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Article
Biochemistry & Molecular Biology
Soumya Lipsa Rath et al.
Summary: The emergence of new SARS-CoV-2 variants poses a threat to the human population, and assessing their severity is challenging. This study compares the interaction of the wild-type and the latest Omicron variant using molecular dynamics simulations, revealing diverse changes in the properties of the mutated protein complex. These findings enhance our understanding of the binding mechanism between the Omicron variant and the wild-type SARS-CoV-2.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Chaoran Chen et al.
Summary: The CoV-Spectrum website provides support for identifying and tracking new SARS-CoV-2 variants, with flexible mutation search capabilities and analysis on various data sources to understand characteristics and transmission of different variants.
Article
Biochemistry & Molecular Biology
Wanwisa Dejnirattisai et al.
Summary: On November 24, 2021, the sequence of a new SARS-CoV-2 variant, Omicron-B.1.1.529, was announced. Compared to previous variants, Omicron has a higher number of mutations in the Spike (S) protein. Serum neutralization of Omicron by individuals vaccinated or previously infected with Alpha, Beta, Gamma, or Delta variants is significantly reduced or ineffective. Third vaccine doses can boost neutralization titers against Omicron, and high titers are observed in both vaccinated individuals and those infected with the Delta variant. Most potent monoclonal antibodies and antibodies under development are unable to effectively neutralize Omicron due to mutations in its Spike protein. Omicron has structural changes compared to earlier viruses and utilizes mutations that enhance its binding to ACE2, allowing for immune escape. This results in a large number of mutations in the ACE2 binding site and a rebalancing of receptor affinity similar to earlier pandemic viruses.
Article
Biochemistry & Molecular Biology
Markus Hoffmann et al.
Summary: The Omicron variant of SARS-CoV-2 is spreading rapidly and shows resistance to most therapeutic antibodies. It also evades neutralization by antibodies induced by infection or vaccination more efficiently than the Delta variant. This suggests that therapeutic antibodies may not be effective against the Omicron variant, and double vaccination with BNT162b2 may not provide adequate protection against severe disease caused by this variant.
Letter
Cell Biology
Shuai Xia et al.
Article
Medicine, General & Internal
Nicole Wolter et al.
Summary: According to data analysis from South Africa, individuals infected with the omicron variant have a lower likelihood of hospitalization compared to those infected with non-omicron variants. Furthermore, individuals infected with the omicron variant have a lower odds of severe disease compared to individuals infected with the earlier delta variant.
Article
Multidisciplinary Sciences
Bo Meng et al.
Summary: The Omicron variant of SARS-CoV-2 has a higher affinity for ACE2 and can evade neutralizing antibodies more effectively compared to the Delta variant. A third dose of mRNA vaccine can provide enhanced protection. Omicron has lower replication in lung and gut cells and less efficiently cleaves its spike protein compared to Delta.
Article
Multidisciplinary Sciences
Elisabetta Cameroni et al.
Summary: The Omicron variant of SARS-CoV-2 has raised concerns due to its 37 amino acid substitutions in the spike protein, particularly in the receptor-binding domain (RBD), leading to increased binding affinity with human ACE2. Neutralizing activity against Omicron was greatly reduced in convalescent and vaccinated individuals compared to the ancestral virus, but this decrease was less significant after a third vaccine dose. Broadly neutralizing monoclonal antibodies recognizing conserved RBD epitopes may be crucial in combating the Omicron variant and future zoonotic transmissions.
Article
Multidisciplinary Sciences
Sandile Cele et al.
Summary: The study found that the Omicron variant has reduced neutralizing effectiveness in individuals vaccinated with Pfizer BNT162b2, but those who had previously been infected with SARS-CoV-2 showed better neutralization against Omicron.
Article
Multidisciplinary Sciences
Rigel Suzuki et al.
Summary: The Omicron variant of SARS-CoV-2 has spread rapidly in several countries and has shown lower fusogenicity and attenuated pathogenicity compared to the Delta variant.
Article
Multidisciplinary Sciences
Lihong Liu et al.
Summary: The B.1.1.529/Omicron variant of SARS-CoV-2, initially detected in southern Africa, has rapidly spread globally and is expected to become dominant due to its enhanced transmissibility in the coming weeks. This variant poses a threat to the efficacy of current COVID-19 vaccines and antibody therapies due to its significant antibody resistance. Even individuals who have received vaccines and booster doses may have reduced neutralizing activity against B.1.1.529.
Article
Biochemistry & Molecular Biology
Laura A. VanBlargan et al.
Summary: The emergence of the B.1.1.529 Omicron variant raises concerns about the efficacy of antibody countermeasures. This study shows that some of the antibodies currently in clinical use may lose their ability to neutralize the Omicron variant.
Letter
Medicine, General & Internal
Shirley Collie et al.
Summary: Preliminary data from a test-negative study design in South Africa showed that two doses of the BNT162b2 vaccine had an efficacy of 50 to 70% against hospitalization caused by the omicron variant in Gauteng province.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Letter
Medicine, General & Internal
Heba N. Altarawneh et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Multidisciplinary Sciences
Dhiraj Mannar et al.
Summary: The newly reported Omicron variant shows new salt bridges and hydrogen bonds formed by mutated residues in the receptor binding domain, compensating for reduced ACE2 binding affinity. It also exhibits increased antibody evasion, which likely contributes to its rapid spread.
Article
Virology
Frederic Grabowski et al.
Summary: Omicron, a highly mutated variant of SARS-CoV-2, has rapidly spread and approached fixation in South Africa and has been detected worldwide. Its exponential growth and short doubling time may be attributed to its ability to evade immunity and infect both recovered and vaccinated individuals. The growth rate of Omicron compared to Delta is considerably higher, indicating a potential for larger epidemic outbreaks.
Article
Immunology
Hanjun Zhao et al.
Summary: The Omicron variant of SARS-CoV-2 has distinct virological characteristics compared to the Delta variant. It replicates more slowly and its entry pathway is mediated primarily through the endocytic pathway instead of TMPRSS2 pathway. This difference in entry pathway may have implications for the clinical manifestations or severity of the disease.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Immunology
Youchun Wang et al.
Summary: The Omicron variant shows greater potential for immune escape compared to other variants, suggesting a significant impact on immunity from previous infections and vaccines.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Virology
Christoph Jung et al.
Summary: The recently identified Omicron variant of SARS-CoV-2 is the fifth variant of concern and is characterized by significant changes in the viral Spike protein, possibly leading to increased transmission efficiency and evasion of neutralizing antibodies. Despite quickly outcompeting the Delta variant, Omicron appears to be overall less pathogenic than other variants.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sophie M-C Gobeil et al.
Summary: The SARS-CoV-2 Omicron variant, aided by extensive spike protein mutation, has surpassed the previously dominant Delta variant. Cryo-EM structures of the Omicron and Delta spikes reveal the conformational impacts of mutations, with the Omicron spike showing a tightly packed RBD organization and increased flexibility at the fusion peptide site.
News Item
Infectious Diseases
Sharmila Devi
LANCET INFECTIOUS DISEASES
(2022)
Editorial Material
Medicine, General & Internal
Penny L. Moore et al.
Summary: South Africa has relatively low Covid-19 vaccine coverage, but there may be a high prevalence of underlying seropositivity due to previous infection. Seropositivity could be related to the severity of disease caused by new variants.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Article
Multidisciplinary Sciences
Matthew McCallum et al.
Summary: The SARS-CoV-2 Omicron variant evades antibody-mediated immunity and exhibits enhanced affinity for host cells due to accumulation of spike mutations and remodeling of interactions with the ACE2 receptor.
Article
Multidisciplinary Sciences
Antoni G. Wrobel et al.
Summary: Recently emerged variants of SARS-CoV-2, such as Alpha and Beta, have spike glycoproteins with multiple substitutions that increase transmission and resistance to neutralizing antibodies. The spike proteins of these variants have acquired mutations that affect receptor binding and stability upon binding. This research provides insights into the evolution of the virus and its ability to transmit in humans.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Jun Zhang et al.
Summary: The Omicron variant of SARS-CoV-2 has a high number of mutations, which requires a higher level of ACE2 receptor for membrane fusion and shows increased resistance to neutralizing antibodies. This suggests that Omicron has acquired the ability to evade host immunity through excessive mutations.
Article
Multidisciplinary Sciences
Yunlong Cao et al.
Summary: Omicron sublineages BA.2.12.1, BA.4 and BA.5 have higher transmissibility and increased evasion of neutralizing antibodies compared to the BA.2 lineage. They exhibit similar binding affinities to the ACE2 receptor as BA.2. BA.1 infection after vaccination boosts humoral immune memory against wild-type SARS-CoV-2, but these antibodies are largely evaded by BA.2 and BA.4/BA.5 variants.
Article
Cell Biology
Victoria Stalls et al.
Summary: This study determines the cryoelectron microscopy structures of the Spike (S) protein of the Omicron BA.2 sub-lineage of the SARS-CoV-2 virus and compares it with the BA.1 sub-lineage. The BA.2 S protein exhibits tighter packing and improved thermostability due to mutations in the receptor-binding domain (RBD). The closed state of BA.2 S enhances RBD interactions and shows reduced accessibility of the fusion peptide to antibodies compared to BA.1.
Article
Multidisciplinary Sciences
Sho Iketani et al.
Summary: The identification of the Omicron variant of SARS-CoV-2 in Botswana in November 2021 sparked concern due to the spike protein alterations that could potentially evade antibodies. Further studies showed that the Omicron sublineages, BA.1+R346K and BA.2, are antigenically similar to the wild-type virus and pose similar risks to the effectiveness of current vaccines. BA.2 also demonstrated resistance to many neutralizing monoclonal antibodies, highlighting the challenges in developing effective therapeutic options.
Article
Infectious Diseases
Laura Espenhain et al.
Article
Biochemistry & Molecular Biology
Changshuo Wei et al.
Summary: The study suggests that the rapid accumulation of mutations in the SARS-CoV-2 Omicron variant may have originated from humans jumping to mice and then back to humans, indicating an inter-species evolutionary trajectory.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Immunology
Lydia Riepler et al.
Summary: Neutralizing antibodies are crucial for protection against viruses like SARS-CoV-2. This study compared four different assays for detecting these antibodies and found that they were all robust and yielded comparable results, indicating their reliability.
Article
Multidisciplinary Sciences
Fabian Zech et al.
Summary: By exchanging residue 403 between RaTG13 and SARS-CoV-2 spike proteins, researchers demonstrated the impact on binding to human ACE2 and entry of pseudotyped viruses. This finding suggests the potential of vaccination to protect against future zoonotic diseases.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Shihui Sun et al.
Summary: The study presents a novel mouse-adapted SARS-CoV-2 strain, MASCp36, as a model for investigating the pathogenicity, evolution, and adaptation of the virus. Through deep sequencing and cryo-electron microscopy analysis, the molecular basis of structural changes and receptor binding mechanism at a biological level are revealed.
NATURE COMMUNICATIONS
(2021)
Article
Virology
Jingyou Yu et al.
Summary: The study outlines a method to generate a highly infectious SARS-CoV-2 pseudovirus for evaluating humoral immunity, antibody therapeutics, and vaccines. The SDCT13-based pseudovirus neutralization assay exhibits key characteristics including linearity, limit of detection, and assay precision. This assay is adaptable for emerging SARS-CoV-2 variants and crucial for the development of vaccines and immune-based therapeutics.
JOURNAL OF VIROLOGY
(2021)
Article
Medicine, General & Internal
Kun Huang et al.
Summary: By passaging SARS-CoV-2 in BALB/c mice, researchers obtained a mouse-adapted virus strain with increased infectivity and severe interstitial pneumonia in mice; mutations Q493K and Q498H in the RBD of the virus enhanced its binding affinity to mouse ACE2; the study tentatively confirmed the antiviral activity of TLR7/8 agonist Resiquimod against SARS-CoV-2 in vitro and in vivo.
Article
Multidisciplinary Sciences
Delphine Planas et al.
Summary: The SARS-CoV-2 B.1.617 Delta variant, first identified in India in 2020, has become dominant in some regions and is spreading to many countries. This variant shows resistance to certain monoclonal antibodies and antibodies in convalescent sera, as well as reduced neutralization by some COVID-19 vaccines. Administration of two doses of the vaccine is needed for a neutralizing response against the Delta variant.
Article
Chemistry, Multidisciplinary
Terra Sztain et al.
Summary: Through simulations, the study reveals the mechanism of spike protein receptor binding domain (RBD) opening in SARS-CoV-2 infection, highlighting the crucial role of N-glycan in facilitating RBD opening. This research represents a milestone in ensemble pathway simulations and provides a foundation for understanding the fundamental mechanisms of viral entry and infection.
Review
Genetics & Heredity
Kaiming Tao et al.
Summary: The emergence of multiple SARS-CoV-2 variants has significant impacts on the epidemiological and clinical aspects of the COVID-19 pandemic, including increased virus transmission rates, heightened risk of reinfection, and reduced effectiveness of neutralizing antibodies and vaccines. These variants have introduced new challenges to COVID-19 research, necessitating additional avenues of laboratory, epidemiological, and clinical studies.
NATURE REVIEWS GENETICS
(2021)
Review
Microbiology
William T. Harvey et al.
Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Biology
Fang Tian et al.
Summary: Research indicates that the N501Y mutation in SARS-CoV-2 variants strengthens its interaction with ACE2, leading to an increased transmission rate, highlighting the need for close monitoring of future mutations in the virus' RBD.
Review
Immunology
Lianpan Dai et al.
Summary: The urgent need for vaccines to control the COVID-19 pandemic has led to the rapid development of multiple vaccine candidates, with some showing positive results in late-stage clinical trials. This article discusses the viral elements used in these candidates, the reasons why they are good targets for the immune system, and their implications for protective immunity. Dai and Gao highlight the importance of selecting the right viral targets in vaccine development to ensure an effective immune response and the overall safety and efficacy of the vaccine.
NATURE REVIEWS IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Daniel Wrapp et al.
Article
Microbiology
Michael Letko et al.
NATURE MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Alexandra C. Walls et al.
Article
Biochemistry & Molecular Biology
Markus Hoffmann et al.
Article
Biochemistry & Molecular Biology
Bette Korber et al.
Article
Biochemistry & Molecular Biology
Leonid Yurkovetskiy et al.
Article
Biochemical Research Methods
James Hadfield et al.
Article
Virology
Pavel Sagulenko et al.
Article
Immunology
Florian I. Schmidt et al.
JOURNAL OF EXPERIMENTAL MEDICINE
(2016)
Article
Chemistry, Physical
ACT van Duin et al.
JOURNAL OF PHYSICAL CHEMISTRY A
(2001)
