Omicron (B.1.1.529 variant of SARS-CoV-2); an emerging threat: Current global scenario

Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron's several subvariants and the current rise of KP.3.1.1 and XEC

The recent COVID-19 pandemic is one of the quickest-evolving pandemics in the world history. Therefore, the evolution of SARS-CoV-2 needs to be tracked consistently. Various VOIs, VOCs, and recent subvariants of Omicron have emerged from the dynamically evolving SARS-CoV-2. Various offspring of the Omicron subvariants have emerged since its origin, including lineages such as BA, BQ, and XBB, as well as more recent subvariants like BA.2.86, JN.1, JN.11.1, KP.3, KP.3.1.1, and XEC. The study evaluated the overall and one year evolutionary patterns, genome diversity, divergence event, transmission and geographical distributions, circulating frequency, entropy diversity, mutational diversity, risk mutations in S-protein and mutational fitness of the subvariants. The study estimated the substitution rate of all variants and subvariants of SARS-CoV-2 since its origin (32.001 × 10-4 subs/year). The geographical distributions of the recent KP.3.1.1 and XEC subvariant indicated its distribution in North America, South America, Europe, and Southeast Asia. Simultaneously, genome mutational landscapes were noted, including Spike and RBD mutations. We found that JN.1, JN.1.11.1, KP.3, KP.3.1.1 and XEC subvariants have gained the highest mutational fitness in Europe and North America. Our study indicates that the rapid evolution and highest frequency of mutational fitness have created a variety of subvariants from Omicron. It also indicates a shift from waves to mini-waves. Finally, our possible explanation is that mutation-driven divergent evolution contributes to the emergence of recent subvariants.

Characterizing HLA-A2-restricted CD8+ T-cell epitopes and immune responses to Omicron variants in SARS-CoV-2-inactivated vaccine recipients

Introduction

Recent surveillance has identified the emergence of the SARS-CoV-2 Omicron ariant, which exhibits the ability to evade multiple neutralizing antibodies generated by prior infection or vaccination. However, significant knowledge gaps remain regarding the CD8 T-cell immune reactivity to the Omicron variant. This study aims to evaluate the characteristics of HLA-A2-restricted CD8 T-cell epitopes from the Omicron variant and analyze epitope-specific CD8 T-cell responses to SARS-CoV-2 inactivated vaccines.

Methods

We conducted a comprehensive analysis of CD8 T-cell responses to SARS-CoV-2 inactivated vaccines, focusing on HLA-A2-restricted epitopes derived from the Omicron variant. Mutant epitopes were evaluated for their impact on antigen presentation and CD8 T-cell immune reactivity. Additionally, we screened for epitopes that exhibited reduced CD8 T-cell responses following the emergence of the Omicron variant.

Results

Our findings revealed that mutant epitopes in the Omicron variant led to escape from antigen presentation and diminished CD8 T-cell immune responses. We identified two epitopes associated with decreased CD8 T-cell reactivity post-Omicron variant emergence. Notably, we discovered an S protein epitope, 67A>V, which demonstrated similar proportions of CD8 T-cell specificity between the ancestral and mutant strains, suggesting its conservation and potential immunogenicity for vaccine development. Furthermore, the third dose of the inactivated vaccine significantly increased the number of epitope-specific CD8 T cells, underscoring the importance of booster doses in enhancing cellular immune responses against the Omicron variant.

Discussion

This study highlights the ability of the Omicron variant to evade CD8 T-cell immune responses through epitope mutations, while also identifying conserved epitopes with potential utility in vaccine design. The observed increase in epitope-specific CD8 T cells following a booster dose emphasizes the critical role of additional vaccinations in strengthening cellular immunity against emerging SARS-CoV-2 variants. These findings provide valuable insights for the development of next-generation vaccines targeting conserved epitopes and optimizing booster strategies.

Exploring binding mechanisms of omicron spike protein with dolutegravir and etravirine by molecular dynamics simulation, principal component analysis, and free binding energy calculations

The COVID-19 pandemic was caused by the SARS-CoV-2 virus, frequent mutations occurred to the wild-type virus resulting in evolved new variants. The WHO classified the new variants as 'Variants of Concern'. SARS-CoV-2 omicron evolved as the dominating variant at the end of 2021. Dolutegravir and etravirine were identified as inhibitors of SARS-CoV-2 entry to host cells in Omicron variants. In this study, combined in silico methods such as molecular docking, molecular dynamics, Principal component analysis, binding-free energy calculations, and Per Residues calculations were applied to investigate the mechanism of the bindings of the two inhibitors. The molecular dynamics results revealed the stability of dolutegravir-spike and etravirine-spike complexes in a similar manner to apo-protein. Dolutegravir and etravirine formed H-bonds and salt bridges with Omicron spike protein. The 2,4-difluoro phenyl moiety of dolutegravir plays an important role in binding the ligand. The binding mode and interactions of the two compounds indicated that Arg403, Tyr449, Tyr453, Arg493, Ser496, Arg498, Thr500, Tyr501, Gln502 and His505 are the key residues. The Principal Component Analyses suggested that no significant conformational changes happened for the two complexes during the simulations. Binding-free energy calculations showed that van der Waals interactions were the most important interactions for ligands' binding. Per-residue free energy decomposition revealed residues Arg493, Arg498, and Tyr501 contributed to the binding of the ligands through H-bonds and salt bridges formation while His505 contributed to H-bonds and Pi-Pi stacking and Phe497 contributed to hydrophobic interactions between ligands and Omicron spike protein.Communicated by Ramaswamy H. Sarma.

Advanced biomaterials for regenerative medicine and their possible therapeutic significance in treating COVID-19: a critical overview

The potential of biomaterials in medical sciences has attracted much interest, especially in promoting tissue regeneration and controlling immune responses. As the COVID-19 pandemic broke out, there was an increased interest in understanding more about how biomaterials could be employed to fight this dreaded disease, especially in the context of regenerative medicine. Out of the numerous regenerative medicine possibilities, stem cells and scaffolding (grafting) technology are two major areas in modern medicine and surgery. Mesenchymal stem cells are useful in tissue repair, tailored therapy and the treatment of COVID-19. Using biomaterials in COVID-19 treatment is intricate and needs multidisciplinary and cross-disciplinary research. Cell-based therapy and organ transplants pose immunological rejection challenges. Immunomodulation enhanced, tumorigenicity decreased, inflammation addressed and tissue damage restricted; bioengineered stem cells need clinical insights and validation. Advanced stem cell-based therapies should ideally be effective, safe and scalable. Cost and scalability shall dictate the dawn of techno-economically feasible regenerative medicine. A globally standard and uniform approval process could accelerate translational regenerative medicine. Researchers, patient advocacy organisations, regulators and biopharmaceutical stakeholders need to join hands for easy navigation of regulatory measures and expeditious market entry of regenerative medicine. This article summarises advances in biomaterials for regenerative medicine and their possible therapeutic benefits in managing infectious diseases like COVID-19. It highlights the significant recent developments in biomaterial design, scaffold construction, and stem cell-based therapies to treat tissue damage and COVID-19-linked immunological dysregulation. It also highlights the potential contribution of biomaterials towards creating novel treatment strategies to manage COVID-19.

Dual-strain dynamics of COVID-19 variants in India: Modeling, analysis, and implications for pandemic control

This study introduces a detailed compartmental model developed to understand the complex dynamics of COVID-19 transmission, focusing on the Delta and Omicron variants in India. The model tracks disease progression through different population compartments, considering factors like vaccination, time-dependent transmission, economic burden and COVID-19 death rates, loss of vaccine-induced immunity, and the transition of asymptomatic cases to recovery. The model is validated against established epidemiological knowledge and real-world data, emphasizing dynamic parameterization and accurate representation of immunity dynamics. The basic reproduction number for both variants is calculated, and sensitivity analysis for various parameters is conducted. Time-dependent parameters are estimated using the discrete inverse method. The study also explores the economic burden, impact of different types of masks, vaccine efficacy, and vaccine-induced immunity through numerical analysis.

Exploring the potential of FDA approved anti-diabetic drugs for repurposing against COVID-19: a core combination of multiple computational strategies and integrated artificial intelligence

The latest variant of coronavirus is omicron. The World Health Organization (WHO) designated variation 'B.1.1.529' named omicron as a variant of concern (VOC) on 26 November 2021. By September 2020, it will have infected over 16 million patients and killed over 600,000 people over the world. This very infectious viral illness still poses a danger to world health; it has also become the greatest problem the world is facing and become the main area of research. The development of vaccines is insufficient to stop their spread and serious effects. Despite several reputable pharmaceutical firms claiming to have developed a cure for COVID-19. For that purpose, the field-based 3D-QSAR model has been used to analyze a series of anti-diabetic drugs to repurpose them against COVID-19. The LOO verified partial least square (PLS) model generates satisfactory q2 (0.4) and r2 (0.5) values. By using this model 10 compounds were screened out of 55 FDA approved anti-diabetic drugs (built-up library). Additionally, these substances were examined using molecular docking screening and ADMET. Finally, the drugs L8, and L23 were discovered to be the lead drugs. Density functional theory at the B3LYP/6-311G* technique was used to examine structural geometries, electronic characteristics, and molecular electrostatic potential (MEP). This work will greatly assist in the detection and development of leads for early drug development to control COVID-19.Communicated by Ramaswamy H. Sarma.

Stem Cell Extracellular Vesicles as Anti-SARS-CoV-2 Immunomodulatory Therapeutics: A Systematic Review of Clinical and Preclinical Studies

BACKGROUND

COVID-19 rapidly escalated into a worldwide pandemic with elevated infectivity even from asymptomatic patients. Complications can lead to severe pneumonia and acute respiratory distress syndrome (ARDS), which are the main contributors to death. Because of their regenerative and immunomodulatory capacities, stem cells and their derived extracellular vesicles (EVs) are perceived as promising therapies against severe pulmonary conditions, including those associated with COVID-19. Herein, we evaluate the safety and efficacy of stem cell EVs in treating COVID-19 and complicating pneumonia, acute lung injury, and ARDS. We also cover relevant preclinical studies to recapitulate the current progress in stem cell EV-based therapy.

METHODS

Using PubMed, Cochrane Central Register of Controlled Trials, Scopus, and Web of Science, we searched for all English-language published studies (2000-2023) that used stem cell EVs as a therapy for COVID-19, ARDS, or pneumonia. The risk of bias (ROB) was assessed for all studies.

RESULTS

Forty-eight studies met our inclusion criteria. Various-sized EVs derived from different types of stem cells were reported as a potentially safe and effective therapy to attenuate the cytokine storm induced by COVID-19. EVs alleviated inflammation and regenerated the alveolar epithelium by decreasing apoptosis, proinflammatory cytokines, neutrophil infiltration, and M2 macrophage polarization. They also prevented fibrin production and promoted the production of anti-inflammatory cytokines and endothelial cell junction proteins.

CONCLUSION

Similar to their parental cells, stem cell EVs mediate lung tissue regeneration by targeting multiple pathways and thus hold promise in promoting the recovery of COVID-19 patients and improving the survival rate of severely affected patients.

What makes SARS-CoV-2 unique? Focusing on the spike protein

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.

A validated LC-MS/MS method for determination of six Anti-SARS-CoV-2 drugs in plasma and its application for a pharmacokinetic study in rats

Antiviral treatment for COVID-19 is considered an effective tool in reducing the rate of severe cases and deaths. As of June 2023, a total of six small molecule antiviral drugs have been conditionally approved for marketing by the National Medical Products Administration (NMPA) within China. In this study, a method of HPLC-MS/MS was established and validated for the determination of six small molecule antiviral drugs in plasma using Lamivudine as an internal standard. The chromatographic separation was performed using gradient elution with an ACE 3 C18-PFP column (3.0 mm × 150 mm, 3 μm), and the mobile phase consisted of deionized water and acetonitrile/water (90:10, v/v), both with 10 mmol/L of ammonium acetate and 0.1 % ammonium hydroxide added. Quantitative analysis of the six small molecule drugs was carried out through selective reaction monitoring based on the positive ion spray ionization mode. The method exhibited excellent precision, accuracy, recovery, and linearity, and it was used to determine the pharmacokinetic characteristics in rats. Our work not only established a bioanalytical method for six small molecule antiviral drugs but also provided scientific references for clinical pharmacokinetic studies.

COVID-19 vaccine acceptance and hesitancy in Indian context: a systematic review and meta-analysis

Vaccination against COVID-19 is vital for achieving herd immunity, and the Government of India has adopted several strategies to achieve coverage. Vaccine hesitancy was identified as a potential obstacle in combating COVID-19. This study aimed to review the COVID-19 vaccine acceptance and hesitancy, and factors associated with vaccine hesitancy based on studies conducted in Indian populations. The data sources (PubMed, Scopus, and Google Scholar) were searched by following PRISMA guidelines, and the search was done in September 2022. We performed a meta-analysis through a random effect model to estimate pooled hesitancy rate with 95% confidence intervals (CI). A total of 3,339 records were searched, of which 46 studies were found to be eligible for inclusion in the review. The included studies covered 65,551 respondents, 55% were female. Studies reported COVID-19 vaccine acceptance rate of 65.7% in January-February 2021, which increased to 92.8% in May-August 2021. Likewise, the rate of vaccine hesitancy in December 2020 was 37%, dropping to 12.1% through November 2021. The estimated pooled COVID-19 vaccine hesitancy was 31% [95% CI: 27% - 36%, I2 = 99.3%]. Most studies highlighted that fear of the vaccine's side effects, efficacy, and safety were major barriers to vaccine acceptance. However, as the review indicates, it is important to consider and address all factors contributing to vaccine hesitancy.

Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants

Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.

Excretion of SARS-CoV-2 RNA in feces has no prognostic benefit in the outcome of COVID-19: A clinical and immunological study

This study explores the correlation between immunological and clinical characteristics in coronavirus disease 2019 (COVID-19) patients with detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in feces, analyzing data from 251 patients admitted to Mostar University Clinical Hospital (UCH) from December 2021 to January 2022. Methods involved reverse transcription quantitative polymerase chain reaction (RT-qPCR) from nasopharyngeal (NP) swabs and feces, alongside serological tests for anti-SARS-CoV-2 spike IgGs. Demographic and clinical data were collected through questionnaires and medical records. The data analyses were performed using SPSS statistical software. Death occurred in 53 patients (21.1%, P < 0.001), mostly in the elderly (47/53, 88.7%, P = 0.001) and immunocompromised (19/53, 35.8%, P = 0.05), particularly those developing acute respiratory insufficiency (ARI) (46/53, 86.8%, P = 0.004), and severe/critical disease (46/53, 86.8%, P = 0.002). Among the patients with positive anti-SARS-CoV-2 IgG antibodies (86/251, 34.3%, P < 0.001), 41 (47.7%) were vaccinated and 45 (52.3%) unvaccinated (P = 0.666), showing no significant differences in clinical outcomes or mortality. Unvaccinated patients with a negative antibody titer had a higher incidence of ARI (96/123, 78%, P = 0.029) and intensive care unit (ICU) admission (22/123, 17.9%, P = 0.026), than those with a positive antibody titer. Forty-seven (62.7%) patients, out of the 75 hospitalized who provided a feces sample, were positive for SARS-CoV-2 RNA (P = 0.028), without statistical differences between fecal SARS-CoV-2 positive and negative groups regarding vaccination status (15/47, 31.9%, P = 0.493), antibody status (18/47, 38.3%, P = 0.628), or death outcome (5/47, 10.6%, P = 0.706). In conclusion, unvaccinated hospitalized patients with a severe COVID-19 presentation and a negative anti-spike SARS-CoV-2 IgG titer had adverse outcomes more frequently. This suggests cautious consideration for the diagnostic use of fecal samples compared to NP swabs.

A pilot study on Paxlovid therapy for hemodialysis patients with severe acute respiratory syndrome coronavirus 2 infections

We aimed to investigate the safety and efficacy of nirmatrelvir/ritonavir (Paxlovid) therapy for hemodialysis-dependent patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Thirteen hemodialysis patients infected with the Omicron variant of SARS-CoV-2 from April 3 to May 30, 2022, were recruited. Laboratory parameters and chest CT (computed tomography) imaging were analyzed. The treatment group included six patients who received 150 mg/100 mg of Paxlovid orally once daily for 5 days, whereas the control group included seven patients who received basic treatment. No serious adverse reactions or safety events were recorded. Four control patients progressed to moderate disease, and none in the treatment group showed progression of chest CT findings (P < 0.05). Paxlovid therapy tended toward early viral clearance and low viral load on Day 8. Moreover, 83.3% of the patients in the treatment group and 57.1% of the patients in the control group turned negative within 22 days. In the Paxlovid treatment group, we found significantly increased levels of lymphocytes (P=0.03) and eosinophils (P=0.02) and decreased levels of D-dimer on Day 8 compared with those on Day 1. Paxlovid therapy showed a potential therapeutic effect with good tolerance in hemodialysis patients. The optimal dose and effectiveness evaluation must be further investigated in a largeer cohort.

Dysregulation of intracellular redox homeostasis by the SARS-CoV-2 ORF6 protein

SARS-CoV-2 has evolved several strategies to overcome host cell defenses by inducing cell injury to favour its replication. Many viruses have been reported to modulate the intracellular redox balance, affecting the Nuclear factor erythroid 2-Related Factor 2 (NRF2) signaling pathway. Although antioxidant modulation by SARS-CoV-2 infection has already been described, the viral factors involved in modulating the NRF2 pathway are still elusive. Given the antagonistic activity of ORF6 on several cellular pathways, we investigated the role of the viral protein towards NRF2-mediated antioxidant response. The ectopic expression of the wt-ORF6 protein negatively impacts redox cell homeostasis, leading to an increase in ROS production, along with a decrease in NRF2 protein and its downstream controlled genes. Moreover, when investigating the Δ61 mutant, previously described as an inactive nucleopore proteins binding mutant, we prove that the oxidative stress induced by ORF6 is substantially related to its C-terminal domain, speculating that ORF6 mechanism of action is associated with the inhibition of nuclear mRNA export processes. In addition, activation by phosphorylation of the serine residue at position 40 of NRF2 is increased in the cytoplasm of wt-ORF6-expressing cells, supporting the presence of an altered redox state, although NRF2 nuclear translocation is hindered by the viral protein to fully antagonize the cell response. Furthermore, wt-ORF6 leads to phosphorylation of a stress-activated serine/threonine protein kinase, p38 MAPK, suggesting a role of the viral protein in regulating p38 activation. These findings strengthen the important role of oxidative stress in the pathogenesis of SARS-CoV-2 and identify ORF6 as an important viral accessory protein hypothetically involved in modulating the antioxidant response during viral infection.

Role of available COVID-19 vaccines in reducing deaths and perspective for next generation vaccines and therapies to counter emerging viral variants: an update

The COVID-19 disease wreaked havoc all over the world causing more than 6 million deaths out of over 519 million confirmed cases. It not only disturbed the human race health-wise but also caused huge economic losses and social disturbances. The utmost urgency to counter pandemic was to develop effective vaccines as well as treatments that could reduce the incidences of infection, hospitalization and deaths. The most known vaccines that could help in managing these parameters are Oxford-AstraZeneca (AZD1222), Pfizer-BioNTech (BNT162b2), Moderna (mRNA-1273) and Johnson & Johnson (Ad26.COV2.S). The effectiveness of AZD1222 vaccine in reducing deaths is 88% in the age group 40-59 years, touching 100% in the age group 16-44 years & 65-84 years. BNT162b2 vaccine also did well in reducing deaths due to COVID-19 (95% in the age group 40-49 years and 100% in the age group 16-44 years. Similarly, mRNA-1273 vaccine showed potential in reducing COVID-19 deaths with effectiveness ranging from 80.3 to 100% depending upon age group of the vaccinated individuals. Ad26.COV2.S vaccine was also 100% effective in reducing COVID-19 deaths. The SARS-CoV-2 emerging variants have emphasized the need of booster vaccine doses to enhance protective immunity in vaccinated individuals. Additionally, therapeutic effectiveness of Molnupiravir, Paxlovid and Evusheld are also providing resistance against the spread of COVID-19 disease as well as may be effective against emerging variants. This review highlights the progress in developing COVID-19 vaccines, their protective efficacies, advances being made to design more efficacious vaccines, and presents an overview on advancements in developing potent drugs and monoclonal antibodies for countering COVID-19 and emerging variants of SARS-CoV-2 including the most recently emerged and highly mutated Omicron variant.

COVID-19 vaccines and their underbelly: Are we going the right way?

Background

Historically, a critical aetiological agent of health concern stays till eternity after its discovery, so shall it be with the COVID-19 outbreak. It has transformed human life to a 'new normal' with huge tolls on the social, psychological, intellectual and financial spheres.

Aim

This perspective aimed to collate numerous reported COVID-19 vaccine-associated adverse events and the predisposing factors. It focussed on the efficacy of mix-n-match (cocktail) vaccines to effectively counter COVID-19 infection to facilitate future research and possible interventions.

Material and Methods

Databases like Scopus, Pubmed and the Web-of-science were searched for published literature on 'adverse events associated with COVID-19 vaccine'. The reports and updates from health agencies like the WHO and CDC were also considered for the purpose. The details with respect to the adverse events associated with COVID-19 vaccination and the predisposing factors were compiled to obtain insights and suggest possible future directions in vaccine research.

Results

India stood strong to manage its health resources in time and turned into a dominant global vaccine supplier at a time when healthcare infrastructure of many countries was still significantly challenged. Developing indigenous vaccines and the vaccination drive in India were its major achievements during the second and the subsequent COVID-19 waves. The fully indigenous Covaxin vaccine, primarily as an emergency intervention, was successfully rapidly launched. Similar such vaccines for emergency use were developed elsewhere as well. However, all of these reached the marketplace with a 'emergency use only' tag, without formal clinical trials and other associated formalities to validate and verify them as these would require much longer incubation time before they are available for human use.

Discussion

Many adverse events associated with either the first or the second/booster vaccination doses were reported. Evidently, these associated adverse events were considered as 'usually rare' or were often underreported. Without the additional financial or ethical burden on the vaccine companies, fortunately, the Phase IV (human) clinical trials of their manufactured vaccines are occurring by default as the human population receives these under the tag 'emergency use'. Thus, focused and collaborative strategies to unveil the molecular mechanisms in vaccine-related adverse events in a time-bound manner are suggested.

Conclusion

Reliable data particularly on the safety of children is lacking as majority of the current over-the-counter COVID-19 vaccines were for emergency use. Many of these were still in their Phase III and Phase IV trials. The need for a mutant-proof, next-gen COVID-19 vaccine in the face of vaccine-associated adverse events is opined.

Psychometric properties of the Coronavirus Anxiety Scale based on Classical Test Theory (CTT) and Item Response Theory (IRT) models among Chinese front-line healthcare workers

BACKGROUND

Since March 2022, the COVID-19 epidemic has rebounded widely and frequently in China. Healthcare workers have faced grand challenges such as soaring COVID-19 patients, being busy with the nucleic acid screening of all the populations in the epidemic areas every day, and testing positive for COVID-19, all of which contributed to anxiety easily according to the Conservation of Resources theory. However, anxiety among healthcare workers is not only associated with personal health but also adversely affects the quality of health services. Therefore, it is crucial to search for suitable tools to monitor the anxiety related to COVID-19 among healthcare workers. The current study aimed to test the Coronavirus Anxiety Scale (CAS) in Chinese healthcare workers.

METHODS

The current study employed a cross-sectional design. The CAS was translated into Chinese. Then, according to Classical Test Theory (CTT) and Item Response Theory (IRT) models, the psychometric properties of the Chinese version were measured among 811 healthcare workers.

RESULTS

The split-half reliability was 0.855. The Cronbach's α coefficient was 0.895. The retest coefficient was 0.901 with 10 days as the retest interval. The content validity index was 0.920. In exploratory factor analysis, one common factor was extracted and explained 72.559% of the total variance. All item load values on the common factor ranged from 0.790 to 0.885, and the communality of each item ranged from 0.625 to 0.784. With confirmatory factor analysis, the single factor model showed an excellent goodness-of-fit, chi-square/degree of freedom (χ2/df) = 3.339, goodness of fit index (GFI) = 0.992, adjusted goodness of fit index (AGFI) = 0.975, root-mean-square error of approximation (RMSEA) = 0.054, root mean square residual (RMR) = 0.005, incremental fit index (IFI) = 0.967, Tucker-Lewis index (TLI) = 0.932, and comparative fit index (CFI) = 0.966. The multiple-group confirmatory factor analysis revealed the invariance measuring anxiety of COVID-19 was in similar ways across ages, hospital degrees, and professional titles. With convergent validity, the CAS was positively correlated with post-traumatic stress disorder (r = 0.619, P < 0.001), fear of COVID (r = 0.550, P < 0.001), and depression (r = 0.367, P < 0.001). According to IRT models, the results showed that all item discrimination parameters were higher than 1.70 and difficulty parameters ranged from 1.13 to 2.83.

CONCLUSION

The Chinese version of CAS has good psychometric properties in healthcare workers after China adjusted the COVID-19 management measures during the COVID-19 Omicron epidemic, and can be used for assessing the anxiety associated with COVID-19 in Chinese healthcare workers.

COVID-19-associated candidiasis and the emerging concern of Candida auris infections

The incidence of COVID-19-associated candidiasis (CAC) is increasing, resulting in a grave outcome among hospitalized patients with COVID-19. The most alarming condition is the increasing incidence of multi-drug resistant Candida auris infections among patients with COVID-19 worldwide. The therapeutic strategy towards CAC caused by common Candida species, such as Candida albicans, Candida tropicalis, and Candida glabrata, is similar to the pre-pandemic era. For non-critically ill patients or those with a low risk of azole resistance, fluconazole remains the drug of choice for candidemia. For critically ill patients, those with a history of recent azole exposure or with a high risk of fluconazole resistance, echinocandins are recommended as the first-line therapy. Several novel therapeutic agents alone or in combination with traditional antifungal agents for candidiasis are potential options in the future. However, for multidrug-resistant C. auris infection, only echinocandins are effective. Infection prevention and control policies, including strict isolation of the patients carrying C. auris and regular screening of non-affected patients, are suggested to prevent the spread of C. auris among patients with COVID-19. Whole-genome sequencing may be used to understand the epidemiology of healthcare-associated candidiasis and to better control and prevent these infections.

Safety, tolerability, pharmacokinetics, and immunogenicity of JMB2002-an antibody against COVID-19: a phase 1 clinical trial in healthy Chinese adults

BACKGROUND

The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and subsequent Coronavirus Disease 2019 (COVID-19) pandemic has resulted in a significant global public health burden, leading to an urgent need for effective therapeutic strategies. Monoclonal antibodies (mAbs) are a potentially effective therapeutic option. We identified a potent antibody JMB2002 against the SARS-CoV-2 receptor binding domain. JMB2002 has demonstrated therapeutic efficacy in a SARS-CoV-2 infected rhesus macaque model.

METHODS

We conducted a randomized, double-blind, phase 1 trial to evaluate the JMB2002's safety, tolerability, pharmacokinetics, and immunogenicity in healthy Chinese adults. Participants were randomly assigned to one of four cohorts with sequential dose, administrated intravenously with JMB2002 or placebo, and followed up for 85 ± 5 days.

RESULTS

40 participants were recruited and completed in the study. Eight (25.0%) participants experienced 13 treatment emergent adverse events (TEAEs) that were drug-related. No serious adverse events (SAEs), dose limiting events (DLTs), or adverse events of special interest (AESIs), such as infusion related/allergic reactions, were observed, and no drop out due to adverse events (AEs) occurred. There was no significant safety difference observed between JMB2002 and the placebo, suggesting it was well tolerated. The AUC_0-∞, AUC_0 - t of JMB2002 infusion increased dose-dependently from 5 mg/kg to 50 mg/kg while there is also a linear trend between doses and C_max.

CONCLUSION

Therefore, JMB2002 was well tolerated after administration of a single dose in the range of 5 mg/kg to 50 mg/kg in healthy Chinese adults.

TRIAL REGISTRATION

ChiCTR2100042150 at https://www.chictr.org.cn/searchproj.aspx (14/01/2021).

Genomic evolution of the SARS-CoV-2 Variants of Concern: COVID-19 pandemic waves in India

SARS-CoV-2 has mutated rapidly since its first case report in Wuhan, China, leading to the emergence of an indefinite number of variants. India has witnessed three waves of the COVID-19 pandemic. The country saw its first wave of SARS-CoV-2 illness from late January 2020 to February 2021. With a peak surge of cases in mid-September 2020, India recorded more than 11 million cases and a death toll of more than 0.165 million at this time. India faced a brutal second wave driven by the emergence of highly infectious SARS-CoV-2 variants B.1.617.2 (Delta variant) and the third wave with the leading cause of BA.2 (Omicron variant), which has led to an unprecedented rise in COVID-19 cases in the country. On September 14, 2022, India recorded a cumulative 44.51 million cases of COVID-19 with more than 0.528 million deaths. The discovery of common circulating mutants is facilitated by genome sequencing. The changes in the Spike surface glycoprotein recombinant binding domains served as the critical alterations, resulting in enhanced infectivity and transmissibility, with severe clinical effects. Further, the predominant mutation in the SARS-CoV-2 spike protein; the D614G strains served as a model for vaccine development. The mutation of the Wuhan strain to the Variant of Concern led to a significant increase in SARS-CoV-2 infections. In addition, there was a shift in the age group affected by SARS-CoV-2 variant infection. The current review summarized the COVID-19 pandemic's Variant of Concern and the advent of SARS-CoV-2 in India.

Mediating effect of resilience and fear of COVID-19 on the relationship between social support and post-traumatic stress disorder among campus-quarantined nursing students: a cross-sectional study

BACKGROUND

The emergency of Omicron variants, spreading in China and worldwide, has sparked a new wave of the coronavirus disease 2019 (COVID-19) pandemic. The high infectivity and persistence of the pandemic may trigger some degrees of post-traumatic stress disorder (PTSD) for nursing students experiencing indirect trauma exposure to the epidemic, which hinders the role transition from students to qualified nurses and exacerbates the health workforce shortage. Thus, it's well worth an exploration to understand PTSD and its underlying mechanism. Specifically, PTSD, social support, resilience, and fear of COVID-19 were selected after widely literature review. This study aimed to investigate the relationship between social support and PTSD among nursing students during COVID-19, to address the mediating role of resilience and fear of COVID-19 between social support and PTSD, and to provide practical guidance for nursing students' psychological intervention.

METHODS

From April 26 to April 30, 2022, 966 nursing students from Wannan Medical College were selected by the multistage sampling method to fill the Primary Care PTSD Screen for the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), Brief Resilience Scale, Fear of COVID-19 Scale, and Oslo 3 Items Social Support Scale. Data were analyzed by descriptive statistics, spearman's correlation analysis, regression analysis, and path analysis.

RESULTS

15.42% of nursing students had PTSD. There were significant correlations between social support, resilience, fear of COVID-19, and PTSD (r =-0.291 ~ 0.353, P <0.001). Social support had a direct negative effect on PTSD (β =-0.216; 95% confidence interval, CI: -0.309~-0.117), accounting for 72.48% of the total effect. Analysis of mediating effects revealed that social support influenced PTSD through three indirect pathways: the mediated effect of resilience was statistically significant (β =-0.053; 95% CI: -0.077~-0.031), accounting for 17.79% of the total effect; the mediated effect of fear of COVID-19 was statistically significant (β =-0.016; 95% CI: -0.031~-0.003), accounting for 5.37% of the total effect; the chain mediating effect of resilience and fear of COVID-19 was statistically significant (β =-0.013; 95% CI: -0.022~-0.006), accounting for 4.36% of the total effect.

CONCLUSION

The social support of nursing students not only directly affects PTSD, but also indirectly affects PTSD through the separate and chain mediating effect of resilience and fear of COVID-19. The compound strategies targeted at boosting perceived social support, fostering resilience, and controlling fear of COVID-19 are warranted for reducing PTSD.

Safety and immunogenicity of a protein subunit COVID-19 vaccine (ZF2001) in healthy children and adolescents aged 3-17 years in China: a randomised, double-blind, placebo-controlled, phase 1 trial and an open-label, non-randomised, non-inferiority, phase 2 trial

BACKGROUND

ZF2001 is a recombinant protein subunit vaccine against SARS-CoV-2 that has been approved for use in China, Colombia, Indonesia, and Uzbekistan in adults aged 18 years or older, but not yet in children and adolescents younger than 18 years. We aimed to evaluate the safety and immunogenicity of ZF2001 in children and adolescents aged 3-17 years in China.

METHODS

The randomised, double-blind, placebo-controlled, phase 1 trial and the open-label, non-randomised, non-inferiority, phase 2 trial were done at the Xiangtan Center for Disease Control and Prevention (Hunan Province, China). Healthy children and adolescents aged 3-17 years, without a history of SARS-CoV-2 vaccination, without a history of COVID-19, without COVID-19 at the time of the study, and without contact with patients with confirmed or suspected COVID-19 were included in the phase 1 and phase 2 trials. In the phase 1 trial, participants were divided into three groups according to age (3-5 years, 6-11 years, and 12-17 years). Each group was randomly assigned (4:1), using block randomisation with five blocks, each with a block size of five, to receive three 25 μg doses of the vaccine, ZF2001, or placebo intramuscularly in the arm 30 days apart. The participants and investigators were masked to treatment allocation. In the phase 2 trial, participants received three 25 μg doses of ZF2001 30 days apart and remained stratified by age group. For phase 1, the primary endpoint was safety and the secondary endpoint was immunogenicity (humoral immune response on day 30 after the third vaccine dose: geometric mean titre [GMT] of prototype SARS-CoV-2 neutralising antibodies and seroconversion rate, and geometric mean concentration [GMC] of prototype SARS-CoV-2 receptor-binding domain [RBD]-binding IgG antibodies and seroconversion rate). For phase 2, the primary endpoint was the GMT of SARS-CoV-2 neutralising antibodies with seroconversion rate on day 14 after the third vaccine dose, and the secondary endpoints included the GMT of RBD-binding antibodies and seroconversion rate on day 14 after the third vaccine dose, the GMT of neutralising antibodies against the omicron BA.2 subvariant and seroconversion rate on day 14 after the third vaccine dose, and safety. Safety was analysed in participants who received at least one dose of the vaccine or placebo. Immunogenicity was analysed in the full-analysis set (ie, participants who received at least one dose and had antibody results) by intention to treat and in the per-protocol set (ie, participants who completed the whole vaccination course and had antibody results). Non-inferiority in the phase 2 trial (neutralising antibody titre of participants from this trial aged 3-17 years vs that of participants aged 18-59 years from a separate phase 3 trial) for clinical outcome assessment was based on the geometric mean ratio (GMR) and was considered met if the lower bound of the 95% CI for the GMR was 0·67 or greater. These trials are registered with ClinicalTrials.gov, NCT04961359 (phase 1) and NCT05109598 (phase 2).

FINDINGS

Between July 10 and Sept 4, 2021, 75 children and adolescents were randomly assigned to receive ZF2001 (n=60) or placebo (n=15) in the phase 1 trial and were included in safety and immunogenicity analyses. Between Nov 5, 2021, and Feb 14, 2022, 400 participants (130 aged 3-7 years, 210 aged 6-11 years, and 60 aged 12-17 years) were included in the phase 2 trial and were included in the safety analysis; six participants were excluded from the immunogenicity analyses. 25 (42%) of 60 participants in the ZF2001 group and seven (47%) of 15 participants in the placebo group in phase 1, and 179 (45%) of 400 participants in phase 2, had adverse events within 30 days after the third vaccination, without a significant difference between groups in phase 1. Most adverse events were grade 1 or 2 (73 [97%] of 75 in the phase 1 trial, and 391 [98%] of 400 in the phase 2 trial). One participant in the phase 1 trial and three in the phase 2 trial who received ZF2001 had serious adverse events. One serious adverse event (acute allergic dermatitis) in the phase 2 trial was possibly related to the vaccine. In the phase 1 trial, on day 30 after the third dose, in the ZF2001 group, seroconversion of neutralising antibodies against SARS-CoV-2 was observed in 56 (93%; 95% CI 84-98) of 60 participants, with a GMT of 176·5 (95% CI 118·6-262·8), and seroconversion of RBD-binding antibodies was observed in all 60 (100%; 95% CI 94-100) participants, with a GMC of 47·7 IU/mL (95% CI 40·1-56·6). In the phase 2 trial, on day 14 after the third dose, seroconversion of neutralising antibodies against SARS-CoV-2 was seen in 392 (99%; 95% CI 98-100) participants, with a GMT of 245·4 (95% CI 220·0-273·7), and seroconversion of RBD-binding antibodies was observed in all 394 (100%; 99-100) participants, with a GMT of 8021 (7366-8734). On day 14 after the third dose, seroconversion of neutralising antibodies against the omicron subvariant BA.2 was observed in 375 (95%; 95% CI 93-97) of 394 participants, with a GMT of 42·9 (95% CI 37·9-48·5). For the non-inferiority comparison of participants aged 3-17 years with those aged 18-59 years for SARS-CoV-2 neutralising antibodies, the adjusted GMR was 8·6 (95% CI 7·0-10·4), with the lower bound of the GMR greater than 0·67.

INTERPRETATION

ZF2001 is safe, well tolerated, and immunogenic in children and adolescents aged 3-17 years. Vaccine-elicited sera can neutralise the omicron BA.2 subvariant, but with reduced activity. The results support further studies of ZF2001 in children and adolescents.

FUNDING

Anhui Zhifei Longcom Biopharmaceutical and the Excellent Young Scientist Program from National Natural Science Foundation of China.

TRANSLATION

For the Chinese translation of the abstract see Supplementary Materials section.

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development

Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases and over 6.7 million deaths have been attributed to successive waves of SARS-CoV-2 infections as of 29th January 2023. Similar to other RNA viruses, SARS-CoV-2 is more susceptible to genetic evolution and spontaneous mutations over time, resulting in the continual emergence of variants with distinct characteristics. Spontaneous mutations of SARS-CoV-2 variants increase its transmissibility, virulence, and disease severity and diminish the efficacy of therapeutics and vaccines, resulting in vaccine-breakthrough infections and re-infection, leading to high mortality and morbidity rates. Materials and methods: In this study, we evaluated 10,531 whole genome sequences of all reported variants globally through a computational approach to assess the spread and emergence of the mutations in the SARS-CoV-2 genome. The available data sources of NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) and NextStrain (https://nextstrain.org/) were searched for tracking SARS-CoV-2 mutations, analysed using the PROVEAN, Polyphen-2, and Predict SNP mutational analysis tools and validated by Machine Learning models. Result: Compared to the Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 mutations in the SARS-CoV-2 genome. We determined that the Omicron variant had 6,307 mutations (retrieved sequence:1947), including 67.8% unique mutations, more than any other variant evaluated in this study. The spike protein of the Omicron variant harboured 876 mutations, including 443 deleterious mutations. Among these deleterious mutations, 187 were common and 256 were unique non-synonymous mutations. In contrast, after analysing 1,884 sequences of the Delta variant, we discovered 4,468 mutations, of which 66% were unique, and not previously reported in other variants. Mutations affecting spike proteins are mostly found in RBD regions for Omicron, whereas most of the Delta variant mutations drawn to focus on amino acid regions ranging from 911 to 924 in the context of epitope prediction (B cell & T cell) and mutational stability impact analysis protruding that Omicron is more transmissible. Discussion: The pathogenesis of the Omicron variant could be prevented if the deleterious and persistent unique immunosuppressive mutations can be targeted for vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor and track the continuously evolving nature of SARS-CoV-2 strains, the associated genetic variants, and their implications for developing effective control and prophylaxis strategies.

Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies

Newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously posing high global public health concerns and panic resulting in waves of coronavirus disease 2019 (COVID-19) pandemic. Depending on the extent of genomic variations, mutations and adaptation, few of the variants gain the ability to spread quickly across many countries, acquire higher virulency and ability to cause severe disease, morbidity and mortality. These variants have been implicated in lessening the efficacy of the current COVID-19 vaccines and immunotherapies resulting in break-through viral infections in vaccinated individuals and recovered patients. Altogether, these could hinder the protective herd immunity to be achieved through the ongoing progressive COVID-19 vaccination. Currently, the only variant of interest of SARS-CoV-2 is Omicron that was first identified in South Africa. In this review, we present the overview on the emerging SARS-CoV-2 variants with a special focus on the Omicron variant, its lineages and hybrid variants. We discuss the hypotheses of the origin, genetic change and underlying molecular mechanism behind higher transmissibility and immune escape of Omicron variant. Major concerns related to Omicron including the efficacy of the current available immunotherapeutics and vaccines, transmissibility, disease severity, and mortality are discussed. In the last part, challenges and strategies to counter Omicron variant, its lineages and hybrid variants amid the ongoing COVID-19 pandemic are presented.

COVID-19 patients' clinical profile and outcome with respect to their vaccination status: A prospective observational multicentre cohort study during third wave in Western India

PURPOSE

To understand the benefits of COVID-19 vaccination (Covishield, Covaxin) on clinical features and outcome of COVID-19 during the third wave in India.

MATERIALS AND METHODS

The primary study aim was to describe the clinical profile and outcome of COVID-19 regarding their vaccination and to identify risk factors for disease progression in vaccinated patients. This was a prospective observational multicentric study of COVID-19 attended by Infectious Disease physicians during January 15, 2022 to February 15, 2022. Adult patients with positive RT-PCR or rapid antigen test for COVID-19 were enrolled. Patient received treatment as per local institutional protocol. Chi square test for categorical and Mann Whitney test for continuous variables were applied for the analysis. Logistic regression was used to calculate adjusted odds ratios.

RESULTS

A total of 788 patients were included in analysis out of 883 enrolled patients from 13 centers across Gujarat. By the end of two weeks' follow up, 22 patients (2.8%) had expired. The Median age of subjects was 54 years, with a (55.8%) male. 90% of the subjects were vaccinated, majority (77%) of them had received 2 doses of vaccine with Covishield (659, 93%). Mortality among the non-vaccinated was significantly (11.4%) higher than vaccinated (1.8%). Logistic regression analysis showed numbers of comorbidities (p ​= ​0.027), baseline higher WBC count (p ​= ​0.02), higher NLR (p ​= ​0.016), and Ct value (p ​= ​0.046) were associated with mortality while vaccination was associated with survival (p ​= ​0.001). The factors associated with mortality among vaccinated were age, comorbidities, baseline higher WBC, NLR, and CRP.

CONCLUSIONS

Omicron variant was associated with mild symptoms. Clinical and laboratory risk factors for getting severe disease with Omicron variant were the same with previous SARS CoV-2 strain. Two doses of vaccine protect people against severe disease and death. Age, comorbidities, baseline leucocytosis, high NLR, elevated CRP are the risk factors for poor outcome in vaccinated patients.

Reproduction numbers of SARS-CoV-2 Omicron subvariants

Estimating the effective reproduction number of Omicron subvariants is crucial for evaluating the effectiveness of control measures, and adjusting control measures promptly. We conducted a systematic review to synthesize the evidence from estimates of the reproduction numbers for Omicron subvariants, and estimated their effective reproduction number.

Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern

This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).

Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus's genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August-22 October 2021) and 1.435 × 10-3 (95% HPD  =  1.021 × 10-3 - 1.869 × 10-3) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September-28 November 2021) and 1.074 × 10-3 (95% HPD  =  6.444 × 10-4 - 1.586 × 10-3) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health.

Emergence of SARS-CoV-2 Omicron variant and strategies for tackling the infection

INTRODUCTION

Nowadays, emerging SARS-CoV-2 Omicron, the novel highly mutated VOC, has quickly spread as the dominant variant in over 190 countries worldwide through the first part of 2022, which is influencing the infectivity, transmissibility, pathogenicity, and severity of COVID-19 pandemic. Additionally, clinical cases and experimental studies have reported that Omicron variant likely leads to weakened immune protection elicited by infection, antibody therapies, and vaccines. The new wave, from late February, 2022, was escalated abruptly by higher levels of transmission of Omicron BA.2 sublineage in China.

METHODS AND RESULTS

Following a systematic database search, this review summarizes the salient features of Omicron sublineages, and their impact on transmissibility, disease severity as well as the efficacy of the available vaccines and treatment against the Omicron.

CONCLUSION

We hope this study will provide a scientific reference for alleviating the burden of COVID-19.

Omicron BA.2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India

Background

Recent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India.

Methods

Whole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7.

Results

The mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men.

Conclusion

The current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.

Genomic and epidemiologic surveillance of SARS-CoV-2 in Southern Brazil and identification of a new Omicron-L452R sublineage

Recently, SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in Botswana in November 2021. In a short period of time, this highly mutated variant replaced the previous dominant Delta variant, causing an exponential increase in the number of COVID-19 cases, resulting in a new wave of pandemic. This current research article aims to analyze and summarize information about the genetic characteristics, amino acid mutations and epidemiological data providing scientific findings to enrich the SARS-CoV-2 knowledge. More importantly, we describe here, for the first time, the identification of a new Omicron variant of concern: Omicron-L452R in Brazil.

Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2?

Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid the serious containment efforts against COVID-19 that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has been identified as a highly modified, contagious, and crucial variant among the five VOCs of SARS-CoV-2. The increased affinity of the spike protein (S-protein), and host receptor, angiotensin converting enzyme-2 (ACE-2), due to a higher number of mutations in the receptor-binding domain (RBD) of the S-protein has been proposed as the primary reason for the decreased efficacy of majorly available vaccines against the Omicron variant and the increased transmissible nature of the Omicron variant. Because of its significant competitive advantage, the Omicron variant and its sublineages swiftly surpassed other variants to become the dominant circulating lineages in a number of nations. The Omicron variant has been identified as a prevalent strain in the United Kingdom and South Africa. Furthermore, the emergence of recombinant variants through the conjunction of the Omicron variant with other variants or by the mixing of the Omicron variant's sublineages/subvariants poses a major threat to humanity. This raises various issues and hazards regarding the Omicron variant and its sublineages, such as an Omicron variant breakout in susceptible populations among fully vaccinated persons. As a result, understanding the features and genetic implications of this variant is crucial. Hence, we explained in depth the evolution and features of the Omicron variant and analyzed the repercussions of spike mutations on infectiousness, dissemination ability, viral entry mechanism, and immune evasion. We also presented a viewpoint on feasible strategies for precluding and counteracting any future catastrophic emergence and spread of the omicron variant and its sublineages that could result in a detrimental wave of COVID-19 cases.

Breakthrough cases of Omicron and Delta variants of SARS-CoV-2 during the fifth wave in Pakistan

COVID-19 pandemic has severely affected Pakistan with 1,557,134 cases as of August 4, 2022. However, the data regarding breakthrough infections in Pakistan is scant. Hence, the objective was to analyze SARS-CoV-2 breakthrough infections with respect to vaccines and variants during the fifth wave in Pakistan. Therefore, the Department of Virology (NIH, Pakistan) genotyped 2,467 randomly selected individuals between November 2021 and February 2022 using the SNPsig^® SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK). P681R and K417N mutations were used to distinguish delta and omicron. Data on the patient's age, gender, date of collection, variant, and vaccination status were analyzed using Statistical Package for Social Sciences (SPSS) software. Among 2,467 genotyped samples, Omicron was detected in 58.6% (n = 1445), Delta in 40.4% (n = 998) and undetermined/wildtype variant in 24 samples. The vaccination status of omicron-positive patients showed (49.7%; n = 718/1445) and Delta-positive patients (39.67%; n = 396/998) to be fully vaccinated. Of note, a high percentage 85% of breakthrough cases (n = 947) were identified among fully vaccinated individuals (n = 1114). Among them, 85.9% (n = 617/718) belonged to omicron and 83.3% (n = 330/396) to delta. Moreover, 76.7% (n = 855) of vaccinated individuals (n = 1114) received Sinopharm (n = 432) and Sinovac (n = 423) vaccines. The majority of breakthrough subjects who contracted Omicron were vaccinated with Sinopharm (93.0%, n = 256) and delta with Cansino (100%, n = 44). Individuals vaccinated with Sinovac showed the most frequent breakthrough cases for both Omicron and Delta variant between the 4th and 6th months (n = 278) after primary vaccination as compared to the 7th to 9th months (n = 24) category. While in case of Sinopharm, maximum breakthrough cases occurred between 7th to 9th months (n = 234) as compared to the 4th to 6th months (n = 120) after primary vaccination. Omicron and Delta breakthrough cases in men (n = 364 and 193) are more frequently seen than women (n = 253 and 138) respectively and breakthrough majority cases (n = 392) occurred in individuals aged 18-33 years. Breakthrough cases limiting monitoring in Pakistan impose a substantial constraint on policymakers' ability to take timely effective decisions. Since the current study consists of only a 2,467-genotyped sample, comprehensive data should be analyzed.

Fear-Responses to Bat-Originating Coronavirus Pandemics with Respect to Quarantines Gauged in Relation to Postmodern Thought—Implications and Recommendations

Fear-responses to bat-originating coronavirus pandemics with respect to quarantine imposition are gathered and interpreted from large datasets, identified and disseminated by media. Responses are effectively gauged using postmodern thought with a continuum ranging from people’s resilience to define their own perspectives to public views being socially conditioned from media persistence in maintaining fear. Public responses to the 2003 SARS pandemic generally presumed and supported resilience of citizens’ perspectives. In contrast, from late 2019 to mid-2022, public responses to the COVID-19 pandemic were media-determined, promoting fear. In this regard, reactions to the COVID-19 quarantines are contrasted to the hospital isolations of SARS. The primary source of the difference was the major polarizing influence by social media of the WHO policy makers’ pronouncements and of healthcare providers’ statements directing media spotlight in their guidance of public response to COVID-19 throughout the pandemic, unlike during SARS. An investigation of cognitive bias regarding the psychological and societal implications related to this migration from resilience to fear regarding public responses to novel bat-originating coronavirus pandemics elicits recommendations concerning future quarantine dictates. These recommendations are dependent on appropriate encouragement of hopeful resilience through evidence based practice with respect to one extreme of the postmodern thought continuum.

Evolving trend change during the COVID-19 pandemic

Coronavirus disease (COVID-19) has caused unimaginable damage to public health and socio-economic structures worldwide; thus, an epidemiological depiction of the global evolving trends of this disease is necessary. As of March 31, 2022, the number of cases increased gradually over the four waves of the COVID-19 pandemic, indicating the need for continuous countermeasures. The highest total cases per million and total deaths per million were observed in Europe (240,656.542) and South America (2,912.229), despite these developed countries having higher vaccination rates than other continents, such as Africa. In contrast, the lowest of the above two indices were found in undeveloped African countries, which had the lowest number of vaccinations. These data indicate that the COVID-19 pandemic is positively related to the socio-economic development level; meanwhile, the data suggest that the vaccine currently used in these continents cannot completely prevent the spread of COVID-19. Thus, rethinking the feasibility of a single vaccine to control the disease is needed. Although the number of cases in the fourth wave increased exponentially compared to those of the first wave, ~43.1% of deaths were observed during the first wave. This was not only closely linked to multiple factors, including the inadequate preparation for the initial response to the COVID-19 pandemic, the gradual reduction in the severity of additional variants, and the protection conferred by prior infection and/or vaccination, but this also indicated the change in the main driving dynamic in the fourth wave. Moreover, at least 12 variants were observed globally, showing a clear spatiotemporal profile, which provides the best explanation for the presence of the four waves of the pandemic. Furthermore, there was a clear shift in the trend from multiple variants driving the spread of disease in the early stage of the pandemic to a single Omicron lineage predominating in the fourth wave. These data suggest that the Omicron variant has an advantage in transmissibility over other contemporary co-circulating variants, demonstrating that monitoring new variants is key to reducing further spread. We recommend that public health measures, along with vaccination and testing, are continually implemented to stop the COVID-19 pandemic.

A Systematic Review on the Emergence of Omicron Variant and Recent Advancement in Therapies

With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as compared to another variant of concern, with a total of 50 mutations, 30 of which are present on its spike protein alone. These mutations have led to immune escape and more transmissibility compared to other variants, including the Delta variant. A cluster of mutations (H655Y, N679K, and P681H) present in the Omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of the anti-viral and mAbs drugs. However, two monoclonal antibody drugs, Sotrovimab and Evusheld, are authorized for emergency use in COVID-19 patients. This virus is not fading away soon. The easiest solution and least expensive measure to fight against this pandemic are to follow the appropriate COVID-19 protocols. There is a need to strengthen the level of research for the development of potential vaccines and anti-viral drugs. It is also important to monitor and expand the genomic surveillance to keep track of the emergence of new variants, thus avoiding the spread of new diseases worldwide. This article highlights the emergence of the new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), and the vast number of mutations in its protein. In addition, recent advancements in drugs approved by FDA to treat COVID patients have been listed and focused in this paper.

Molecular modelling and simulation techniques to investigate the effects of fungal metabolites on the SARS-CoV-2 RdRp protein inhibition

Various protein/receptor targets have been discovered through in-silico research. They are expanding rapidly due to their extensive advantage of delivering new drug candidates more quickly, efficiently, and at a lower cost. The automation of organic synthesis and biochemical screening will lead to a revolution in the entire research arena in drug discovery. In this research article, a few fungal metabolites were examined through an in-silico approach which involves major steps such as (a) Molecular Docking Analysis, (b) Drug likeness and ADMET studies, and (c) Molecular Dynamics Simulation. Fungal metabolites were taken from Antibiotic Database which showed antiviral effects on severe viral diseases such as HIV. Docking, Lipinski's, and ADMET analyses investigated the binding affinity and toxicity of five metabolites: Chromophilone I, iso; F13459; Stachyflin, acetyl; A-108836; Integracide A (A-108835). Chromophilone I, iso was subjected to additional analysis, including a 50 ns MD simulation of the protein to assess the occurring alterations. This molecule's docking data shows that it had the highest binding affinity. ADMET research revealed that the ligand might be employed as an oral medication. MD simulation revealed that the ligand–protein interaction was stable. Finally, this ligand can be exploited to develop SARS-CoV-2 therapeutic options. Fungal metabolites that have been studied could be a potential source for future lead candidates. Further study of these molecules may result in creating an antiviral drug to battle the SARS-CoV-2 virus.

Omicron: Understanding the Latest Variant of SARS-CoV-2 and Strategies for Tackling the Infection

The new variant of concern of SARS-CoV-2, namely Omicron, has triggered global fear recently. To date, our knowledge of Omicron, particularly of how S glycoprotein mutations affect the infectivity of the virus and the severity of the infection, is far from complete. This hinders our ability to treat the disease and to predict the future state of SARS-CoV-2 threats to well-being and economic stability. Despite this, efforts have been made to unveil the routes of transmission and the efficiency of existing vaccines in tackling Omicron. This article reviews the latest understanding of Omicron and the current status of the use of vaccines and drugs for infection control. It is hoped that this article can offer insights into the development of more effective measures to tackle the pandemic.

Clinical Characteristics and Outcomes of Critically Ill Patients with 1, 2 and 3 doses of Vaccination against COVID-19 in Australia

Background

Vaccination has been shown to be highly effective in preventing death and severe disease from severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. Currently few studies have directly compared vaccinated and unvaccinated patients with severe COVID‐19 in the intensive care unit (ICU).

Aims

Our aim was to compare the clinical characteristics and outcomes of vaccine recipients and unvaccinated patients with SARS‐CoV‐2 infection admitted to the ICU in a nationwide setting.

Materials and Methods

Data were extracted from the Short PeRiod IncideNce sTudy of Severe Acute Respiratory Infection Australia, in 57 ICUs during Delta and Omicron predominant periods of the COVID‐19 pandemic. The primary outcome was in‐hospital mortality. Secondary outcomes included duration of mechanical ventilation, ICU length of stay, hospital length of stay, and ICU mortality.

Results

2,970 patients were admitted to ICU across participating sites from 26 June 2021 to 8 February 2022. 1,134 (38.2%) patients were vaccine recipients, and 1,836 (61.8%) patients were unvaccinated. Vaccine recipients were older, more comorbid, and less likely to require organ support. Unadjusted in‐hospital mortality was greater in the vaccinated cohort. After adjusting for age, gender and comorbid status, no statistically significant association between in‐hospital or ICU mortality, and vaccination status, was apparent.

Conclusion

We found COVID‐19 infection can cause severe disease and death in vaccine recipients, though comorbid status and older age were significant contributors to mortality. Organ support requirements and the number of deaths were highest in the unvaccinated cohort.

This article is protected by copyright. All rights reserved.

Assessment of SARS-CoV-2 Infected Patients and Their Clinical Outcomes During the Third Wave in India: A Single-Center Observational Study

Background

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that emerged from the Chinese mainland has spread throughout the world affecting the normal lives of the people. Both developed and developing nations have been equally affected and coronavirus disease-19 (COVID-19) resulted in the death of millions of people worldwide. The virus is undergoing mutations and is evolving into variants that are responsible for wave after wave. This study was carried out to assess the clinical outcomes of people infected with the novel virus during the third wave of the COVID-19 pandemic in India.

Methods

The study was carried out between November 2021 and January 2022 and included 100 consecutive patients attending the hospital attached to the BLDE (Deemed to be University) Shri B.M. Patil Medical College, Bijapur, Karnataka, South India. All patients included in the study returned a positive report in a real-time polymerase chain reaction (RT-PCR). The patient details collected included age, sex, cycle threshold (Ct) values for envelope (E)/nucleocapsid (N), and Orf1b (open reading frame 1b) genes, hospitalization status, vaccine status, C-reactive protein (CRP), D-dimer, interleukin-6 (IL-6), and final clinical outcome. The data were entered into Microsoft Office Excel sheets, and statistical inferences were drawn using SPSS 24 (IBM Corp., Armonk, NY).

Results

Of the 100 patients included in the study, only 14 (14%) patients were vaccinated. The patient's mean age was 34.22±17.50. Among the vaccinated patients, the majority had taken COVISHIELD™ (85.71%) compared to COVAXIN^® (14.29%). Only 14% of patients were symptomatic, and the mean Ct values among all the patients were 29.92±3.74 (E gene/N gene) and 27.6±4.78 (Orf1B gene). Eight (8%) patients were hospitalized, and all the patients recovered from the infection. Among the hospitalized patients, six (75%) were vaccinated. The mean age of the hospitalized patients was 43.8±14.25 years. The mean CRP, D-dimer, and IL-6 concentrations among the hospitalized patients were noted to be 22.375±16.58 mg/L, 654.325±577.24 ng/mL, and 5.075±2.15 ng/mL, respectively.

Conclusion

The study results demonstrate that despite unvaccinated status, most patients in the third wave had only suffered from asymptomatic infection. Moreover, people who developed a clinical infection and those who required hospitalization had an uneventful recovery irrespective of their vaccination status.

Development of a simple genotyping method based on indel mutations to rapidly screen SARS-CoV-2 circulating variants: Delta, Omicron BA.1 and BA.2

The high need of rapid and flexible tools that facilitate the identification of circulating SARS-CoV-2 Variants of Concern (VOCs) remains crucial for public health system monitoring.

Here, we develop allele-specific (AS)-qPCR assays targeting three recurrent indel mutations, ΔEF156–157, Ins214EPE and ΔLPP24–26, in spike (S) gene to identify the Delta VOC and the Omicron sublineages BA.1 and BA.2, respectively.

After verification of the analytical specificity of each primer set, two duplex qPCR assays with melting curve analysis were performed to screen 129 COVID-19 cases confirmed between December 31, 2021 and February 01, 2022 in Sfax, Tunisia.

The first duplex assay targeting ΔEF156–157 and Ins214EPE mutations successfully detected the Delta VOC in 39 cases and Omicron BA.1 in 83 cases. All the remaining cases (n = 7) were identified as Omicron BA.2, by the second duplex assay targeting Ins214EPE and ΔLPP24–26 mutations. The results of the screening method were in perfect concordance with those of S gene partial sequencing. In conclusion, our findings provide a simple and flexible screening method for more rapid and reliable monitoring of circulating VOCs. We highly recommend its implementation to guide public health policies.

Interconnectedness Is Associated with a Greater Sense of Civic Duty and Collective Action Participation through Transcendental Awareness and Compassion during COVID-19

The COVID-19 pandemic has a unprecedented impact on the way individuals make sense of the interconnected nature of themselves in relation to the world. This study investigated the mediating role of transcendental awareness and compassion in the association of interconnectedness with a sense of civic duty and collective action participation during COVID-19 using a longitudinal design. A total of 336 young adult participants were recruited at baseline and were asked to complete measures of interconnectedness, transcendental awareness, compassion, civic duty, and collective action participation at three time points over a 6-month period. Path analysis was used to test the hypothesized mediation model. The results showed that compassion fully mediated the positive association between interconnectedness and collective action participation and partially mediated the positive association between interconnectedness and civic duty. Transcendental awareness also partially mediated the positive association between interconnectedness and civic duty but not collective action participation. This study highlighted the potential of interconnectedness in promoting civic duty and engagement in collective action through transcendental awareness and compassion during the COVID-19 pandemic.

Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience

OBJECTIVES

To assess the severity of symptoms, duration of infection and viral loads of health-care workers (HCWs) who tested positive for Coronavirus disease 2019 (COVID-19) during Omicron's prevalence, in regard to vaccination and previous infection.

METHODS

During 2 weeks of highest rate of COVID-19 cases in Bosnia and Herzegovina, the positive nasopharyngeal swabs were analysed in 141 HCWs by reverse transcription quantitative PCR, targeting four different genes: RdRp, E, N and nsp14. Uniformed questionnaire was used to collect relevant sociodemographic and epidemiological data from HCWs divided into four groups: unvaccinated/not previously infected (group 1); unvaccinated/previously infected (group 2); vaccinated/not previously infected (group 3); and vaccinated/previously infected (group 4).

RESULTS

We observed that occurrence of fever and smell or taste loss were more frequent in group 1 (86.4% and 25%) and group 3 (76.9% and 19.2%), in comparison to group 2 (64.4% and 6.7%) and group 4 (69.2% and 3.8%), (p = 0.023 and p = 0.003). Although statistically not significant, group 2 (61.9%), group 3 (65.4%), and group 4 (70.8%) experienced negativization within 7 days of positive RT-qPCR test, whereas 51.2% of HCWs from group 1 tested negative later on. There is no significant difference between all four groups regarding Ct values of analysed genes.

CONCLUSION

During Omicron's prevalence, the vaccination had less substantial effect on symptomatic disease among HCWs, while fever and loss of smell or taste were considerably less likely to occur upon reinfection. Since viral loads and negativization periods do not seem to significantly vary, irrespective of pre-existing immunity, systemic vaccination and mask-wearing should still be considered among HCWs.

COVID-19 Omicron variant - Time for airborne precautions

Genetic mutations in SARS-CoV-2 have resulted in variants with more transmissibility and partial resistance to COVID-19 vaccines, as seen in the recently classified variant of concern (VOC) “Omicron”. The rapid spread has raised concerns about Omicron being airborne, which leads to a high risk of contamination in public premises, particularly among the frontline healthcare workers. Mandatory usage of protective face masks and respirators is highly recommended in order to break the chain of transmission. Furthermore, health authorities need to reassess the modes of transmission of VOCs and provide updated guidelines to the general public for its prevention.

Impaired detection of omicron by SARS-CoV-2 rapid antigen tests

Since autumn 2020, rapid antigen tests (RATs) have been implemented in several countries as an important pillar of the national testing strategy to rapidly screen for infections on site during the SARS-CoV-2 pandemic. The current surge in infection rates around the globe is driven by the variant of concern (VoC) omicron (B.1.1.529). Here, we evaluated the performance of nine SARS-CoV-2 RATs in a single-centre laboratory study. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 1.77 × 106 to 7.03 × 107 RNA copies subjected to the RAT for omicron compared to 1.32 × 105 to 2.05 × 106 for delta. To score positive in these point-of-care tests, up to 10-fold (LoD50) or 101-fold (LoD95) higher virus loads were required for omicron- compared to delta-containing samples. The rates of true positive test results for omicron samples in the highest virus load category (Ct values < 25) ranged between 31.4 and 77.8%, while they dropped to 0-8.3% for samples with intermediate Ct values (25-30). Of note, testing of expanded virus stocks suggested a comparable RAT sensitivity of both VoCs, questioning the predictive value of this type of in vitro-studies for clinical performance. Given their importance for national test strategies in the current omicron wave, awareness must be increased for the reduced detection rate of omicron infections by RATs and a short list of suitable RATs that fulfill the minimal requirements of performance should be rapidly disclosed.

Outpatient treatment options to address the SARS-CoV-2 variant Omicron

INTRODUCTION

: On November 26, 2021, the World Health Organization's Technical Advisory Group on SARS-CoV-2 Virus Evolution designated PANGO lineage B.1.1.529 a variant of concern and gave it the designation Omicron. The following day, the United Kingdom reported its first two cases of Omicron, a novel variant that was thought to be more transmissible than other variants such as Delta, Beta, and Alpha.

AREAS COVERED

: Omicron has since become the dominant variant around the world, accounting for unprecedented case counts and hospitalizations. Omicron's high rate of spread has been attributed to a variety of factors, including enhanced replication in the upper airways (bronchi) as well as immune evasion.

EXPERT OPINION

: These intrinsic factors have implications for the approach to treatment. Monoclonal antibody therapies, which were highly effective against prior SARS-CoV-2 variants, were rendered largely ineffective against Omicron, and other antiviral options remain severely limited due to supply issues. This manuscript reviews the landscape of Omicron therapeutics and looks ahead to examine how these treatments and others may be used in the future to address the expanding threat of the Omicron variant.