The omicron variant of SARS-CoV-2: Understanding the known and living with unknowns

Antibiotics daptomycin interacts with S protein of SARS-CoV-2 to promote cell invasion of Omicron (B1.1.529) pseudovirus

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed enormous challenges to global public health. The use of antibiotics has greatly increased during the SARS-CoV-2 epidemic owing to the presence of bacterial co-infection and secondary bacterial infections. The antibiotics daptomycin (DAP) is widely used in the treatment of infectious diseases caused by gram-positive bacteria owing to its highly efficient antibacterial activity. It is pivotal to study the antibiotics usage options for patients of coronavirus infectious disease (COVID-19) with pneumonia those need admission to receive antibiotics treatment for bacterial co-infection in managing COVID-19 disease. Herein, we have revealed the interactions of DAP with the S protein of SARS-CoV-2 and the variant Omicron (B1.1.529) using the molecular docking approach and Omicron (B1.1.529) pseudovirus (PsV) mimic invasion. Molecular docking analysis shows that DAP has a certain degree of binding ability to the S protein of SARS-CoV-2 and several derived virus variants, and co-incubation of 1-100 μM DAP with cells promotes the entry of the PsV into human angiotensin-converting enzyme 2 (hACE2)-expressing HEK-293T cells (HEK-293T-hACE2), and this effect is related to the concentration of extracellular calcium ions (Ca2+). The PsV invasion rate in the HEK-293T-hACE2 cells concurrently with DAP incubation was 1.7 times of PsV infection alone. In general, our findings demonstrate that DAP promotes the infection of PsV into cells, which provides certain reference of antibiotics selection and usage optimization for clinicians to treat bacterial coinfection or secondary infection during SARS-CoV-2 infection.

Clinical characteristics of 4,520 paediatric patients infected with the SARS-CoV-2 omicron variant, in Xi'an, China

Background and objective

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has broad tissue tropism and high transmission, which are likely to perpetuate the pandemic. The study aim to analyze the clinicopathogenic characteristics in paediatric patients.

Methods

In this single-centre study, we retrospectively included all confirmed cases infected by SARS-CoV-2 infection at Xi'an Children's Hospital, China, from 1 December to 31 December 2022. The demographic, clinical, laboratory, and radiological features of the patients were analysed.

Results

A total of 4,520 paediatric patients with SARS-CoV-2 omicron variant infections were included. Of these, 3,861 (85.36%) were outpatients, 659 (14.64%) were hospitalised patients, and nine patients (0.20%) died. Of the nine patients who died, five were diagnosed with acute necrotising encephalopathy (ANE). The most common symptoms were fever in 4,275 (94.59%) patients, cough in 1,320 (29.20%) patients, convulsions in 610 (13.50%) patients, vomiting in 410 (9.07%) patients, runny nose/coryza in 277 (6.13%) patients, hoarseness of voice in 273 (6.04%) patients. A blood cell analysis showed a slight elevation of monocytes (mean: 11.14 ± 0.07%). The main diagnoses for both outpatients and inpatients were respiratory infection with multisystem manifestations.

Conclusions

A high incidence of convulsions is a typical characteristic of children infected with SARS-CoV-2. Five of the nine COVID-19 fatalities were associated with ANE. This indicates that nervous system damage in children with SARS-CoV-2 infection is more significant.

Immune escape of SARS-CoV-2 variants to therapeutic monoclonal antibodies: a system review and meta-analysis

BACKGROUND

Omicron's high transmissibility and variability present new difficulties for COVID-19 vaccination prevention and therapy. In this article, we analyzed the sensitivity of vaccine-induced antibodies as well as the effect of booster vaccinations against Omicron sublineages.

METHODS

We looked for Randomized Controlled Trials and cohort studies that reported the COVID-19 vaccines against Omicron sublineages up to 28 July 2022 through PubMed, the Cochrane Library, EMBASE, and Web of Science. Quantitative synthesis was carried out using Stata 16.0 and RevMa5.3, then the serum NT50 and antibody sensitivity to neutralize Omicron sublineages were assessed before and after booster vaccination. This study was registered with PROSPERO number CRD42022350477.

RESULTS

This meta-analysis included 2138 patients from 20 studies, and the booster vaccination against Omicron sublineages showed a significant difference compared to 2 dosage: BA.1/BA.1.1 (SMD = 0.80, 95% CI: 0.75-0.85, P = 0.00), BA.2/BA.2.12.1 (SMD = 0.77, 95% CI: 0.69-0.85, P = 0.00), BA.3 (SMD = 0.91, 95% CI: 0.83-1.0, P = 0.00), and BA.4/5 (SMD = 0.77, 95% CI: 0.60-0.94, P = 0.00). The sensitivity of vaccines-induced antibodies decreased by at least 5-folds after booster vaccination, particularly in the case of BA.4/5 which had the most notable decline in vaccine effectiveness.

CONCLUSION

After the booster vaccination, the NT50 and the neutralization ability of vaccine-induced antibodies increased, but the susceptibility of antibodies decreased compared with the control virus, which may be a clue for future Omicron sublineages prevention.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World

SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient transmission, severity, and immune evasion properties. The World Health Organization has given these variants names according to the letters of the Greek Alphabet, starting with the Alpha (B.1.1.7) variant, which emerged in 2020, followed by the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. This review explores the genetic variation among different VOCs of SARS-CoV-2 and how the emergence of variants made a global impact on the pandemic.

Source identification via contact tracing in the presence of asymptomatic patients

Inferring the source of a diffusion in a large network of agents is a difficult but feasible task, if a few agents act as sensors revealing the time at which they got hit by the diffusion. One of the main limitations of current source identification algorithms is that they assume full knowledge of the contact network, which is rarely the case, especially for epidemics, where the source is called patient zero. Inspired by recent implementations of contact tracing algorithms, we propose a new framework, which we call Source Identification via Contact Tracing Framework (SICTF). In the SICTF, the source identification task starts at the time of the first hospitalization, and initially we have no knowledge about the contact network other than the identity of the first hospitalized agent. We may then explore the network by contact queries, and obtain symptom onset times by test queries in an adaptive way, i.e., both contact and test queries can depend on the outcome of previous queries. We also assume that some of the agents may be asymptomatic, and therefore cannot reveal their symptom onset time. Our goal is to find patient zero with as few contact and test queries as possible. We implement two local search algorithms for the SICTF: the LS algorithm, which has recently been proposed by Waniek et al. in a similar framework, is more data-efficient, but can fail to find the true source if many asymptomatic agents are present, whereas the LS+ algorithm is more robust to asymptomatic agents. By simulations we show that both LS and LS+ outperform previously proposed adaptive and non-adaptive source identification algorithms adapted to the SICTF, even though these baseline algorithms have full access to the contact network. Extending the theory of random exponential trees, we analytically approximate the source identification probability of the LS/ LS+ algorithms, and we show that our analytic results match the simulations. Finally, we benchmark our algorithms on the Data-driven COVID-19 Simulator (DCS) developed by Lorch et al., which is the first time source identification algorithms are tested on such a complex dataset.

SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron's viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron's transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.

Prevalence, clinical course and outcomes of COVID-19 in peritoneal dialysis (PD) patients: a single-center experience

INTRODUCTION

There are limited data on the effects of COVID-19 on peritoneal dialysis (PD) patients. This study aimed to describe the impact of COVID-19 on the PD population.

METHODS

A monocentric retrospective observational study was conducted on 146 consecutive PD patients followed from January 2020 to March 2022 at the University Hospital of Modena, Italy.

RESULTS

Twenty-seven (18.4%) PD patients experienced 29 episodes of SARS-CoV-2 infection, corresponding to an incidence rate of 0.16 episodes/patient-year. Median age of COVID-19 patients was 60.4 (interquartile range [IQR] 50.2-66.5) years. In unvaccinated patients (n. 9), COVID-19 was always symptomatic and manifested with fever (100%) and cough (77.7%). COVID-19 caused hospital admission of three (33.3%) patients and two (22.2%) died of septic shock. COVID-19 was symptomatic in 83.3% of vaccinated subjects (n.18) and manifested with fever (61.1%) and cough (55.6%). Hospital admission occurred in 27.8% of the subjects but all were discharged home. Median SARS-CoV-2 shedding was 32 and 26 days in the unvaccinated and vaccinated groups, respectively. At the end of the follow-up, COVID-19 triggered the shift from PD to HD in two subjects without affecting the residual renal function of the remaining patients. Overall, COVID-19 caused an excess death of 22.2%. COVID-19 vaccination refusal accounted for only 1.6% in this cohort of patients.

CONCLUSION

COVID-19 incident rate was 0.16 episodes/patient-year in the PD population. About one-third of the patients were hospitalized for severe infection. Fatal outcome occurred in two (7.4%) unvaccinated patients. A low vaccination refusal rate was observed in this population.

Effect of Double Mutation (L452R and E484Q) on the Binding Affinity of Monoclonal Antibodies (mAbs) against the RBD-A Target for Vaccine Development

The COVID-19 pandemic, caused by SARS-CoV-2, emerges as a global health problem, as the viral genome is evolving rapidly to form several variants. Advancement and progress in the development of effective vaccines and neutralizing monoclonal antibodies are promising to combat viral infections. In the current scenario, several lineages containing "co-mutations" in the receptor-binding domain (RBD) region of the spike (S) protein are imposing new challenges. Co-occurrence of some co-mutations includes delta (L452R/T478K), kappa (L452R/E484Q), and a common mutation in both beta and gamma variants (E484K/N501Y). The effect of co-mutants (L452R/E484Q) on human angiotensin-converting enzyme 2 (hACE2) binding has already been elucidated. Here, for the first time, we investigated the role of these RBD co-mutations (L452R/E484Q) on the binding affinity of mAbs by adopting molecular dynamics (MD) simulation and free-energy binding estimation. The results obtained from our study suggest that the structural and dynamic changes introduced by these co-mutations reduce the binding affinity of the viral S protein to monoclonal antibodies (mAbs). The structural changes imposed by L452R create a charged patch near the interfacial surface that alters the affinity towards mAbs. In E484Q mutation, polar negatively charged E484 helps in the formation of electrostatic interaction, while the neutrally charged Q residue affects the interaction by forming repulsive forces. MD simulations along with molecular mechanics-generalized Born surface area (MMGBSA) studies revealed that the REGN 10933, BD-368-2, and S2M11 complexes have reduced binding affinity towards the double-mutant RBD. This indicates that their mutant (MT) structures have a stronger ability to escape from most antibodies than the wild type (WT). However, EY6A Ab showed higher affinity towards the double MT-RBD complex as compared to the WT. However, no significant effect of the per-residue contribution of double-mutated residues was observed, as this mAb does not interact with the region harboring L452 and E484 residues.

Review of SARS-COV-2 Systemic Impact: Building the Case for Sepsis via Virus in the Circulatory System

SARS-COV-2 can contribute to long term consequences associated with sepsis and circulatory dysfunction. In this insightful paper, we highlight the emerging pathophysiology utilizing two case examples. Both systemic and organ specific features are discussed. In addition, a novel laboratory assay is presented that identified SARS-COV-2 in the circulation using conserved SARS ion channels rather than the spike protein. The presentation is linked to the pathophysiology with the emphasis for early recognition and continued research. This paper will serve as a catalyst for continued discovery.

Omicron variant of SARS-CoV-2: a review of existing literature

On November 24th, 2021 a case of a new viral variant of SARS-CoV-2 was reported by South Africa and Botswana to WHO, which later was designated as the variant of concern on 26th November 2021. It has around 60 mutations (50 non synonymous, 8 synonymous, and 2 non coding) as compared to the original parent strain of Wuhan. Different hypotheses have been put forward as an explanation for the origin like reverse zoonosis i.e. animal to human transmission, origin from an immune compromised patient or use of highly mutagenic drug like molnupiravir as treatment. A huge spike in cases around the globe is suggestive of a high rate of infectivity and transmissivity as compared to the previous known variants. With whatever cases have been documented so far, it is said that omicron causes mostly mild clinical illnesses and there is a less chance of hospitalization according to the clinicians. Among the reported cases, there were already vaccinated patients also. So there is a possibility that omicron might be able to evade the vaccine induced immunity due to a huge number of mutations (especially in the spike protein sequences). Until new vaccines specific to the pathogen are being developed, the coverage of the currently acceptable vaccines should be increased so that none is deprived of the mandatory doses and a third booster dose might help to reduce the chances of serious complications of this new strain beforehand. So an equal focus on the host and environment is required along with the pathogen.

Development and evaluation of an online training program based on the O-AMAS teaching model for community pharmacists in the post-COVID-19 era

Background

Formerly, the community pharmacists' work was mainly focused on drug supply. However, during the COVID-19 epidemic outbreak, community pharmacists in Wuhan played an important role in control and prevention of SARS-CoV-2 and in providing pharmaceutical care. Due to a lack of adequate knowledge and skills, many community pharmacists were not able to cope with healthcare work timely and efficiently. To improve community pharmacists' specialized knowledge and enhance their professional competence through systemic training in the post-COVID-19 era.

Methods

Based on the O-AMAS (Objective, Activation, Multi-learning, Assessment and Summary) teaching model and flipped classroom, an online continuing training program containing four sections was developed. It was a semi-experimental study with no control group. Quantitative tests before and after training as well as questionnaire were used to evaluate the outcome of this training program for community pharmacists.

Results

A total of twenty-six community pharmacists were invited to participate in continuing education, and twenty-five trainees finished this training program with a completion rate of 96.2 %. Quantitative tests before and after training and anonymous questionnaires were carried out to comprehensively evaluate the outcomes of this training program. Compared with the test scores before training (61.6 ± 6.6), the score after training was statistically higher, reaching 80.9 ± 7.5 (P < 0.001). Twenty-three questionnaires were received (returns ratio, 92.0%). Notably, most of the pharmacists were satisfied with the training program. The percentage of positive responses for each item in this anonymous questionnaire was more than 85 %.

Conclusion

It was suggested that the O-AMAS model and the flipped classroom-based continuing educational program achieved the expected training effects. It is a promising on-the-job training approach for pharmacy continuing education. Moreover, our study also demonstrated that online learning had advantages of no geographic constraints, flexible learning beyond time and easy interaction, over traditional face-to-face training style, especially in the post-pandemic era.

SARS-CoV-2 Omicron and its current known unknowns: A narrative review

The emergence of the SARS-CoV-2 Omicron variant (B.1.1.529) has created great global distress. This variant of concern shows multiple sublineages, importantly B.1.1.529.1 (BA.1), BA.1 + R346K (BA.1.1), and B.1.1.529.2 (BA.2), each with unique properties. However, little is known about this new variant, specifically its sub-variants. A narrative review was conducted to summarise the latest findings on transmissibility, clinical manifestations, diagnosis, and efficacy of current vaccines and treatments. Omicron has shown two times higher transmission rates than Delta and above ten times more infectious than other variants over a similar period. With more than 30 mutations in the spike protein's receptor-binding domain, there is reduced detection by conventional RT-PCR and rapid antigen tests. Moreover, the two-dose vaccine effectiveness against Delta and Omicron variants was found to be approximately 21%, suggesting an urgent need for a booster dose to prevent the possibility of breakthrough infections. However, the current vaccines remain highly efficacious against severe disease, hospitalisation, and mortality. Japanese preliminary lab data elucidated that the Omicron sublineage BA.2 shows a higher illness severity than BA.1. To date, the clinical management of Omicron remains unchanged, except for monoclonal antibodies. Thus far, only Bebtelovimab could sufficiently treat all three sub-variants of Omicron. Further studies are warranted to understand the complexity of Omicron and its sub-variants. Such research is necessary to improve the management and prevention of Omicron infection.

Comparison of epidemiological characteristics and transmissibility of different strains of COVID-19 based on the incidence data of all local outbreaks in China as of March 1, 2022

Background

The epidemiological characteristics and transmissibility of Coronavirus Disease 2019 (COVID-19) may undergo changes due to the mutation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) strains. The purpose of this study is to compare the differences in the outbreaks of the different strains with regards to aspects such as epidemiological characteristics, transmissibility, and difficulties in prevention and control.

Methods

COVID-19 data from outbreaks of pre-Delta strains, the Delta variant and Omicron variant, were obtained from the Chinese Center for Disease Control and Prevention (CDC). Case data were collected from China's direct-reporting system, and the data concerning outbreaks were collected by on-site epidemiological investigators and collated by the authors of this paper. Indicators such as the effective reproduction number (R _eff), time-dependent reproduction number (R _t), rate of decrease in transmissibility (RDT), and duration from the illness onset date to the diagnosed date (D _ID )/reported date (D _IR ) were used to compare differences in transmissibility between pre-Delta strains, Delta variants and Omicron variants. Non-parametric tests (namely the Kruskal-Wallis H and Mean-Whitney U tests) were used to compare differences in epidemiological characteristics and transmissibility between outbreaks of different strains. P < 0.05 indicated that the difference was statistically significant.

Results

Mainland China has maintained a "dynamic zero-out strategy" since the first case was reported, and clusters of outbreaks have occurred intermittently. The strains causing outbreaks in mainland China have gone through three stages: the outbreak of pre-Delta strains, the outbreak of the Delta variant, and outbreaks involving the superposition of Delta and Omicron variant strains. Each outbreak of pre-Delta strains went through two stages: a rising stage and a falling stage, Each outbreak of the Delta variant and Omicron variant went through three stages: a rising stage, a platform stage and a falling stage. The maximum R _eff value of Omicron variant outbreaks was highest (median: 6.7; ranged from 5.3 to 8.0) and the differences were statistically significant. The RDT value of outbreaks involving pre-Delta strains was smallest (median: 91.4%; [IQR]: 87.30-94.27%), and the differences were statistically significant. The D _ID and D _IR for all strains was mostly in a range of 0-2 days, with more than 75%. The range of duration for outbreaks of pre-Delta strains was the largest (median: 20 days, ranging from 1 to 61 days), and the differences were statistically significant.

Conclusion

With the evolution of the virus, the transmissibility of the variants has increased. The transmissibility of the Omicron variant is higher than that of both the pre-Delta strains and the Delta variant, and is more difficult to suppress. These findings provide us with get a more clear and precise picture of the transmissibility of the different variants in the real world, in accordance with the findings of previous studies. R _eff is more suitable than R _t for assessing the transmissibility of the disease during an epidemic outbreak.

Charlson comorbidity index, neutrophil-to-lymphocyte ratio and undertreatment with renin-angiotensin-aldosterone system inhibitors predict in-hospital mortality of hospitalized COVID-19 patients during the omicron dominant period

Purpose

To investigate the clinical predictors of in-hospital mortality in hospitalized patients with Coronavirus disease 2019 (COVID-19) infection during the Omicron period.

Methods

All consecutive hospitalized laboratory‐confirmed COVID-19 patients between January and May 2022 were retrospectively analyzed. All patients underwent accurate physical, laboratory, radiographic and echocardiographic examination. Primary endpoint was in-hospital mortality.

Results

74 consecutive COVID-19 patients (80.0 ± 12.6 yrs, 45.9% males) were included. Patients who died during hospitalization (27%) and those who were discharged alive (73%) were separately analyzed. Compared to patients discharged alive, those who died were significantly older, with higher comorbidity burden and greater prevalence of laboratory, radiographic and echographic signs of pulmonary and systemic congestion. Charlson comorbidity index (CCI) (OR 1.76, 95%CI 1.07-2.92), neutrophil-to-lymphocyte ratio (NLR) (OR 1.24, 95%CI 1.10-1.39) and absence of angiotensin-converting enzyme inhibitors (ACEI)/angiotensin II receptor blockers (ARBs) therapy (OR 0.01, 95%CI 0.00-0.22) independently predicted the primary endpoint. CCI ≥7 and NLR ≥9 were the best cut-off values for predicting mortality. The mortality risk for patients with CCI ≥7, NLR ≥9 and not in ACEI/ARBs therapy was high (86%); for patients with CCI <7, NLR ≥9, with (16.6%) or without (25%) ACEI/ARBs therapy was intermediate; for patients with CCI <7, NLR <9 and in ACEI/ARBs therapy was of 0%.

Conclusions

High comorbidity burden, high levels of NLR and the undertreatment with ACEI/ARBs were the main prognostic indicators of in-hospital mortality. The risk stratification of COVID-19 patients at hospital admission would help the clinicians to take care of the high-risk patients and reduce the mortality.

Computational Analysis of Short Linear Motifs in the Spike Protein of SARS-CoV-2 Variants Provides Possible Clues into the Immune Hijack and Evasion Mechanisms of Omicron Variant

Short linear motifs (SLiMs) are short linear sequences that can mediate protein–protein interaction. Mimicking eukaryotic SLiMs to compete with extra- or intracellular binding partners, or to sequester host proteins is the crucial strategy of viruses to pervert the host system. Evolved proteins in viruses facilitate minimal protein–protein interactions that significantly affect intracellular signaling networks. Unfortunately, very little information about SARS-CoV-2 SLiMs is known, especially across SARS-CoV-2 variants. Through the ELM database-based sequence analysis of spike proteins from all the major SARS-CoV-2 variants, we identified four overriding SLiMs in the SARS-CoV-2 Omicron variant, namely, LIG_TRFH_1, LIG_REV1ctd_RIR_1, LIG_CaM_NSCaTE_8, and MOD_LATS_1. These SLiMs are highly likely to interfere with various immune functions, interact with host intracellular proteins, regulate cellular pathways, and lubricate viral infection and transmission. These cellular interactions possibly serve as potential therapeutic targets for these variants, and this approach can be further exploited to combat emerging SARS-CoV-2 variants.

The Omicron variant of concern: The genomics, diagnostics, and clinical characteristics in children

Since WHO announced the COVID-19 pandemic in March 2020, SARS-CoV-2 has undergone several mutations, with the most recent variant first identified in South Africa in November 2021, the SARS-CoV-2 variant of concern (VOC B.1.1.529) named by WHO as Omicron. To date, it has undergone more mutations compared to previous SARS-CoV-2 variants, particularly, in the S gene that encodes the spike protein, which can cause S gene target failure in some PCR kits. Since its discovery, the Omicron variant has caused a sharp rise in COVID-19 cases worldwide and was responsible for a record of 15 million new COVID-19 cases reported globally in a single week, although this may be an underestimate. Since January 2022, Omicron subvariants with variable genetic characteristics, BA.1, BA.1.1, BA.2, BA.3, BA.4, BA.5, and BA.2.12.2 have been identified, with several countries reporting BA.1.1 was the major subvariant (27.42%), followed by BA.2 (25.19%). At the begining of May 2022, BA.2.12.1 mostly (42%) was detected in the United States. Like adults, the clinical manifestations of the Omicron variant in children are similar to the previous variants consisting of fever, cough, vomiting, breathing difficulties, and diarrhea, with some reports on croup-like symptoms and seizures. Though it presents apparently milder disease than the Delta variant, it is significantly more contagious and has caused more hospitalizations, especially in unvaccinated children younger than 5 years and unvaccinated or incompletely vaccinated adults. However, there is insufficient evidence yet to distinguish the Omicron variant from the other variants based solely on the clinical manifestations, therefore, this review presents a brief literature review of the most current evidence and data related to Omicron.

The Vaccine Efficacy Against the SARS-CoV-2 Omicron: A Systemic Review and Meta-Analysis

Background

COVID-19 is a respiratory illness caused by SARS-CoV-2. The most recent variant is Omicron (line B.1.1.529), which was first identified in South Africa in November 2021. The concern with this variant is the ineffectiveness of vaccines currently available. We aim to systematically evaluate the effectiveness of the currently available COVID-19 vaccines and boosters for the Omicron variant.

Methods

We searched the PubMed, Embase, the Cochrane Library and Web of Science databases from inception to June 5th, 2022. Studies that examined the effectiveness of SARS-CoV-2 vaccines against the Omicron variant infection were included. Random-effects model was used to estimate the pooled vaccine effectiveness against the Omicron variant.

Results

A total of 13 studies were included to evaluate the effectiveness of the vaccine against the Omicron variant, and 11 studies were included to compare the effectiveness between the two-dose and three-dose (booster) vaccinations. Full vaccination (two-dose with or without booster) showed a protective effect against the Omicron variant compared to no vaccination (OR = 0.62, 95% CI: 0.56–0.69), while the effectiveness decreased significantly over 6 months after the last dose. The two-dose vaccination plus booster provided better protection against the Omicron variant compared to the two-dose vaccination without booster (OR = 0.60, 95% CI: 0.52–0.68). Additional analysis was performed for the most commonly used vaccines in the United Staes: BNT162b2(Pfizer) (OR = 0.65, 95% CI: 0.52–0.82) and mRNA-1273(Moderna) (OR = 0.67, 95% CI: 0.58–0.88) vaccines in the US, which showed similar effectiveness compared to no vaccination.

Conclusions

The full dose of SARS-CoV-2 vaccination effectively reduces infection from the SARS-CoV-2 Omicron variant; however, the effectiveness wanes over time. The booster vaccine provides additional protection against the Omicron variant.

Towards Control and Oversight of SARS‐CoV‐2 Diagnosis and Monitoring through Multiplexed Quantitative Electroanalytical Immune Response Biosensors

The development of versatile and sensitive biotools to quantify specific SARS‐CoV‐2 immunoglobulins in SARS‐CoV‐2 infected and non‐infected individuals, built on the surface of magnetic microbeads functionalized with nucleocapsid (N) and in‐house expressed recombinant spike (S) proteins is reported. Amperometric interrogation of captured N‐ and S‐specific circulating total or individual immunoglobulin (Ig) isotypes (IgG, IgM, and IgA), subsequently labelled with HRP‐conjugated secondary antibodies, was performed at disposable single or multiplexed (8×) screen‐printed electrodes using the HQ/HRP/H₂O₂ system. The obtained results using N and in‐house expressed S ectodomains of five SARS‐CoV‐2 variants of concern (including the latest Delta and Omicron) allow identification of vulnerable populations from those with natural or acquired immunity, monitoring of infection, evaluation of vaccine efficiency, and even identification of the variant responsible for the infection.

OMICRON: Virology, immunopathogenesis, and laboratory diagnosis

Since its emersion, coronavirus disease 2019 (COVID-19) has been a significant global dilemma. Several mutations in the severe acute respiratory virus (SARS-Co-2) genome has given rise to different variants with various levels of transmissibility, severity and mortality. Up until November 2021, the variants of concern declared by the World Health Organization were Alpha, Beta, Delta and Gamma. Since then, a novel variant named Omicron (B.1.1.529) has been developed. BA.1, BA.1.1, BA.2 and BA.3 are four known subvariants of Omicron. The Omicron variant involves new mutations in its spike protein, most of which are in its receptor binding site, and increase its transmissibility and decrease its antibody and vaccine response. Understanding the virology and mutations of Omicron is necessary for developing diagnostic and therapeutic methods. Moreover, important issues, such as the risk of re-infection, the response to different kinds of vaccines, the need for a booster vaccine dose and the increased risk of Omicron infection in pediatrics, need to be addressed. In this article, we provide an overview of the biological and immunopathological properties of Omicron and its subvariants, its clinical signs and symptoms, Omicron and pediatrics, vaccines against Omicron, re-infection with Omicron, diagnostic approaches and specific challenges of Omicron in the successful control and management of the rapid global spread of this variant.

Omicron - The new SARS-CoV-2 challenge?

SARS-CoV-2 virus has infected nearly 300 M people worldwide and has been associated with over 6 M deaths by March 2022. Since the virus emergence in December 2019 in Wuhan, several new mutations have been described. The World Health Organization has developed a working name for these emerging variants according to their impact on the worldwide population. In this context a high alert has been paid to variants of concern (VOC) due to their high infectiousness and transmissibility patterns. The most recent VOC, Omicron (B.1.1.529), has become dominant in the shortest time ever and has placed Europe under an overwhelming and unprecedented number of new cases. This variant has numerous mutations in regions that are associated with higher transmissibility, stronger viral binding, affinity and antibody escape. Moreover, the mutations and deletions present in the spike protein suggest that the SARS-CoV-2 specific attachment inhibitors may not be the best option for Omicron therapy. Omicron is the dominant variant circulating worldwide and, at the end of February 2022, it was responsible for nearly all sequences reported to GISAID. Omicron is made up of several sublineages, where the most common are BA.1 and BA.2 (or Nextstrain clade 21K and 21L, respectively). At a global level, it is possible to say that the proportion of BA.2 has been increasing relative to BA.1 and in some countries it has been replacing it at high rates. In order to better assess the Omicron effectiveness on antibody escape, spread and infectious ability it is of the highest relevance to maintain a worldwide tight surveillance. Even though this variant has been associated with a lower death rate, it is important to highlight that the number of people becoming infected is concerning and that further unpredictable mutations may emerge as the number of infected people rises.

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.

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.

Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic

Since the appearance in the late of December 2019, SARS-CoV-2 is rapidly evolving and mutating continuously, giving rise to various variants with variable degrees of infectivity and lethality. The virus that initially appeared in China later mutated several times, wreaking havoc and claiming many lives worldwide amid the ongoing COVID-19 pandemic. After Alpha, Beta, Gamma, and Delta variants, the most recently emerged variant of concern (VOC) is the Omicron (B.1.1.529) that has evolved due to the accumulation of high numbers of mutations especially in the spike protein, raising concerns for its ability to evade from pre-existing immunity acquired through vaccination or natural infection as well as overpowering antibodies-based therapies. Several theories are on the surface to explain how the Omicron has gathered such a high number of mutations within less time. Few of them are higher mutation rates within a subgroup of population and then its introduction to a larger population, long term persistence and evolution of the virus in immune-compromised patients, and epizootic infection in animals from humans, where under different immune pressures the virus mutated and then got reintroduced to humans. Multifaceted approach including rapid diagnosis, genome analysis of emerging variants, ramping up of vaccination drives and receiving booster doses, efficacy testing of vaccines and immunotherapies against newly emerged variants, updating the available vaccines, designing of multivalent vaccines able to generate hybrid immunity, up-gradation of medical facilities and strict implementation of adequate prevention and control measures need to be given high priority to handle the on-going SARS-CoV-2 pandemic successfully.

Severe Acute Respiratory Syndrome Coronavirus 2 Variants—Possibility of Universal Vaccine Design: A Review

Both novel and conventional vaccination strategies have been implemented worldwide since the onset of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite various medical advances in the treatment and prevention of the spread of this contagious disease, it remains a major public health threat with a high mortality rate. As several lethal SARS-CoV-2 variants continue to emerge, the development of several vaccines and medicines, each with certain advantages and disadvantages, is underway. Additionally, many modalities are at various stages of research and development or clinical trials. Here, we summarize emerging SARS-CoV-2 variants, including delta, omicron, and “stealth omicron,” as well as available oral drugs for COVID-19. We also discuss possible antigen candidates other than the receptor-binding domain protein for the development of a universal COVID-19 vaccine. The present review will serve as a helpful resource for future vaccine and drug development to combat COVID-19.

Towards Control and Oversight of SARS‐CoV‐2 Diagnosis and Monitoring through Multiplexed Quantitative Electroanalytical Immune Response Biosensors

The development of versatile and sensitive biotools to quantify specific SARS‐CoV‐2 immunoglobulins in SARS‐CoV‐2 infected and non‐infected individuals, built on the surface of magnetic microbeads functionalized with nucleocapsid (N) and in‐house expressed recombinant spike (S) proteins is reported. Amperometric interrogation of captured N‐ and S‐specific circulating total or individual immunoglobulin (Ig) isotypes (IgG, IgM, and IgA), subsequently labelled with HRP‐conjugated secondary antibodies, was performed at disposable single or multiplexed (8×) screen‐printed electrodes using the HQ/HRP/H₂O₂ system. The obtained results using N and in‐house expressed S ectodomains of five SARS‐CoV‐2 variants of concern (including the latest Delta and Omicron) allow identification of vulnerable populations from those with natural or acquired immunity, monitoring of infection, evaluation of vaccine efficiency, and even identification of the variant responsible for the infection.

Clinical Characteristics of COVID-19 Patients Infected by the Omicron Variant of SARS-CoV-2

Background

Currently, as the omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surges amid the coronavirus disease 2019 (COVID-19) pandemic, its clinical characteristics with intrinsic severity and the protection from vaccination have been understudied.

Methods

We reported 169 COVID-19 patients that were infected with the omicron variant of SARS-CoV-2 and hospitalized in Suzhou, China, from February to March 2022, with their demographic information, medical/immunization history, clinical symptom, and hematological profile. At the same time, patients with none/partial (one-dose), full (two-dose) and three-dose vaccination were also compared to assess the vaccine effectiveness.

Findings

For the omicron COVID-19 patients included in this study, their median age was 33.0 [interquartile range (IQR): 24.0-45.5], 53.3% were male and the median duration from illness onset to hospitalization was 2 days. Hypertension, bronchitis, and diabetes were the leading comorbidities among patients. While the common clinical symptoms included cough, fever, expectoration, and fatigue, etc., asymptomatic patients took up a significant portion (46.7%). For hematological parameters, most values revealed the alleviated pathogenicity induced by the omicron variant infection. No critically ill or deceased patients due to COVID-19 infection were reported in this study.

Interpretation

Our results supported that the viremic effect of the omicron variant became milder than the previous circulating variants, while full vaccination or booster shot was greatly desired for an effective protection against clinical severity.

Clinical and translational values of spatial transcriptomics

The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with molecular alterations, defining in situ intercellular molecular communications and knowledge on spatiotemporal molecular medicine. The present article overviews the development of ST and aims to evaluate clinical and translational values for understanding molecular pathogenesis and uncovering disease-specific biomarkers. We compare the advantages and disadvantages of sequencing- and imaging-based technologies and highlight opportunities and challenges of ST. We also describe the bioinformatics tools necessary on dissecting spatial patterns of gene expression and cellular interactions and the potential applications of ST in human diseases for clinical practice as one of important issues in clinical and translational medicine, including neurology, embryo development, oncology, and inflammation. Thus, clear clinical objectives, designs, optimizations of sampling procedure and protocol, repeatability of ST, as well as simplifications of analysis and interpretation are the key to translate ST from bench to clinic.

Successive Pandemic Waves with Different Virulent Strains and the Effects of Vaccination for SARS-CoV-2

One hundred years after the flu pandemic of 1918, the world faces an outbreak of a new severe acute respiratory syndrome, caused by a novel coronavirus. With a high transmissibility, the pandemic has spread worldwide, creating a scenario of devastation in many countries. By the middle of 2021, about 3% of the world population had been infected and more than 4 million people had died. Different from the H1N1 pandemic, which had a deadly wave and ceased, the new disease is maintained by successive waves, mainly produced by new virus variants and the small number of vaccinated people. In the present work, we create a version of the SIR model using the spatial localization of persons, their movements, and considering social isolation probabilities. We discuss the effects of virus variants, and the role of vaccination rate in the pandemic dynamics. We show that, unless a global vaccination is implemented, we will have continuous waves of infections.

In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack

The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.

Clinical Characteristics of 40 Patients Infected With the SARS-CoV-2 Omicron Variant in Korea

Since severe acute respiratory syndrome-coronavirus-2 variant B.1.1.529 (omicron) was first reported to the World Health Organization on November 24, 2021, the cases of the omicron variant have been detected in more than 90 countries over the last month. We investigated the clinical and epidemiological characteristics of the first 40 patients with the omicron variant who had been isolated at the National Medical Center in South Korea during December 4-17, 2021. The median age of the patients was 39.5 years. Twenty-two patients (55%) were women. Seventeen patients (42.5%) were fully vaccinated, and none were reinfected with the omicron. Eighteen (45%) had recent international travel history. Half of the patients (19, 47.5%) were asymptomatic, while the others had mild symptoms. Six patients (15%) showed lung infiltrations on chest image; however, none required supplemental oxygen. These mild clinical features are consistent with recent case reports on the omicron variant from other countries.

Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.