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

The Inhibitory Potential of Ferulic Acid Derivatives against the SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics, and ADMET Evaluation

The main protease (Mpro) of SARS-CoV-2 is an appealing target for the development of antiviral compounds, due to its critical role in the viral life cycle and its high conservation among different coronaviruses and the continuously emerging mutants of SARS-CoV-2. Ferulic acid (FA) is a phytochemical with several health benefits that is abundant in plant biomass and has been used as a basis for the enzymatic or chemical synthesis of derivatives with improved properties, including antiviral activity against a range of viruses. This study tested 54 reported FA derivatives for their inhibitory potential against Mpro by in silico simulations. Molecular docking was performed using Autodock Vina, resulting in comparable or better binding affinities for 14 compounds compared to the known inhibitors N3 and GC376. ADMET analysis showed limited bioavailability but significantly improved the solubility for the enzymatically synthesized hits while better bioavailability and druglikeness properties but higher toxicity were observed for the chemically synthesized ones. MD simulations confirmed the stability of the complexes of the most promising compounds with Mpro, highlighting FA rutinoside and compound e27 as the best candidates from each derivative category.

COVID-19 Vaccines' Protection Over Time and the Need for Booster Doses; a Systematic Review

Introduction

Controversies existed regarding the duration of COVID-19 vaccines' protection and whether receiving the usual vaccine doses would be sufficient for long-term immunity. Therefore, we aimed to systematically review the studies regarding the COVID-19 vaccines' protection three months after getting fully vaccinated and assess the need for vaccine booster doses.

Methods

The relevant literature was searched using a combination of keywords on the online databases of PubMed, Scopus, Web of Science, and Cochrane on September 17th, 2021. The records were downloaded and the duplicates were removed. Then, the records were evaluated in a two-step process, consisting of title/abstract and full-text screening processes, and the eligible records were selected for the qualitative synthesis. We only included original studies that evaluated the efficacy and immunity of COVID-19 vaccines three months after full vaccination. This review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement to ensure the reliability of results.

Results

Out of the 797 retrieved records, 12 studies were included, 10 on mRNA-based vaccines and two on inactivated vaccines. The majority of included studies observed acceptable antibody titers in most of the participants even after 6 months; however,it appeared that the titers could also decrease in a considerable portion of people. Due to the reduction in antibody titers and vaccine protection, several studies suggested administering the booster dose, especially for older patients and those with underlying conditions, such as patients with immunodeficiencies.

Conclusion

Studies indicated that vaccine immunity decreases over time, making people more susceptible to contracting the disease. Besides, new variants are emerging, and the omicron variant is continuing to spread and escape from the immune system, indicating the importance of a booster dose.

Multi-Faceted Analysis of COVID-19 Epidemic in Korea Considering Omicron Variant: Mathematical Modeling-Based Study

BACKGROUND

The most recent variant of concern, omicron (B.1.1.529), has caused numerous cases worldwide including the Republic of Korea due to its fast transmission and reduced vaccine effectiveness.

METHODS

A mathematical model considering age-structure, vaccine, antiviral drugs, and influx of the omicron variant was developed. We estimated transmission rates among age groups using maximum likelihood estimation for the age-structured model. The impact of non-pharmaceutical interventions (NPIs; in community and border), quantified by a parameter μ in the force of infection, and vaccination were examined through a multi-faceted analysis. A theory-based endemic equilibrium study was performed to find the manageable number of cases according to omicron- and healthcare-related factors.

RESULTS

By fitting the model to the available data, the estimated values of μ ranged from 0.31 to 0.73, representing the intensity of NPIs such as social distancing level. If μ < 0.55 and 300,000 booster shots were administered daily from February 3, 2022, the number of severe cases was forecasted to exceed the severe bed capacity. Moreover, the number of daily cases is reduced as the timing of screening measures is delayed. If screening measure was intensified as early as November 24, 2021 and the number of overseas entrant cases was contained to 1 case per 10 days, simulations showed that the daily incidence by February 3, 2022 could have been reduced by 87%. Furthermore, we found that the incidence number in mid-December 2021 exceeded the theory-driven manageable number of daily cases.

CONCLUSION

NPIs, vaccination, and antiviral drugs influence the spread of omicron and number of severe cases in the Republic of Korea. Intensive and early screening measures during the emergence of a new variant is key in controlling the epidemic size. Using the endemic equilibrium of the model, a formula for the manageable daily cases depending on the severity rate and average length of hospital stay was derived so that the number of severe cases does not surpass the severe bed capacity.

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.

Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India

Background

The massive increase in COVID-19 infection had generated a second wave in India during May–June 2021 with a critical pandemic situation. The Delta variant (B.1.617.2) was a significant factor during the second wave. Conversely, the UK had passed through the crucial phase of the pandemic from November to December 2020 due to B.1.1.7. The study tried to comprehend the pandemic response in the UK and India to the spread of the B.1.1.7 (Alpha, UK) variant and B.1.617.2 (Delta, India) variant.

Methods

This study was performed in three directions to understand the pandemic response of the two emerging variants. First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R). Second, we performed evolutionary epidemiology using molecular phylogenetics, scatter plots of the cluster evaluation, country-wise transmission pattern, and frequency pattern. Third, the receptor binding pattern was analyzed using the Wuhan reference strain and the other two variants.

Results

The study analyzed the country-wise and region-wise genome sequences and their submission pattern, molecular phylogenetics, scatter plot of the cluster evaluation, country-wise geographical distribution and transmission pattern, frequency pattern, entropy diversity, and mutational landscape of the two variants. The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations. The study found increased molecular interactivity between hACE2-RBD binding of B.1.1.7 and B.1.617.2 compared to the Wuhan reference strain. Our receptor binding analysis showed a similar indication pattern for hACE2-RBD of these two variants. However, B.1.617.2 offers slightly better stability in the hACE2-RBD binding pattern through MD simulation than B.1.1.7.

Conclusion

The increased hACE2-RBD binding pattern of B.1.1.7 and B.1.617.2 might help to increase the infectivity compared to the Wuhan reference strain.

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.

Comparative evaluation of authorized drugs for treating Covid-19 patients

Background and Aims

Vaccines are the first line of defense against coronavirus disease 2019 (Covid-19). However, the antiviral drugs provide a new tool to fight the Covid-19 pandemic. Here we aimed for a comparative evaluation of authorized drugs for treating Covid-19 patients.

Methods

We searched in PubMed and Google Scholar using keywords and terms such as Covid, SARS-CoV-2, Coronavirus disease 2019, therapeutic management, hospitalized Covid-19 patients, Covid-19 treatment. We also gathered information from reputed newspapers, web portals, and websites. We thoroughly observed, screened, and included the studies relevant to our inclusion criteria. We included only the United States Food and Drug Administration (FDA) authorized drugs for this review.

Results

We found that molnupiravir and paxlovid are available for oral use, and remdesivir is for only hospitalized patients. Paxlovid is a combination of nirmatrelvir and ritonavir, nirmatrelvir is a protease inhibitor (ritonavir increases the concentration of nirmatrelvir), and the other two (remdesivir and molnupiravir) are nucleoside analog prodrugs. Remdesivir and molnupiravir doses do not need to adjust in renal and hepatic impairment. However, the paxlovid dose adjustment is required for mild to moderate renal or hepatic impaired patients. Also, the drug is not allowed for Covid-19 patients with severe renal or hepatic impairment. Preliminary studies showed oral antiviral drugs significantly reduce hospitalization or death among mild to severe patients. Moreover, the US FDA has approved four monoclonal antibodies for Covid-19 treatment. Studies suggest that these drugs would reduce the risk of hospitalization or severity of symptoms. World Health Organization strongly recommended the use of corticosteroids along with other antiviral drugs for severe or critically hospitalized patients.

Conclusion

All authorized drugs are effective in inhibiting viral replication for most SARS-CoV-2 variants. Therefore, along with vaccines, these drugs might potentially aid in fighting the Covid-19 pandemic.

Immune Response to SARS-CoV-2 Vaccines

COVID-19 vaccines have been developed to confer immunity against the SARS-CoV-2 infection. Prior to the pandemic of COVID-19 which started in March 2020, there was a well-established understanding about the structure and pathogenesis of previously known Coronaviruses from the SARS and MERS outbreaks. In addition to this, vaccines for various Coronaviruses were available for veterinary use. This knowledge supported the creation of various vaccine platforms for SARS-CoV-2. Before COVID-19 there are no reports of a vaccine being developed in under a year and no vaccine for preventing coronavirus infection in humans had ever been developed. Approximately nine different technologies are being researched and developed at various levels in order to design an effective COVID-19 vaccine. As the spike protein of SARS-CoV-2 is responsible for generating substantial adaptive immune response, mostly all the vaccine candidates have been targeting the whole spike protein or epitopes of spike protein as a vaccine candidate. In this review, we have compiled the immune response to SARS-CoV-2 infection and followed by the mechanism of action of various vaccine platforms such as mRNA vaccines, Adenoviral vectored vaccine, inactivated virus vaccines and subunit vaccines in the market. In the end we have also summarized the various adjuvants used in the COVID-19 vaccine formulation.

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.

Chinese University Students' Awareness and Acceptance of the COVID-19 Vaccine: A Cross-Sectional Study

Purpose

The emergence of the mutant virus has exacerbated the COVID-19 epidemic, and vaccines remain an effective and viable means of resistance. As a socially influential young group, university students’ awareness and acceptance of the COVID-19 vaccine are crucial to achieving herd immunity. This study aimed to assess the awareness and acceptance of the COVID-19 vaccine among Chinese university students and identify possible factors associated with their awareness level and vaccine hesitancy.

Patients and Methods

An anonymous cross-sectional survey was conducted among Chinese university students between 10 and 28 June 2021. We collected information on the demographic characteristics, awareness and acceptance of the COVID-19 vaccine, and influencing factors. Sleep disturbances and anxiety disorders were also evaluated. Multinomial logistic regression analyses were performed.

Results

Among the 721 participants (aged 18 to 23 years) with a female predominance (68.9%), 40.4% of cases exhibited moderate awareness the COVID-19 vaccine, and 87.4% of cases expressed high acceptance of the vaccine. Participants’ awareness of the COVID-19 vaccine was associated with gender, ethnicity, region of residence, grade level, satisfaction with current state of pandemic control, the perceived likelihood of a COVID-19 pandemic rebound, the source number of COVID-19 information, concerns about differences in vaccine manufacturers, acceptance of current state-approved vaccines and insomnia level. Furthermore, age, preferred channels for vaccination and the acceptance of current state-approved vaccines were significantly associated with their acceptance of the vaccine.

Conclusion

This study reflected Chinese university students’ high acceptance, but insufficient awareness of the COVID-19 vaccine, some students have insomnia and anxiety problems. These require the government to take measures such as individualized publicity and education, adding professional psychological counseling courses to improve the university students’ awareness of vaccines and public health events, and comprehensively promote vaccination to cope with the ever-changing situation of the COVID-19 epidemic.

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

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

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.

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

Background

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

Methods

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

Results

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

Conclusions

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

SARS‐CoV‐2 and its variants of concern including Omicron: looks like a never ending pandemic

The ongoing COVID‐19 pandemic caused by SARS‐CoV‐2 is associated with high morbidity and mortality. This zoonotic virus has emerged in Wuhan of China in December 2019 from bats and pangolins probably and continuing the human‐to‐human transmission globally since last two years. As there is no efficient approved treatment, a number of vaccines were developed at an unprecedented speed to counter the pandemic. Moreover, vaccine hesitancy is observed that may be another possible reason for this never ending pandemic. In the meantime, several variants and mutations were identified and causing multiple waves globally. Now the safety and efficacy of these vaccines are debatable and recommended to determine whether vaccines are able to interrupt transmission of SARS‐CoV‐2 variant of concern (VOC). Moreover, the VOCs continue to emerge that appear more transmissible and less sensitive to virus‐specific immune responses. In this overview, we have highlighted various drugs and vaccines used to counter this pandemic along with their reported side effects. Moreover, the preliminary data for the novel VOC “Omicron” are discussed with the existing animal models.

Omicron variant losing its critical mutations in the receptor-binding domain

Recently the Omicron This article is protected by copyright. All rights reserved.

Outpatient surveillance programme for health workers with COVID 19 in Mexico: an observational study of ambulatory treatment and early hospitalization

Introduction:

International guidelines recommend hospital care for patients with severe Coronavirus disease (COVID-19), but fragile health care systems struggle to cope with high number of admissions, placing patients at risk of receiving substandard care. We describe an outpatient ambulatory surveillance and treatment strategy (OPAT) for health care workers (HCWs) with severe COVID-19 during low hospital bed availability periods in Mexico City.

Methods:

In this observational, descriptive, retrospective study, we included HCWs with severe disease for whom there were no hospital beds available at the time of evaluation. We provided daily assessments by infectious disease specialists, daily ambulatory steroid, oral thromboprophylaxis and domiciliary low-dose oxygen. We recorded the number of patients who recovered, were hospitalized or died on follow-up.

Results:

From 18 March 2020 to 16 July 2021, 1739 HCWs attended our service. A total of 540 were diagnosed with COVID-19. Seventy-four had severe COVID-19 and needed hospitalization. Immediate hospitalization was not possible in 56 patients who were sent to the OPAT and included in our study. Twenty-four patients subsequently required hospitalization and 32 recovered as outpatients.

Conclusions:

We describe a feasible and safe outpatient management strategy for HCWs with severe COVID-19 in a low-resource setting.

Characteristics of the SARS-CoV-2 Omicron (B.1.1.529) Variant and Emerging Impact on Global Public Health

The discovery of the SARS-CoV-2 Omicron (B.1.1.529) variant has sparked alarm globally because of its rapid rate of infection and trespassing acquired immunity due to vaccination or natural infection. This heavily mutated variant is rapidly spreading around the world. Infected individuals with the Omicron variant may suffer from flu-like symptoms, and infected with the Delta variant frequently report low oxygen levels, high pulse rates, and a loss of smell and taste. Also, the Omicron variant causes asymptomatic or mild disease so far, and not any severe illness as like Delta, and this new variant has a 15% to 80% reduced risk of hospitalization than the Delta variant. Scientists are worried about the possibility of escaping the immunity by the Omicron variants and subvariants among fully vaccinated and recovered COVID-19 patients. Two doses of available vaccines are found to be partially ineffective in protecting this new variant, therefore, the third dose as a booster is recommended to enhance antibody level. Moreover, some antiviral drugs significantly reduce hospitalization or death among mild to severe COVID-19 patients. All authorized antiviral drugs are effective against viral replication for most SARS-CoV-2 variants, and particularly some monoclonal antibodies may not now be effective in treating COVID-19 patients. There is an urgent need to update existing vaccines, develop more effective and newer vaccines as well as additional monoclonal antibodies to counter Omicron. Therefore, along with close monitoring of Omicron characteristics, the present study suggests that health safety guidelines, mass immunization, early diagnosis, and search for effective antiviral drugs should be the approaches to fight against newer SARS-CoV-2 variants.

Indiscriminate Use of Antibiotics for COVID-19 Treatment in South Asian Countries is a Threat for Future Pandemics Due to Antibiotic Resistance

The COVID-19 pandemic has put enormous strain on the global public health and healthcare systems. Here we aimed to assess the prevalence and impact of indiscriminate use of antibiotics for COVID-19 treatment in south Asian countries. We observed the indiscriminate use of antibiotics in south Asian countries and other similar parts of the world. Along with vaccines, people in poor and developing countries have been taking antibiotics and some other medications without proper jurisdiction during the waves of the COVID-19 pandemic. We all know that COVID-19 is a viral disease, and only a few patients might have bacterial co-infections. Therefore, the role of antibiotics is ambiguous in most COVID-19 cases. Consequently, the overuse of antibiotics would cause antimicrobial resistance that has the potential to become a 2-edged sword after the COVID-19 pandemic era. Our findings emphasize the judicious use of antibiotics in COVID-19 therapy, especially in poor and developing countries across the globe.

The Upsurge of Diarrhea Amid COVID-19 Pandemic Makes Matter Worse in Bangladesh: A Call to Action

We have seen an alarming increase in diarrhea prevalence amid Coronavirus Disease-2019 (COVID-19) in Bangladesh. Healthcare professionals might face difficulty in diagnosis as these two infectious diseases have some common symptoms. Though there are confirmatory diagnostic tests for individual cases, there are chances of misdiagnosis as co-infections occur. Here we presented distinct clinical features of diarrhea and COVID-19 for differential diagnosis. We demonstrated the common overlapping symptoms of these two infectious diseases to facilitate fast diagnosis of patients. Also, we have discussed possible reasons for this upsurge of diarrheal infections in Bangladesh. Finally, we have made some recommendations based on our findings for managing this upsurge of diarrheal disease during the COVID-19 pandemic in Bangladesh. The healthcare authorities should take immediate measures before the tremendous twin effects of these two infectious diseases.