The Emergence of Omicron: Challenging Times Are Here Again!

Development of an ancestral DC and TLR4-inducing multi-epitope peptide vaccine against the spike protein of SARS-CoV and SARS-CoV-2 using the advanced immunoinformatics approaches

The oldest human coronavirus that started pandemics is severe acute respiratory syndrome virus (SARS-CoV). While SARS-CoV was eradicated, its new version, SARS-CoV2, caused the global pandemic of COVID-19. Evidence highlights the harmful events orchestrated by these viruses are mediated by Spike (S)P protein. Experimental epitopes of the S protein which were overlapping and ancestral between SARS-CoV and SARS-CoV-2 were obtained from the immune epitopes database (IEDB). The epitopes were then assembled in combination with a 50 S ribosomal protein L7/L12 adjuvant, a Mycobacterium tuberculosis-derived element and mediator of dendritic cells (DCs) and toll-like receptor 4 (TLR4). The immunogenic sequence was modeled by the GalaxyWeb server. After the improvement and validation of the protein structure, the physico-chemical properties and immune simulation were performed. To investigate the interaction with TLR3/4, Molecular Dynamics Simulation (MDS) was used. By merging the 17 B- and T-lymphocyte (HTL/CTL) epitopes, the vaccine sequence was created. Also, the Ramachandran plot presented that most of the residues were located in the most favorable and allowed areas. Moreover, SnapGene was successful in cloning the DNA sequence linked to our vaccine in the intended plasmid. A sequence was inserted between the XhoI and SacI position of the pET-28a (+) vector, and simulating the agarose gel revealed the existence of the inserted gene in the cloned plasmid with SARS vaccine (SARSV) construct, which has a 6565 bp in length overall. In terms of cytokines/IgG response, immunological simulation revealed a strong immune response. The stabilized vaccine showed strong interactions with TLR3/4, according to Molecular Dynamics Simulation (MDS) analysis. The present ancestral vaccine targets common sequences which seem to be valuable targets even for the new variant SARS-CoV-2.

Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants

Post-market surveillance of test performance is a critical function of public health agencies and clinical researchers that ensures tests maintaining diagnostic characteristics following their regulatory approval. Changes in product quality, manufacturing processes over time, or the evolution of new variants may impact product performance. During the COVID-19 pandemic, a plethora of point-of-care tests (POCTs) was released onto the Canadian market. This study evaluated the performance characteristics of several of the most widely distributed POCTs in Canada, including four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT). All tests were challenged with 149 SARS-CoV-2 clinical positives, including multiple variants up to and including Omicron XBB.1.5, as well as 29 clinical negatives. Results were stratified based on whether the isolate was Omicron or pre-Omicron as well as by reverse transcriptase quantitative PCR Ct value. The test performance of each POCT was consistent with the manufacturers' claims and showed no significant decline in clinical performance against any of the variants tested. These findings provide continued confidence in the results of these POCTs as they continue to be used to support decentralized COVID-19 testing. This work demonstrates the essential role of post-market surveillance in ensuring reliability in diagnostic tools.IMPORTANCEPost-market surveillance of diagnostic test performance is critical to ensure their reliability after regulatory approval. This is especially critical in the context of the COVID-19 pandemic as the use of point-of-care tests (POCTs) became widespread. Our study focused on four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT) that were widely distributed across Canada, assessing their performance using many SARS-CoV-2 variants, including up to Omicron subvariant XBB.1.5. Overall, we found no significant difference in performance against any variant, reinforcing confidence in their use. As concerns in test efficacy have been raised by news outlets, particularly regarding the BTNX Rapid Response, this work is even more timely and crucial. Our research offers insights into the performance of widely used COVID-19 POCTs but also highlights the necessity for post-market surveillance.

Epidemiological Features of Hepatitis C in China From 2015 to 2021: Insights From National Surveillance Data

The COVID-19 pandemic overwhelmed national health care systems, not least in the context of hepatitis elimination. This study investigates the effects of the pandemic response on the incidence rate, mortality rate, and case fatality rate (CFR) for hepatitis C virus (HCV) cases in China. We extracted the number of hepatitis C cases and HCV-related deaths by month and year for 2015 to 2021 in China and applied two proportional tests to analyze changes in the average yearly incidence rates, mortality rates, and CFRs for 2015 to 2020. We used the autoregressive integrated moving average model to predict these three rates for 2020 based on 2015 to 2019 HCV data. The incidence of hepatitis C decreased by 7.11% and 1.42% (P < .001) in 2020 and 2021, respectively, compared with 2015 to 2019, while it increased by 6.13% (P < .001) in 2021 relative to 2020. The monthly observed incidence in 2020 was significantly lower (-26.07%) than predicted. Meanwhile, no differences in mortality rate or CFR were observed between 2021, 2020, and 2015 to 2019. Our findings suggested that nonpharmaceutical interventions and behavioral changes to mitigate COVID-19 could have reduced hepatitis C incidence and accelerated China's implementation of a plan to eliminate HCV infection.

RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

Three years of COVID-19 in children that attend the Mexican Social Security Institute's 1,350 child day-care centers, 2020-2023

Background

Studies have suggested that children are less likely than adults to develop COVID-19; however, with the emergence of SARS-CoV-2 variants, hospitalization and death due to this cause have increased among the youngest ones.

Methods

Retrospective, descriptive analytical study of the COVID-19 cases, hospitalizations and deaths occurred in children under five years who attended in Child Day-Care Centers (Centros de Atención Infantil-CAIs) of the Mexican Social Security Institute (IMSS) from 20th July 2020 to 31st March 2023. Results were compared with Mexico's and the US's national-level data. Incidence, attack (children and workers) and mortality rates were estimated. The risks of getting sick, being hospitalized and dying due to COVID-19 were calculated by year.

Results

There were 4,369 COVID-19 cases among children from IMSS CAIs; 67 (1.5%) required hospitalization and only two deaths were reported (0.04%). Both at IMSS CAIs and at a national level in Mexico and the US, the highest incidences of COVID-19 among children under five years occurred during Omicron prevalence. The attack rate among workers (32.93%) was higher than children (4.99%). Hospitalization and mortality rates in the US decreased since the anti-COVID 19 vaccine was introduced in children older than six months, unlike the rates in Mexico, where the vaccine for this age group was not available. By the year 2020, the children that attended the IMSS CAIs were 77.3% less likely to be hospitalized; 80.9% in 2021, 93.2% in 2022, and 77.7% by March 2023, compared to same age children in Mexico. In 2021, the children that attended IMSS CAIs were 90.6% less likely to die due to COVID-19, and by March 2023, this likelihood was 34.3% lower than the rest of children in this age group in Mexico.

Conclusions

Children that attended IMSS CAIs had a smaller risk of hospitalization and death due to COVID-19. However, the high rates of hospitalization and death due to SARS-CoV-2 in children under five years in our country point to the need and urgency of vaccination against this virus in this age group, as well as of the adherence to strict detection and medical referral protocols.

Contribution of rumination and psychological resilience to post-traumatic growth of front-line healthcare workers in mobile cabin hospitals under Normalized epidemic Prevention and Control Requirements

To understand the level of post-traumatic growth (PTG) and influencing factors among front-line healthcare workers (HCWs) working in mobile cabin hospitals treating patients with Coronavirus Disease 2019 (COVID-19) under the Normalized Epidemic Prevention and Control Requirements adopted in China. A random sampling method was used to select 540 HCWs of the Chongqing-aid-Shanghai medical team from April to May 2022 as the study participants. Participants completed a general information questionnaire, the Post-traumatic Growth Inventory-Chinese version (PTGI-C), the Chinese version of the Connor-Davidson Resilience Scale (CD-RISC) and the Chinese Event Related Rumination Inventory (C-ERRI). Among the 540 included HCWs, 83.15 % were nurses and 78.89 % were women. The average scores for PTG (62.25 ± 16.73) and psychological resilience (64.22 ± 15.38) were at moderate levels, and the average score for rumination was low (21.62 ± 10.77). Pearson correlation analysis showed that CD-RISC and C-ERRI scores were positive with the PTGI-C score (r = 0.528, 0.316, P < 0.001). Multiple linear regression analysis identified psychological training or intervention during the COVID-19 epidemic (β = 2.353, P = 0.044), psychological resilience (β = 0.525, P < 0.001) and deliberate rumination (β = 0.732, P < 0.001) as factors significantly associated with the PTG of front-line HCWs, which together explained 36.8 % of the total variance in PTG (F[5,539] = 63.866, P < 0.001). In general, psychological resilience and deliberate rumination can promote PTG among HCWs and can be improved by strengthening psychological training and interventions for HCWs working under the Normalized Epidemic Prevention and Control Requirements.

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.

SARS-CoV-2 variants infectivity prediction and therapeutic peptide design using computational approaches

The outbreak of severe acute respiratory coronavirus 2 (SARS-CoV-2) has created a public health emergency globally. SARS-CoV-2 enters the human cell through the binding of the spike protein to human angiotensin converting enzyme 2 (ACE2) receptor. Significant changes have been reported in the mutational landscape of SARS-CoV-2 in the receptor binding domain (RBD) of S protein, subsequent to evolution of the pandemic. The present study examines the correlation between the binding affinity of mutated S-proteins and the rate of viral infectivity. For this, the binding affinity of SARS-CoV and variants of SARS-CoV-2 towards ACE2 was computationally determined. Subsequently, the RBD mutations were classified on the basis of the number of strains identified with respect to each mutation and the resulting variation in the binding affinity was computationally examined. The molecular docking studies indicated a significant correlation between the Z-Rank score of mutated S proteins and the rate of infectivity, suitable for predicting SARS-CoV-2 infectivity. Accordingly, a 30-mer peptide was designed and the inhibitory properties were computationally analyzed. Single amino acid-wise mutation was performed subsequently to identify the peptide with the highest binding affinity. Molecular dynamics and free energy calculations were then performed to examine the stability of the peptide-protein complexes. Additionally, selected peptides were synthesized and screened using a colorimetric assay. Together, this study developed a model to predict the rate of infectivity of SARS-CoV-2 variants and propose a potential peptide that can be used as an inhibitor for the viral entry to human.Communicated by Ramaswamy H. Sarma.

A third (booster) dose of the inactivated SARS-CoV-2 vaccine elicits immunogenicity and T follicular helper cell responses in people living with HIV

Introduction

This study sought to explore the immunogenicity of a booster dose of an inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine in people living with human immunodeficiency virus (HIV) and identify the factors affecting the magnitude of anti-SARS-CoV-2 antibody levels.

Materials and methods

A total of 34 people living with HIV (PLWH) and 34 healthy donors (HD) were administered a booster dose of the same SARS-CoV-2 vaccine. Anti-SARS-CoV-2 antibody and immunoglobulin G (IgG) levels were measured using the SARS-CoV-2 S protein neutralizing antibody Enzyme-Linked Immunosorbent Assay (ELISA) and 2019-nCov IgG Chemiluminescent Immunoassay Microparticles, respectively. Spearman correlation analysis was used to measure the correlation between laboratory markers and neutralizing antibody and IgG levels. Peripheral blood mononuclear cells (PBMCs) were extracted from each subject using density gradient centrifugation and the numbers of memory T and T follicular helper (Tfh) cells were determined using flow cytometry.

Results

PLWH had a marked reduction in CD4 and B cell levels that was accompanied by a lower CD4/CD8 T cell ratio. However, those who received a supplementary dose of inactivated SARS-CoV-2 vaccines exhibited antibody positivity rates that were analogous to levels previously observed. The booster vaccine led to a reduction in IgG and neutralizing antibody levels and the amplitude of this decline was substantially higher in the PLWH than HD group. Correlation analyses revealed a strong correlation between neutralizing antibody levels and the count and proportion of CD4 cells. Anti-SARS-CoV-2 IgG antibody levels followed a similar trend. The expression of memory T and Tfh cells was considerably lower in the PLWH than in the HD group.

Discussion

PLWH had an attenuated immune response to a third (booster) administration of an inactivated SARS-CoV-2 vaccine, as shown by lower neutralizing antibody and IgG levels. This could be attributed to the reduced responsiveness of CD4 cells, particularly memory T and cTfh subsets. CD4 and cTfh cells may serve as pivotal markers of enduring and protective antibody levels. Vaccination dose recalibration may be critical for HIV-positive individuals, particularly those with a lower proportion of CD4 and Tfh cells.

Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity

Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.

GDF-15 (a biomarker for metformin) and the risk of COVID-19: A two-sample Mendelian randomization study

BACKGROUND

Regarding the impact of metformin on COVID-19, there are currently varying opinions from multiple studies. Growth differentiation factor 15 (GDF-15) is a biomarker of metformin use and dosage, and we used two-sample Mendelian randomization (MR) to assess the causal effect of GDF-15 (metformin) on COVID-19 susceptibility, hospitalization, and severe COVID-19, thereby guiding the selection of glucose-lowering agents for diabetic patients during the COVID-19 pandemic.

METHODS

Two sets of genetic tools were utilized for MR analysis, derived from publicly available genetic data. The first set was GDF-15 genome-wide association study (GWAS) data from a study with 5440 participants, while the second set was COVID-19 GWAS data from the Host Genetics Initiative (HGI) GWAS meta-analysis. The primary method used to assess causal effects was random effects inverse variance weighted estimation. Complementary methods included weighted median and MR-Egger analyses. Sensitivity analysis was performed using Cochran Q tests, MR-Egger intercept tests, MR-PRESSO, leave-one-out analyses, and funnel plots.

RESULTS

GDF-15 increased the risk of severe COVID-19 in patients (OR = 1.10, 95% CI 1.03-1.19; P = .006); there was no causal effect of GDF-15 on hospitalization for COVID-19 (OR = 1.02, 95% CI 0.96-1.07; P = .47) or susceptibility to COVID-19 in the general population (OR = 1.010, 95% CI 0.988-1.034; P = .354).

CONCLUSIONS

Our study supports the notion that GDF-15 increases the risk of severe COVID-19 in patients. However, there is no causal relationship between GDF-15 and hospitalization or susceptibility to COVID-19.

Pre-Existing Allergies Patients with Higher Viral Load and Longer Recovery Days Infected by SARS-CoV-2 Omicron BA.2 in Shanghai, China, 2022

Background

It is not known whether the viral load and the number of days to negative nucleic acid increased in patients with a history of allergy during the COVID-19 pandemic.

Objective

To investigate the impact of allergy labels on SARS-CoV-2 Omicron outcomes.

Methods

This retrospective cohort study included 62,293 patients with mild Omicron infection between April 9, 2022, and May 31, 2022. Using 1:2 propensity score matching, we identified 2177 COVID-19 patients with a history of allergy and 4254 COVID-19 patients with no history of allergy. The differences in viral load, days to nucleic acid turning negative, and clinical symptoms were compared between the two groups.

Results

Compared with the group with no allergies, the number of days before negative nucleic acid conversion of COVID-19 patients with allergies was significantly higher, the viral load was significantly higher, and the cumulative negative conversion rates at 5-10 days were all lower (p < 0.01). Patients with a history of allergy to antibiotics had higher viral load and more days with negative nucleic acid levels (p < 0.001). Subgroup analysis revealed that the viral load in penicillin-allergic and cephalosporins-allergic patients was significantly compared to patients without any history of allergies (p < 0.05).

Conclusion

Patients with a history of allergy have a more significant viral load and a longer duration of nucleic acid negative conversion upon COVID-19 infection, particularly those allergic to antibiotics.

Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future

Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.

Longitudinal analysis of memory Tfh cells and antibody response following CoronaVac vaccination

The inactivated vaccine CoronaVac is one of the most widely used COVID-19 vaccines globally. However, the longitudinal evolution of the immune response induced by CoronaVac remains elusive compared with other vaccine platforms. Here, we recruited 88 healthy individuals who received 3 doses of CoronaVac vaccine. We longitudinally evaluated their polyclonal and antigen-specific CD4+ T cells and neutralizing antibody response after receiving each dose of vaccine for over 300 days. Both the second and third doses of vaccine induced robust spike-specific neutralizing antibodies, with a third vaccine further increasing the overall magnitude of antibody response and neutralization against Omicron sublineages B.1.1.529, BA.2, BA.4/BA.5, and BA.2.75.2. Spike-specific CD4+ T cells and circulating T follicular helper (cTfh) cells were markedly increased by the second and third dose of CoronaVac vaccine, accompanied by altered composition of functional cTfh cell subsets with distinct effector and memory potential. Additionally, cTfh cells were positively correlated with neutralizing antibody titers. Our results suggest that CoronaVac vaccine-induced spike-specific T cells are capable of supporting humoral immunity for long-term immune protection.

Roadmap to recovery: Implemented and attitude toward school reopening strategies during the COVID-19 pandemic, a scoping review

The novel coronavirus disease 2019 (COVID-19) has had various financial and life impacts on the world's population. Schools' regular activity and function during the pandemic require balancing the repercussions of suspending in-person education versus health threats. Furthermore, children are one of the prominent victims of the restricted quarantine strategies' effects, which may make them vulnerable to various mental health problems. In this study, we reviewed previously reported strategies and roadmaps regarding the reopening of schools during the COVID-19 pandemic. The following databases were searched from October to December 2021, via multi-step search strategies for "COVID-19," "coronavirus," "school reopening," "roadmaps," "reopening," and "reopening strategies": Google Scholar, PubMed, Scopus, and Web of Science. A total of five papers with roadmaps focusing on reopening schools were included in this study. Fundamental issues and principles of these reviewed roadmaps were: 1) protecting the high-risk students and staff physically and mentally, 2) accelerating the vaccination of essential workers, staff, parents, and students, and 3) improving the COVID-19 testing capacity. Roadmaps for the reopening of the schools should describe some phases and steps for their strategies. Current roadmaps have not mentioned any phases and timelines for this process. Describing some health metrics in the roadmaps for progressing to the next step or returning to the previous ones is also necessary for all roadmaps and should be considered in further studies.

Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants

Viruses are a major cause of mortality and socio-economic downfall despite the plethora of biopharmaceuticals designed for their eradication. Conventional antiviral therapies are often ineffective. Live-attenuated vaccines can pose a safety risk due to the possibility of pathogen reversion, whereas inactivated viral vaccines and subunit vaccines do not generate robust and sustained immune responses. Recent studies have demonstrated the potential of strategies that combine nanotechnology concepts with the diagnosis, prevention, and treatment of viral infectious diseases. The present review provides a comprehensive introduction to the different strains of viruses involved in respiratory diseases and presents an overview of recent advances in the diagnosis and treatment of viral infections based on nanotechnology concepts and applications. Discussions in diagnostic/therapeutic nanotechnology-based approaches will be focused on H1N1 influenza, respiratory syncytial virus, human parainfluenza virus type 3 infections, as well as COVID-19 infections caused by the SARS-CoV-2 virus Delta variant and new emerging Omicron variant.

Cost-effectiveness of Paxlovid in reducing severe COVID-19 and mortality in China

Objectives

To assess the cost-effectiveness of Paxlovid in reducing severe COVID-19 and its associated morality, and to investigate the affordable price of Paxlovid in China.

Materials and methods

Using a Markov model, two interventions by Paxlovid prescription (with and without prescription) were compared in terms of COVID-19-related clinical outcomes and economic loss. COVID-related costs were collected from the societal perspective. Effectiveness data were obtained from literature. The primary outcomes were total social cost, disability adjusted life-years (DALYs) and net monetary benefit (NMB). Scenario analyses were performed to investigate the affordable price of Paxlovid in China. Deterministic sensitivity analyses (DSA) and probabilistic sensitivity analysis (PSA) were performed to verify the model robustness.

Results

Compared with the non-Paxlovid cohort, the NMBs of the Paxlovid cohort were only higher in the subgroup of patients aged over 80 years old, regardless of their vaccination status. Our scenario analysis found that, the price ceiling of Paxlovid/box for it to be cost-effective was RMB 8,993 (8,970-9,009) in those aged over 80 years old who were not vaccinated, which is the highest; and was RMB 35 (27-45) in those aged 40-59 years old who were vaccinated, which is the lowest. Sensitivity analyses found that the incremental NMB for the vaccinated people aged over 80 years was most sensitive to the efficacy of Paxlovid and the cost-effectiveness probability of Paxlovid increased with its decreasing price.

Conclusion

Under the current marketing price of Paxlovid/box (RMB 1,890), using Paxlovid was only cost-effective in people aged over 80 years old regardless of their vaccination status.

Data sharing: A Long COVID perspective, challenges, and road map for the future

'Long COVID' is the term used to describe the phenomenon in which patients who have survived a COVID-19 infection continue to experience prolonged SARS-CoV-2 symptoms. Millions of people across the globe are affected by Long COVID. Solving the Long COVID conundrum will require drawing upon the lessons of the COVID-19 pandemic, during which thousands of experts across diverse disciplines such as epidemiology, genomics, medicine, data science, and computer science collaborated, sharing data and pooling resources to attack the problem from multiple angles. Thus far, there has been no global consensus on the definition, diagnosis, and most effective treatment of Long COVID. In this work, we examine the possible applications of data sharing and data science in general with a view to, ultimately, understand Long COVID in greater detail and hasten relief for the millions of people experiencing it. We examine the literature and investigate the current state, challenges, and opportunities of data sharing in Long COVID research.

Dynamic zero-COVID strategy in controlling COVID-19 in Shanghai, China: A cost-effectiveness analysis

BACKGROUND

The sustainability and generalizability of China's dynamic zero-COVID strategy on eliminating SARS-CoV-2 transmission has casted doubt globally, mainly because it has exacted high social and economic cost. This study aimed to estimate the disease burden during the first wave of Omicron in China and compared the cost-effectiveness of implementing a Real-world strategy (adjusted dynamic zero-COVID strategy) with two simulated strategies (routine and stricter dynamic zero-COVID strategy) to inform appropriate strategies for COVID-19 pandemic control.

METHODS

A dynamic state-transition simulation model was developed to compare the health and cost outcomes between different dynamic zero-COVID strategies. Omicron-related healthcare costs were estimated from the societal perspective. Epidemiological parameter values were derived from data of real-world or generated by model calibration; costs and effectiveness parameter values were informed either by local data or published literature. The primary outcomes were total social cost, disability adjusted life-years (DALYs) and net monetary benefit (NMB). Deterministic sensitivity analyses (DSA) and scenario analyses were performed to assess the model robustness.

RESULTS

The first wave of Omicron in Shanghai resulted in 47,646 DALYs lost and 415 billion RMB losses. At a willingness-to-pay threshold of 173,630 RMB (the GDP per capita of Shanghai in 2021) per DALY saved, the Real-world strategy was considered as the most cost-effective strategy due to its highest NMB (-407 billion). Results from DSA confirmed the robustness of our findings.

CONCLUSION

Our finding supported the Real-world strategy taken by the Shanghai Municipal Government between March 1 and May 21, 2022 to control the first wave of Omicron outbreak. Moreover, our results indicated that whether the Stricter dynamic zero-COVID strategy is worth implementing at the beginning of the COVID-19 outbreak mainly depended on the infection rate of COVID-19 among primary contacts. Our analysis provides important evidence to inform policy makers to make appropriate decisions regarding COVID-19 pandemic management.

Prevalence of taste and smell dysfunction in mild and asymptomatic COVID-19 patients during Omicron prevalent period in Shanghai, China: a cross-sectional survey study

OBJECTIVES

COVID-19, which is caused by SARS-CoV-2, is a severe threat to human health and the economy globally. This study aimed to investigate the prevalence of taste and/or smell dysfunction and associated risk factors in mild and asymptomatic patients with Omicron infection in Shanghai, China.DesignThis was a questionnaire-based cross-sectional study.

SETTING

COVID-19 patients at the makeshift hospital in the Shanghai World Expo Exhibition and Convention Centre were recruited from March to April 2022.

PARTICIPANTS

In total, 686 COVID-19-infected patients who were defined as mild or asymptomatic cases according to the diagnostic criteria of New Coronavirus Pneumonia Prevention and Control Programme ninth edition (National Health Commission of China, 2022) were enrolled.

MEASURES

Data to investigate taste and smell loss and to characterise other symptoms were collected by the modified Chemotherapy-induced Taste Alteration Scale and Sino-Nasal Outcome Test-22 questionnaires. The risk factors for the severity of taste/smell dysfunction were analysed by binary logistic regression models.

RESULTS

379 males (379/686, 55.2%) and 307 females (307/686, 44.8%) completed the questionnaires to record recent changes in taste and smell ability. A total of 302 patients (44%) had chemosensory dysfunction with Omicron infection, of which 22.7% (156/686) suffered from both taste and smell dysfunction. In addition, cough (60.2%), expectoration (40.5%), fever (33.2%) and sore throat (32.5%) were common symptoms during Omicron infection. The quality-of-life-related indicators were negatively associated with participants' self-reported taste and smell dysfunction.

CONCLUSIONS

The prevalence of taste or/and smell dysfunction in patients with Omicron infections was 44%. Individuals with chemosensory dysfunction had significantly higher rates of various upper respiratory influenza-like symptoms, xerostomia and bad breath. Moreover, smell dysfunction was a risk factor for the prevalence of taste dysfunction in patients with Omicron infection.

TRIAL REGISTRATION NUMBER

ChiCTR 2200059097.

Integrative network pharmacology and in silico analyses identify the anti-omicron SARS-CoV-2 potential of eugenol

Eugenol as a natural product is the source of isoniazid, and purified eugenol is extensively used in the cosmetics industry and the productive processes of edible spices. Accumulating evidence suggested that eugenol exerted potent anti-microorganism and anti-inflammation effects. Application of eugenol effectively reduced the risk of atherosclerosis, arterial embolism, and Type 2 diabetes. A previous study confirmed that treatment with eugenol attenuated lung inflammation and improved heart functions in SARS-CoV-2 spike S1-intoxicated mice. In addition to the study, based on a series of public datasets, computational analyses were conducted to characterize the acting targets of eugenol and the functional roles of these targets in COVID-19. The binding capacities of eugenol to conservative sites of SARS-CoV-2 like RNA-dependent RNA polymerase (RdRp) and mutable site as spike (S) protein, were calculated by using molecular docking following the molecular dynamics simulation with RMSD, RMSF, and MM-GBSA methods. The results of network pharmacology indicated that six targets, including PLAT, HMOX1, NUP88, CTSL, ITGB1 andTMPRSS2 were eugenol-SARS-CoV-2 interacting proteins. The omics results of in-silico study further implicated that eugenol increased the expression of SCARB1, HMOX1 and GDF15, especially HMOX1, which were confirmed the potential interacting targets between eugenol and SARS-CoV-2 antigens. Enrichment analyses indicated that eugenol exerted extensive biological effects such as regulating immune infiltration of macrophage, lipid localization, monooxyenase activity, iron ion binding and PPAR signaling. The results of the integrated analysis of eugenol targets and immunotranscription profile of COVID-19 cases shows that eugenol also plays an important role in strengthen of immunologic functions and regulating cytokine signaling. As a complement to the integrated analysis, the results of molecular docking indicated the potential binding interactions between eugenol and four proteins relating to cytokine production/release and the function of T type lymphocytes, including human TLR-4, TCR, NF-κB, JNK and AP-1. Furthermore, results of molecular docking and molecular dynamics (100ns) simulations implicated that stimulated modification of eugenol to the SARS-CoV-2 Omicron Spike-ACE2 complex, especially for human ACE2, and the molecular interaction of eugenol to SARS-CoV-2 RdRp, were no less favorable than two positive controls, molnupiravir and nilotinib. Dynamics (200ns) simulations indicated that the binding capacities and stabilities of eugenol to finger subdomain of RdRp is no less than molnupiravir. However, the simulated binding capacity of eugenol to SARS-CoV-2 wild type RBD and Omicron mutant RBD were less than nilotinib. Eugenol was predicted to have more favor LD50 value and lower cytotoxicity than two positive controls, and eugenol can pass through the blood-brain barrier (BBB). In a brief, eugenol is helpful for attenuating systemic inflammation induced by SARS-CoV-2 infection, due to the direct interaction of eugenol to SARS-CoV-2 proteins and extensive bio-manipulation of pro-inflammatory factors. This study carefully suggests eugenol is a candidate compound of developing drugs and supplement agents against SARS-CoV-2 and its Omicron variants.

The Potential of Nanobodies for COVID-19 Diagnostics and Therapeutics

The infectious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Globally, there have been millions of infections and fatalities. Unfortunately, the virus has been persistent and a contributing factor is the emergence of several variants. The urgency to combat COVID-19 led to the identification/development of various diagnosis (polymerase chain reaction and antigen tests) and treatment (repurposed drugs, convalescent plasma, antibodies and vaccines) options. These treatments may treat mild symptoms and decrease the risk of life-threatening disease. Although these options have been fairly beneficial, there are some challenges and limitations, such as cost of tests/drugs, specificity, large treatment dosages, intravenous administration, need for trained personal, lengthy production time, high manufacturing costs, and limited availability. Therefore, the development of more efficient COVID-19 diagnostic and therapeutic options are vital. Nanobodies (Nbs) are novel monomeric antigen-binding fragments derived from camelid antibodies. Advantages of Nbs include low immunogenicity, high specificity, stability and affinity. These characteristics allow for rapid Nb generation, inexpensive large-scale production, effective storage, and transportation, which is essential during pandemics. Additionally, the potential aerosolization and inhalation delivery of Nbs allows for targeted treatment delivery as well as patient self-administration. Therefore, Nbs are a viable option to target SARS-CoV-2 and overcome COVID-19. In this review we discuss (1) COVID-19; (2) SARS-CoV-2; (3) the present conventional COVID-19 diagnostics and therapeutics, including their challenges and limitations; (4) advantages of Nbs; and (5) the numerous Nbs generated against SARS-CoV-2 as well as their diagnostic and therapeutic potential.

SARS-CoV-2 versus Influenza A Virus: Characteristics and Co-Treatments

For three years, the novel coronavirus disease 2019 (COVID-19) pandemic, caused by infection of the SARS-CoV-2 virus, has completely changed our lifestyles and prepared us to live with this novel pneumonia for years to come. Given that pre-existing flu is caused by the influenza A virus, we have begun unprecedently co-coping with two different respiratory diseases at the same time. Hence, we draw a comparison between SARS-CoV-2 and influenza A virus based on the general characteristics, especially the main variants’ history and the distribution of the two viruses. SARS-CoV-2 appeared to mutate more frequently and independently of locations than the influenza A virus. Furthermore, we reviewed present clinical trials on combined management against COVID-19 and influenza in order to explore better solutions against both at the same time.

Long COVID following Omicron wave in Eastern India-A retrospective cohort study

Long coronavirus disease (COVID) or postacute sequelae of coronavirus disease of 2019 (COVID-19) is widely reported but the data of long COVID after infection with the Omicron variant is limited. This study was conducted to estimate the incidence, characteristics of symptoms, and predictors of long COVID among COVID-19 patients diagnosed during the Omicron wave in Eastern India. The cohort of COVID-19 patients included were adults (≥18 years) diagnosed as severe acute respiratory syndrome coronavirus 2 positive with Reverse Transcription Polymerase Chain Reaction. After 28 days of diagnosis; participants were followed up with a telephonic interview to capture data on sociodemographic, clinical history, anthropometry, substance use, COVID-19 vaccination status, acute COVID-19 symptoms, and long COVID symptoms. The long COVID symptoms were self-reported by the participants. Logistic regression was used to determine the predictors of long COVID. The median follow-up of participants was 73 days (Interquartile range; 67-83). The final analysis had 524 participants' data; among them 8.2% (95% Confidence Interval [CI]: 6%-10.9%) self-reported long COVID symptoms. Fatigue (34.9%) was the most common reported symptom followed by cough (27.9%). In multivariable logistic regression only two predictors were statistically significant-number of acute COVID-19 symptoms ≥ five (Adjusted odds ratio (aOR) = 2.95, 95% CI: 1.30-6.71) and past history of COVID-19 (aOR = 2.66, 95% CI: 1.14-6.22). The proportion of self-reported long COVID is considerably low among COVID-19 patients diagnosed during the Omicron wave in Eastern India when compared with estimates during Delta wave in the same setting.

Vitamin A Deficiency, COVID-19, and Rhino-Orbital Mucormycosis (Black Fungus): An Analytical Perspective

Mucormycosis is a rare but serious opportunistic fungal disease characterized by rhino-orbito-cerebral and pulmonary involvement. It is mainly seen in people with secondary immunosuppression, isolated vitamin A deficiency, measles, and AIDS patients. It showed a rise during the second wave of the COVID-19 epidemic in the spring of 2021 in India, especially in diabetic COVID-19 patients. Vitamin A deficiency is known to cause nutritional immunodeficiency and hence leading the way to increased opportunistic fungal, bacterial, and viral infections. In the eye, it causes keratitis, night blindness, xerophthalmia, conjunctivitis, Bitot spots, keratomalacia, and retinopathy. It also causes decreased tear secretion and deterioration of the anatomical/physiological defense barrier of the eye. The negative impact of vitamin A deficiency has been previously demonstrated in measles, AIDS, and COVID-19. We think that mucormycosis in COVID-19 might be rendered by vitamin A deficiency and that vitamin A supplementation may have preventive and therapeutic values against mucormycosis and other ocular symptoms associated with COVID-19. However, any vitamin A treatment regimen needs to be based on laboratory and clinical data and supervised by medical professionals.

Effects of COVID-19 on Surgical Delays in Patients with Breast Cancer in NYC Public Hospitals: A Multicenter Study

BACKGROUND

Increased time to surgery (TTS) is associated with decreased survival in patients with breast cancer. In early 2020, elective surgeries were canceled to preserve resources for patients with coronavirus disease 2019 (COVID-19). This study attempts to measure the effect of mandated operating room shutdowns on TTS in patients with breast cancer.

PATIENTS AND METHODS

This multicenter retrospective study compares 51 patients diagnosed with breast cancer at four public hospitals from January to June 2020 with 353 patients diagnosed from January 2017 to June 2018. Demographics, tumor characteristics, treatment regimens, and TTS for patients were statistically compared using parametric, nonparametric, and Cox proportional hazards regression modeling.

RESULTS

Across all centers, there was a non-statistically significant increase in median TTS from 59 days in the pre-COVID period to 65 days during COVID (p = 0.9). There was, however, meaningful variation across centers. At center A, the median TTS decreased from 57 to 51 days, center C's TTS decreased from 83 to 64 days, and in center D, TTS increased from 42 to 129 days. In a multivariable Cox proportional hazards model for the pre-COVID versus COVID period effect on TTS, center was an important confounding variable, with notable differences for centers C and D compared with the referent category of center A (p = 0.04, p = 0.006).

CONCLUSION

Data suggest that, while mandated operating room shutdowns did not result in an overall statistically significant delay in TTS, there were important differences between centers, indicating that, even in a unified multicenter public hospital system, COVID-19 may have resulted in delayed and potentially disparate care.

Identification of potential inhibitors of omicron variant of SARS-Cov-2 RBD based virtual screening, MD simulation, and DFT

Emergence of the SARS-CoV-2 Omicron variant of concern (VOC; B.1.1.529) resulted in a new peak of the COVID-19 pandemic, which called for development of effective therapeutics against the Omicron VOC. The receptor binding domain (RBD) of the spike protein, which is responsible for recognition and binding of the human ACE2 receptor protein, is a potential drug target. Mutations in receptor binding domain of the S-protein have been postulated to enhance the binding strength of the Omicron VOC to host proteins. In this study, bioinformatic analyses were performed to screen for potential therapeutic compounds targeting the omicron VOC. A total of 92,699 compounds were screened from different libraries based on receptor binding domain of the S-protein via docking and binding free energy analysis, yielding the top 5 best hits. Dynamic simulation trajectory analysis and binding free energy decomposition were used to determine the inhibitory mechanism of candidate molecules by focusing on their interactions with recognized residues on receptor binding domain. The ADMET prediction and DFT calculations were conducted to determine the pharmacokinetic parameters and precise chemical properties of the identified molecules. The molecular properties of the identified molecules and their ability to interfere with recognition of the human ACE2 receptors by receptor binding domain suggest that they are potential therapeutic agents for SARS-CoV-2 Omicron VOC.

Risk factors for intensive care unit admission and death from COVID-19 in fully vaccinated patients hospitalized for severe COVID-19, Brazil, 2021–2022

Objectives.

To assess factors associated with admission to an intensive care unit (ICU) and death from coronavirus disease 2019 (COVID-19) in fully vaccinated patients with severe COVID-19 in Brazil and the association between ICU admission and death from COVID-19.

Methods.

This was retrospective study of patients hospitalized for COVID-19 from February 12, 2021 to January 10, 2022 across Brazil who were fully vaccinated against COVID-19 before hospitalization. Outcomes were admission in an ICU for COVID-19 and death from COVID-19. Variables evaluated were: sex; age; self-reported skin color; macroregion; comorbidities; time between full vaccination and onset of symptoms; and time between onset of symptoms and hospitalization. A Poisson regression model was used to estimate crude and adjusted risk ratios.

Results.

Of 74 991 patients hospitalized for severe COVID-19, 67.28% were ≥ 70 years and 68.32% had at least one comorbidity. Men, patients aged 60–69 years, and patients aged 18–39 years with obesity had the greatest risk of ICU admission. Patients aged 18–39 years with obesity, diabetes, or renal diseases had the highest risk of death from COVID-19. When age and time between onset of symptoms and hospitalization were considered effect modifiers, patients admitted to an ICU 9–13 days after symptom onset in each age category had the greatest risk of death from COVID-19.

Conclusion.

Although older patients were at greatest risk of ICU admission and death from COVID-19, the difference in the risk of dying from COVID-19 between patients admitted to an ICU and those not admitted was greatest for young adults.

Neurological Manifestations in COVID-19 in Three Waves of the Pandemic: An Inpatient Study from India

Background

Though severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) virus primarily affects respiratory system, neurological involvement is well known.

Aims

To describe the neurological manifestations of coronavirus disease 2019 (COVID-19) during three waves of the pandemic.

Methodology

This was an ambispective observational single-centre study to describe the neurological manifestations of COVID-19 infection among inpatients from a tertiary care referral centre in Western India from March 2020 to January 2022.

Results

Out of 14,822 patients admitted with COVID-19, 307 (2.07%) had neurological manifestations. Neurological manifestations were seen in 1.87% in first wave (onset to 10 Feb 21); 2.37% in second wave (Feb 11, 2021 to Dec 31, 2021) and 6.26% in third wave (Jan 1, 2022 to Jan 31, 2022). The most common neurological manifestations were encephalopathy (34.5%), ischemic stroke (32.1%), and acute symptomatic seizures (8.8%). Encephalopathy (p = 0.028) was more common in first wave while seizures were more common in third wave (p = 0.001). In patients with encephalopathy, hypoxia (p = 0.0001), shock (p = 0.001), renal involvement (p = 0.002), and sepsis (p = 0.033) were associated with higher mortality; while those with no systemic involvement had better survival (p = 0.0001). Among patients with ischemic stroke, 32.1% did not have any traditional vascular risk factors. These patients were 9 years younger and required 6 days less hospitalization than patients of stroke with vascular risk factors.

Conclusion

SARS-CoV-2 produces many central and peripheral nervous system manifestations. Encephalopathy was more common in first wave while acute symptomatic seizures were more common in third wave. Encephalopathy was most common neurological manifestation with progressively higher mortality with increased number of systemic comorbidities. Ischemic stroke was seen in patients who had vascular risk factors as well as in patients without them.

Systematic lung ultrasound in Omicron-type vs. wild-type COVID-19

AIMS

Preliminary data suggested that patients with Omicron-type-Coronavirus-disease-2019 (COVID-19) have less severe lung disease compared with the wild-type-variant. We aimed to compare lung ultrasound (LUS) parameters in Omicron vs. wild-type COVID-19 and evaluate their prognostic implications.

METHODS AND RESULTS

One hundred and sixty-two consecutive patients with Omicron-type-COVID-19 underwent LUS within 48 h of admission and were compared with propensity-matched wild-type patients (148 pairs). In the Omicron patients median, first and third quartiles of the LUS-score was 5 [2-12], and only 9% had normal LUS. The majority had either mild (≤5; 37%) or moderate (6-15; 39%), and 15% (≥15) had severe LUS-score. Thirty-six percent of patients had patchy pleural thickening (PPT). Factors associated with LUS-score in the Omicron patients included ischaemic-heart-disease, heart failure, renal-dysfunction, and C-reactive protein. Elevated left-filling pressure or right-sided pressures were associated with the LUS-score. Lung ultrasound-score was associated with mortality [odds ratio (OR): 1.09, 95% confidence interval (CI): 1.01-1.18; P = 0.03] and with the combined endpoint of mortality and respiratory failure (OR: 1.14, 95% CI: 1.07-1.22; P < 0.0001). Patients with the wild-type variant had worse LUS characteristics than the matched Omicron-type patients (PPT: 90 vs. 34%; P < 0.0001 and LUS-score: 8 [5, 12] vs. 5 [2, 10], P = 0.004), irrespective of disease severity. When matched only to the 31 non-vaccinated Omicron patients, these differences were attenuated.

CONCLUSION

Lung ultrasound-score is abnormal in the majority of hospitalized Omicron-type patients. Patchy pleural thickening is less common than in matched wild-type patients, but the difference is diminished in the non-vaccinated Omicron patients. Nevertheless, even in this milder form of the disease, the LUS-score is associated with poor in-hospital outcomes.

Progress, pitfalls, and path forward of drug repurposing for COVID-19 treatment

On 30 January 2020, the World Health Organization (WHO) declared the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic a public health emergency of international concern. The viral outbreak led in turn to an exponential growth of coronavirus disease 2019 (COVID-19) cases, that is, a multiorgan disease that has led to more than 6.3 million deaths worldwide, as of June 2022. There are currently few effective drugs approved for treatment of SARS-CoV-2/COVID-19 patients. Many of the compounds tested so far have been selected through a drug repurposing approach, that is, by identifying novel indications for drugs already approved for other conditions. We here present an up-to-date review of the main Food and Drug Administration (FDA)-approved drugs repurposed against SARS-CoV-2 infection, discussing their mechanism of action and their most important preclinical and clinical results. Reviewed compounds were chosen to privilege those that have been approved for use in SARS-CoV-2 patients or that have completed phase III clinical trials. Moreover, we also summarize the evidence on some novel and promising repurposed drugs in the pipeline. Finally, we discuss the current stage and possible steps toward the development of broadly effective drug combinations to suppress the onset or progression of COVID-19.

Molecular aspects of Omicron, vaccine development, and recombinant strain XE: A review

The global pandemic of COVID-19 began in December 2019 and is still continuing. The past 2 years have seen the emergence of several variants that were more vicious than each other. The emergence of Omicron (B.1.1.529) proved to be a huge epidemiological concern as the rate of infection of this particular strain was enormous. The strain was identified in South Africa on November 24, 2021 and was classified as a "Variant of Concern" on November 26, 2021. The Omicron variant possessed mutations in the key RBD region, the S region, thereby increasing the affinity of ACE2 for better transmission of the virus. Antibody resistance was found in this variant and it was able to reduce vaccine efficiency of vaccines. The need for a booster vaccine was brought forth due to the prevalence of the Omicron variant and, subsequently, this led to targeted research and development of variant-specific vaccines and booster dosage. This review discusses broadly the genomic characters and features of Omicron along with its specific mutations, evolution, antibody resistance, and evasion, utilization of CRISPR-Cas12a assay for Omicron detection, T-cell immunity elicited by vaccines against Omicron, and strategies to decrease Omicron infection along with COVID-19 and it also discusses on XE recombinant variant and on infectivity of BA.2 subvariant of Omicron.

Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants

The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics.

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.

An investigation of the incidence of post-traumatic stress disorder, turnover intention and psychological resilience among medical staff in a public hospital in China during the outbreak of the omicron variant in the COVID-19 pandemic in 2022

Objective

To investigate the incidence of post-traumatic stress disorder (PTSD), turnover intention and psychological resilience of medical staff during the Outbreak of the Omicron Variant in the COVID-19 pandemic in 2022 and to provide a basis for adopting relevant psychological interventions to reduce medical staff turnover.

Methods

Using the PTSD Checklist-Civilian Version (PCL-C) and a total score ranging from 17 to 85 points, a total score ≥ 38 indicates significant PTSD symptoms and a diagnosis of PTSD. The Chinese version of the Turnover Intention Scale (TIS) has a total score of 6 to 24 points; the higher the score, the stronger the turnover intention. The Chinese version of the Connor-Davidson Resilience Scale (CD-RISC) has a total score of 0 to 100 points, with higher scores indicating a better level of psychological resilience. A total of 443 front-line medical staff working in Chinese public hospitals and still treating all patients normally during COVID-19 were invited via the internet to complete a survey from 15 May to 30 May 2022 in China.

Results

The incidence of PTSD was 14.4%, the total turnover intention score was 13.38 ± 4.08, and the total psychological resilience score was 87.16 ± 18.42. The prevalence of PTSD was higher among medical staff who were married, had children, and were worried about being infected; in addition, the PTSD group had a higher level of education, higher turnover intention, and lower psychological resilience than the non-PTSD group. The total scores for turnover intention and fear of being infected were risk factors for PTSD, while a high total psychological resilience score and high education level were protective factors for PTSD; the differences were statistically significant (all P < 0.05).

Conclusion

Post-traumatic stress disorder among Chinese medical personnel was associated with the marital status, childbirth, education level, turnover intention, and psychological resilience. Among these factors, psychological resilience might be exploited as a protective factor.

COVID-19 vaccines: Update of the vaccines in use and under development

The ongoing COVID-19 pandemic has imposed a series of challenges on the scientific community. One of the biggest was the development of safe and effective vaccines in record time, which could be achieved through a global effort. A topic of great discussion has been the technology surrounding these vaccines: ranging from the well-known inactivated virus vaccines to the latest RNA vaccines. As vaccines became available, another point also came into question: their efficacy and effectiveness against the original Wuhan strain and its variants. Among the numerous variants, 5 of them (Alpha, Beta, Gamma, Delta and, more recently, Omicron) gained greater prominence due to their epidemiological relevance. In this scenario, with numerous variants and several vaccine options, scientific information can often be mismatched. This review aims to provide an overview of the efficacy, effectiveness, and safety of 11 vaccines in use or under development against the original Wuhan strain and the variants of concern identified by the World Health Organisation (WHO). Simultaneously, we aim to explore possible scenarios that can be expected shortly regarding new variants and vaccines. Overall, COVID-19 vaccines have satisfactory efficacy and loss of effectiveness against SARS-CoV-2 variants, especially the Omicron strain.

Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach

Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03258-4.

Clinical Progression and Outcome of Hospitalized Patients Infected with SARS-CoV-2 Omicron Variant in Shanghai, China

Background: Studies on the Omicron variant infection have generally been restricted to descriptions of its initial clinical and epidemiological characteristics. We investigated the timeline-related progression and clinical outcome in hospitalized individuals with the Omicron variant. Methods: We conducted a retrospective, single-centered study including 226 laboratory-confirmed cases with the Omicron variant between 6 April and 11 May 2022 in Shanghai, China. The final date of follow-up was 30 May 2022. Results: Among 226 enrolled patients, the median age was 52 years, and 118 (52.2%) were female. The duration from onset of symptoms to hospitalization was 3 days (interquartile range (IQR): 2–4 days) for symptomatic patients. Cough occurred in 168 patients (74.3%). The median interval to negative reverse-transcriptase PCR tests of nasopharynx swab was 10 days ((IQR): 8–13 days). No radiographic progressions were found in 196 patients on the 7th day after onset of symptoms. The median duration of fever in all participants was 5 days (IQR: 4–6 days). The median PCR conversion time of Paxlovid-treated patients was 8 days (IQR: 7–10 days) compared with that of a traditional Chinese herb medicine lianhuaqingwen (10 days, IQR: 8–13 days) (p = 0.00056). Booster vaccination can significantly decrease the severity of Omicron infection when compared with unvaccinated patients (p = 0.009). In multivariate logistic analysis, erythrocyte sedimentation rate (ESR) (OR = 1.05) was independently related to the severity of the infection. Conclusions: The majority of clinical symptoms of Omicron infection were not severe. Early and aggressive administration of Paxlovid can significantly reduce the PCR conversion time. Booster vaccination should also be highly recommended in the population over 14 years old.

SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength?

The global COVID-19 pandemic continues due to emerging Severe Acute Respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC). Here, we performed comprehensive analysis of in-house sequenced SARS-CoV-2 genome mutations dynamics in the patients infected with the VOCs - Delta and Omicron, within Recovered and Mortality patients. Statistical analysis highlighted significant mutations - T4685A, N4992N, and G5063S in RdRp; T19R in NTD spike; K444N and N532H in RBD spike, associated with Delta mortality. Mutations, T19I in NTD spike, Q493R and N440K in the RBD spike were significantly associated with Omicron mortality. We performed molecular docking for possible effect of significant mutations on the binding of Remdesivir. We found that Remdesivir showed less binding efficacy with the mutant Spike protein of both Delta and Omicron mortality compared to recovered patients. This indicates that mortality associated mutations could have a modulatory effect on drug binding which could be associated with disease outcome.

Advances in COVID-19 Vaccines and New Coronavirus Variants

With the successful development of the Corona Virus Disease 2019 (COVID-19) vaccines and increased vaccination coverage, great progress in global outbreak control has been made in several countries. However, new coronavirus variants emerge and their rapid spread, causing a new wave of economic and social upheaval worldwide. The spread of new coronavirus variants poses a new and enormous challenge to vaccination and pandemic control, so further studies to explore and develop vaccines for the prevention and control virus infection are warranted. In this review, we provide an overview of the most prevalent variants including Omicron, and explore the effectiveness of COVID-19 vaccines against related variants to better understand existing vaccines and to facilitate improved research into new vaccines. In addition, this review discusses existing strategies to increase vaccine efficacy and introduces novel vaccines by the non-injection route.

COVID-19 in children: epidemic issues and candidate vaccines

ABSTRACT

A large-scale vaccination of coronavirus disease-19 (COVID-19) in adults has been conducted for nearly a year, and there is a growing recognition that immunization for children is also essential. It has been months since emergency use of pediatric COVID-19 vaccine was approved, we reviewed the prevalence and transmission of COVID-19 in children. The prevalence of COVID-19 in children is reduced due to vaccination even in a Delta prevalent period, so an increase in the vaccination rate is needed in children. Although the precise role of children in the transmission requires more research to uncover, they likely played a significant role, according to the available literature. We also described four candidate COVID-19 vaccines for children on their safety and immunogenicity and the impact of severe acute respiratory syndrome coronavirus 2 variants on childhood vaccination. Safety issues on pediatric vaccines post-approval, like adverse events following immunization and adverse events of special interest require studies on long-term and effective regulatory mechanisms.

Real-Word Effectiveness of Global COVID-19 Vaccines Against SARS-CoV-2 Variants: A Systematic Review and Meta-Analysis

Background

Currently, promoted vaccinations against SARS-CoV-2 are being given out globally. However, the occurrence of numerous COVID-19 variants has hindered the goal of rapid mitigation of the COVID-19 pandemic by effective mass vaccinations. The real-word effectiveness of the current vaccines against COVID-19 variants has not been assessed by published reviews. Therefore, our study evaluated the overall effectiveness of current vaccines and the differences between the various vaccines and variants.

Methods

PubMed, Embase, Cochrane Library, medRxiv, bioRxiv, and arXiv were searched to screen the eligible studies. The Newcastle-Ottawa scale and the Egger test were applied to estimate the quality of the literature and any publication bias, respectively. The pooled incident rates of different variants after vaccination were estimated by single-arm analysis. Meanwhile, the pooled efficacies of various vaccines against variants were evaluated by two-arm analysis using odds ratios (ORs) and vaccine effectiveness (VE).

Results

A total of 6,118 studies were identified initially and 44 articles were included. We found that the overall incidence of variants post first/second vaccine were 0.07 and 0.03, respectively. The VE of the incidence of variants post first vaccine between the vaccine and the placebo or unvaccinated population was 40% and post second vaccine was 96%, respectively. The sub-single-arm analysis showed a low prevalence rate of COVID-19 variants after specific vaccination with the pooled incidence below 0.10 in most subgroups. Meanwhile, the sub-two-arm analysis indicated that most current vaccines had a good or moderate preventive effect on certain variants considering that the VE in these subgroups was between 66 and 95%, which was broadly in line with the results of the sub-single-arm analysis.

Conclusion

Our meta-analysis shows that the current vaccines that are used globally could prevent COVID-19 infection and restrict the spread of variants to a great extent. We would also support maximizing vaccine uptake with two doses, as the effectiveness of which was more marked compared with one dose. Although the mRNA vaccine was the most effective against variants according to our study, specific vaccines should be taken into account based on the local dominant prevalence of variants.

Immunogenicity of Inactivated SARS-CoV-2 Vaccines in Patients With Rheumatoid Arthritis: A Case Series

Objectives

Attenuated humoral response to mRNA SARS-CoV-2 vaccines has been reported in some patients with autoimmune disease, e.g., rheumatoid arthritis (RA). However, data of immune responses to inactivated SARS-CoV-2 vaccine in the RA population are still unknown. Herein, the safety and immunogenicity of inactivated SARS-CoV-2 vaccines in RA patients were analyzed.

Methods

Seventy five RA patients and 26 healthy controls (HC) were respectively recruited from Yunnan Provincial Hospital of Traditional Chinese Medicine and the community in Kunming city. Neutralizing Antibody (NAb) Test ELISA kit was used to measure the percentage of inhibition. AKA (anti-keratin antibody) positivity was detected using indirect immunofluorescence. Rheumatoid factor (RF)-IgA was detected by ELISA. RF-IgG, RF-IgM, and anti-cyclic citrullinated peptide (CCP) antibodies were measured by chemiluminescence. ESR (erythrocyte sedimentation rate) was detected by ESR analyzer. C-RP (c-reactive protein) was detected by immunoturbidimetry. NEUT% (percentage of neutrophils) and LYMPH% (percentage of percentage) were calculated by a calculation method.

Results

Compared with the HC group, the percentage of inhibition was significantly lower in RA patients receiving two doses of vaccines. Vaccines-induced percentage of inhibition was the lowest in RA patients who had not been vaccinated. In total 80.77% of the HC group had a percentage of inhibition ≧20%, compared with 45.24% of vaccinated RA patients and 6.06% of unvaccinated RA patients. Spearman correlation analysis revealed that antibody responses to SARS-CoV-2 did not differ between RA patients according to their age and disease duration. Furthermore, the results showed that no correlation was found between the percentage of inhibition and indices for RA, including RF-IgA, IgG, IgM; anti-CCP antibody; ESR; C-RP; NEUT% and LYMPH%.

Conclusion

Our study showed inactivated vaccine-induced SARS-COV-2 antibody responses differ in RA patients and healthy subjects, emphasizing the importance of a third or fourth vaccination in RA patients.

Turning point: A new global COVID-19 wave or a signal of the beginning of the end of the global COVID-19 pandemic?

A new variant named Omicron (B.1.1.529), first identified in South Africa, has become of considerable interest to the World Health Organization. This variant differs from the other known major variants, as it carries a large number of unusual mutations, particularly in the spinous process protein and receptor binding domains. Some specific mutation sites make it vaccine resistant, highly infectious, and highly pathogenic. The world fears that the Omicron variant could be even more harmful than the previous major variant, given that it has emerged amid fierce competition to trigger a new global pandemic peak as infections in South Africa rise. However, some epidemiological evidence has emerged that the Omicron variant may produce milder patient symptoms. We speculate if the virulence of the Omicron variant will diminish as transmissibility increases, thereby signaling the beginning of the end for the global COVID-19 pandemic. Based on this view, we make recommendations for COVID-19 mitigation in the present and future. However, it will take a few weeks to determine the true threat posed by the Omicron variant and we need to be fully prepared for future outbreaks, regardless of their severity.

SARS-CoV-2 Omicron Variant: Exploring Healthcare Workers' Awareness and Perception of Vaccine Effectiveness: A National Survey During the First Week of WHO Variant Alert

Background

As the SARS-CoV-2 Omicron variant spreads in several countries, healthcare workers' (HCWs) perceptions and worries regarding vaccine effectiveness and boosters warrant reassessment.

Methods

An online questionnaire among HCWs in Saudi Arabia (KSA) was distributed from Dec 1st-6th 2021 to assess their perceptions, vaccine advocacy to the Omicron variant, and their perception of the effectiveness of infection prevention measures and vaccination to prevent its spread, their Omicron variant related worries in comparison to the other variants, and their agreement with mandatory vaccination in general for adults.

Results

Among the 1,285 HCW participants, two-thirds were female, 49.8 % were nurses, 46.4% were physicians, and 50.0% worked in tertiary care hospitals. 66.9% considered vaccination to be the most effective way to prevent the spread of the Omicron variant and future variants. The respondents however perceived social distancing (78.0%), universal masking (77.8%), and avoiding unnecessary travel (71.4%) as slightly superior to vaccination to prevent the spread of SARS-CoV-2 variants. HCWs aging 55 or older agreed significantly with vaccine ineffectiveness to control Omicron spread, while those who believed in non-pharmacological infection prevention measures agreed significantly with vaccination for that purpose. Male HCWs had a significant agreement with mandatory vaccination of all eligible adult populations. On the other hand, unwilling HCWs to receive the vaccine had strong disagreements with mandatory vaccination.

Conclusions

The current study in the first week of Omicron showed that only two-thirds of HCWs felt that vaccination was the best option to prevent the spread of the Omicron variant, indicating the need for further motivation campaigns for vaccination and booster dose. HCWs had a strong belief in infection prevention measures to contain the spread of SARS-CoV-2 variants that should be encouraged and augmented.

SARS-CoV-2 Omicron variant: Immune escape and vaccine development

New genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) constantly emerge through unmitigated spread of the virus in the ongoing Coronavirus disease 2019 pandemic. Omicron (B.1.1.529), the latest variant of concern (VOC), has so far shown exceptional spread and infectivity and has established itself as the dominant variant in recent months. The SARS-CoV-2 spike glycoprotein is a key component for the recognition and binding to host cell angiotensin-converting enzyme 2 receptors. The Omicron variant harbors a cluster of substitutions/deletions/insertions, and more than 30 mutations are located in spike. Some noticeable mutations, including K417N, T478K, N501Y, and P681H, are shared with the previous VOCs Alpha, Beta, Gamma, or Delta variants and have been proven to be associated with higher transmissibility, viral infectivity, and immune evasion potential. Studies have revealed that the Omicron variant is partially resistant to the neutralizing activity of therapeutic antibodies and convalescent sera, which poses significant challenges for the clinical effectiveness of the current vaccines and therapeutic antibodies. We provide a comprehensive analysis and summary of the epidemiology and immune escape mechanisms of the Omicron variant. We also suggest some therapeutic strategies against the Omicron variant. This review, therefore, aims to provide information for further research efforts to prevent and contain the impact of new VOCs during the ongoing pandemic.

SARS-CoV-2 and Coronavirus Disease Mitigation: Treatment Options, Vaccinations and Variants

COVID-19 is caused by a novel coronavirus (2019-nCoV), which was declared as a pandemic after it emerged in China 2019. A vast international effort has been conducted to prevent and treat COVID-19 due to its high transmissibility and severe morbidity and mortality rates, particularly in individuals with chronic co-morbidities. In addition, polymorphic variants increased the need for proper vaccination to overcome the infectivity of new variants that are emerging across the globe. Many treatment options have been proposed and more than 25 vaccines are in various stages of development; however, the infection peaks are oscillating periodically, which raises a significant question about the effectiveness of the prevention measures and the persistence of this pandemic disease. In this review, we are exploring the most recent knowledge and advances in the treatment and vaccination options as well as the new emerging variants of 2019-nCoV and the possible mitigation of one of the most aggressive pandemics in the last centuries.

SARS-CoV-2 Variants and Clinical Outcomes: A Systematic Review

Background: From the start of the COVID-19 pandemic, new SARS-CoV-2 variants have emerged that potentially affect transmissibility, severity, and immune evasion in infected individuals. In the present systematic review, the impact of different SARS-CoV-2 variants on clinical outcomes is analyzed. Methods: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020. Two databases (PubMed and ScienceDirect) were searched for original articles published from 1 January 2020 to 23 November 2021. The articles that met the selection criteria were appraised according to the Newcastle–Ottawa Quality Assessment Scale. Results: Thirty-three articles were included, involving a total of 253,209 patients and 188,944 partial or complete SARS-CoV-2 sequences. The most reported SARS-CoV-2 variants showed changes in the spike protein, N protein, RdRp and NSP3. In 28 scenarios, SARS-CoV-2 variants were found to be associated with a mild to severe or even fatal clinical outcome, 15 articles reported such association to be statistically significant. Adjustments in eight of them were made for age, sex and other covariates. Conclusions: SARS-CoV-2 variants can potentially have an impact on clinical outcomes; future studies focused on this topic should consider several covariates that influence the clinical course of the disease.