoV-2 pandemic started, it has caused over 5 million deaths and 400 million infected cases, and the world continues to be on high alert for COVID-19. Among the variants of interest and concern of SARS-CoV-2, the current Omicron (B.1.1.529) and stealth Omicron (BA.2) raised serious concerns due to rapid rates of infection caused by numerous mutations in the spike protein, which could escape from the antibody-mediated neutralization and increase the risk of reinfections. Hence, this work aims to describe the most relevant mutations in the SARS-CoV-2 spike protein, discuss vaccine against variant of concerns, describe rare adverse events after COVID-19 vaccination, introduce the most available promising COVID-19 vaccine candidates, and provide few perspectives of the future variants.

Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir

The COVID-19 pandemic continues to be a public health threat. Multiple mutations in the spike protein of emerging variants of SARS-CoV-2 appear to impact on the effectiveness of available vaccines. Specific antiviral agents are keenly anticipated but their efficacy may also be compromised in emerging variants. One of the most attractive coronaviral drug targets is the main protease (M^pro). A promising M^pro inhibitor of clinical relevance is the peptidomimetic nirmatrelvir (PF-07321332). We expressed M^pro of six SARS-CoV-2 lineages (C.37 Lambda, B.1.1.318, B.1.2, B.1.351 Beta, B.1.1.529 Omicron, P.2 Zeta), each of which carries a strongly prevalent missense mutation (G15S, T21I, L89F, K90R, P132H, L205V). Enzyme kinetics reveal that these M^pro variants are catalytically competent to a similar degree as the wildtype. We show that nirmatrelvir has similar potency against the variants as the wildtype. Our in vitro data suggest that the efficacy of the specific M^pro inhibitor nirmatrelvir is not compromised in current COVID-19 variants.

An exploratory study on the propagation of SARS-CoV-2 variants: Omicron is the most predominant variant

As SARS-CoV-2 evolves, it accumulates mutations, which are changes in the genetic code. Because this virus has built-in RNA repair mechanisms, it generates mutations more slowly than some other RNA viruses. Thousands of mutations have emerged since the beginning of the pandemic throughout all virus genomes sequenced to date, resulting in thousands of distinct variants. However, some variants have recently been discovered that appear to increase transmissibility and may affect illness pervasiveness. In this study, we investigated SARS-CoV-2 variants and how countries intervene with them. We also depicted the top 25 countries where the Omicron variant is prevalent, with the UK, US, Denmark, France, and Australia having the top five places as of January 13, 2022. The perception of SARS-CoV-2 variants was investigated in those five countries, and the propagation rate of the Omicron variant was determined to be 51%, 29%, 26%, 15%, and 44% respectively, indicating that the Omicron variant is the most prevalent among the others. Then, a study of SARS-CoV-2 infection test rate based on tests conducted per one million populations with number of sequences in those five countries reveals that 25%, 73%, 1.6%, 4.8%, and 1.5% respectively, it suggests that viral testing should be increased in all five countries since it will help to determine the precise distribution of variants and aid governments in making policy decisions for public safety. We anticipated the production of new variants strains. This research implies that limiting disease transmissions, such as acquiring a COVID-19 vaccine and booster doses for those aged 18 and older, as well as wearing the mask in public places, is the best strategy to prevent the emergence of new variants. This article is protected by copyright. All rights reserved.

Twin combination of Omicron and Delta variant triggering a Tsunami wave of ever high surges in COVID-19 cases: a challenging global threat with a special focus on Indian sub-continent

Due to the continuous emergence of multiple variants of severe acute respiratory syndrome cronavirus-2 (SARS-CoV-2), the Coronavirus disease (COVID-19) pandemic has caused severe morbidity and mortality worldwide in the last two years amidst waves of pandemic within the ongoing pandemic resulting into high global health concerns and adverse socioeconomics impacts. 1-4 Omicron, the recent highly mutated SARS-CoV-2 variant (B.1.1.529), classified as variant of concern (VoC) by WHO on 26 November 2021, is now becoming a dominant strain in several countries and a very massive surge in COVID-19 cases is being faced presently with nearly 300 million cumulative cases and 5.5 million deaths reported as of January 5, 2022 This article is protected by copyright. All rights reserved.

RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor

The COVID-19 pandemic, caused by SARS-CoV-2, has led to catastrophic damage for global human health. The initial step of SARS-CoV-2 infection is the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Constant evolution of SARS-CoV-2 generates new mutations across its genome including the coding region for the RBD in the spike protein. In addition to the well-known single mutation in the RBD, the recent new mutation strains with an RBD "double mutation" are causing new outbreaks globally, as represented by the delta strain containing RBD L452R/T478K. Although it is considered that the increased transmissibility of double-mutated strains could be attributed to the altered interaction between the RBD and ACE2 receptor, the molecular details remain to be elucidated. Using the methods of molecular dynamics simulation, superimposed structural comparison, free binding energy estimation, and antibody escaping, we investigated the relationship between the ACE2 receptor and the RBD double mutants of L452R/T478K (delta), L452R/E484Q (kappa), and E484K/N501Y (beta, gamma). The results demonstrated that each of the three RBD double mutants altered the RBD structure and enhanced the binding of the mutated RBD to ACE2 receptor. Together with the mutations in other parts of the virus genome, the double mutations increase the transmissibility of SARS-CoV-2 to host cells.

The challenges of COVID-19 Delta variant: Prevention and vaccine development

Several SARS-CoV-2 variants have emerged since the pandemic, bringing about a renewed threat to the public. Delta variant (B.1.617.2) was first detected in October 2020 in India and was characterized as variants of concern (VOC) by WHO on May 11, 2021. Delta variant rapidly outcompeted other variants to become the dominant circulating lineages due to its clear competitive advantage. There is emerging evidence of enhanced transmissibility and reduced vaccine effectiveness (VE) against Delta variant. Therefore, it is crucial to understand the features and phenotypic effects of this variant. Herein, we comprehensively described the evaluation and features of Delta variant, summarized the effects of mutations in spike on the infectivity, transmission ability, immune evasion, and provided a perspective on efficient approaches for preventing and overcoming COVID-19.