Related references
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Article
Microbiology
Panke Qu et al.
Summary: The emergence of new Omicron subvariants, including BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2, has shown enhanced neutralization resistance against sera from vaccinated healthcare workers and COVID-19 patients. The mutations N460K, K444T, and F486S play a significant role in driving the increased neutralization resistance of these subvariants. These findings provide insights into the evolution of SARS-CoV-2 Omicron subvariants.
CELL HOST & MICROBE
(2023)
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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
Zhen Cui et al.
Summary: The Omicron variant of SARS-CoV-2 is spreading rapidly worldwide due to its increased fitness, with spike structures that maintain stability for receptor recognition but compromise viral fusion efficiency. By altering amino acids and structures, it evades recognition by most antibodies, facilitating immune escape. The research sheds light on conserved regions for the development of broad-spectrum vaccines.
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.
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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
Kang Wang et al.
Summary: The Omicron variant of SARS-CoV-2 is highly resistant to neutralizing antibodies, which raises concerns about the effectiveness of antibody therapies and vaccines. A study found that individuals who received two or three doses of an inactivated SARS-CoV-2 vaccine had varying rates of seroconversion for neutralizing antibodies. The effectiveness of neutralizing antibodies against Omicron was significantly lower in individuals who received three vaccine doses. However, monoclonal antibodies derived from individuals who received three vaccine doses showed strong neutralizing activity against all variants of concern, including Omicron.
Article
Multidisciplinary Sciences
Yunlong Cao et al.
Summary: The Omicron variant of SARS-CoV-2 contains 15 mutations in the receptor-binding domain, leading to evasion of over 85% of tested neutralizing antibodies. Different epitope groups of neutralizing antibodies are affected to varying degrees by single mutations of Omicron. Antibodies targeting the conserved region of sarbecovirus remain most effective against Omicron.
Article
Biochemistry & Molecular Biology
Daichi Yamasoba et al.
Summary: Research has shown that the Omicron lineage BA.1 has been outpaced by a new Omicron lineage, BA.2, which is more transmissible. Immunity induced by COVID vaccines does not effectively protect against BA.2, similar to BA.1, and BA.2 has notable antigenic differences from BA.1. BA.2 spike shows higher replication efficacy and cell fusion capability compared to BA.1 spike. Infection experiments on hamsters indicate that BA.2 spike-bearing virus is more pathogenic than BA.1 spike-bearing virus. Overall, these findings suggest that the risk of BA.2 to global health is potentially higher than that of BA.1.
Article
Immunology
Zijun Wang et al.
Summary: SARS-CoV-2 infection or vaccination induces neutralizing antibody responses targeting the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the spike protein. This study identifies different groups of neutralizing antibodies, including some that can neutralize the Omicron variant. Structural analysis reveals the mechanism of action of broad neutralizers.
Article
Multidisciplinary Sciences
Ryuta Uraki et al.
Summary: The replicative ability and pathogenicity of Omicron BA.2 variant is similar to that of BA.1 in rodents, but it shows less pathogenicity compared to early SARS-CoV-2 strains. There is a marked reduction in the neutralizing activity of plasma from individuals who had recovered from COVID-19 and vaccine recipients against BA.2 variant.
Article
Cell Biology
Kathryn Westendorf et al.
Summary: A monoclonal antibody named LY-CoV1404 has been successfully isolated, which demonstrates highly potent neutralization against multiple variants of the SARS-CoV-2 virus. The binding site of LY-CoV1404 remains relatively conserved, allowing it to maintain its activity. This finding suggests that LY-CoV1404 has the potential to be an effective therapeutic agent against all known variants.
Article
Immunology
Jasmin Quandt et al.
Summary: The Omicron BA.1 breakthrough infection in BNT162b2-vaccinated individuals showed strong neutralizing activity against Omicron BA.1, BA.2, and previous SARS-CoV-2 variants. The memory B cells induced by the breakthrough infection targeted epitopes shared broadly among variants. The vaccination-imprinted memory B cell pool was capable of remodeling in response to heterologous SARS-CoV-2 spike glycoprotein exposure. However, variants that acquire alterations at conserved sites may have increased susceptibility to immune escape.
SCIENCE IMMUNOLOGY
(2022)
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Aekkachai Tuekprakhon et al.
Summary: The Omicron variant of SARS-CoV-2 has rapidly spread globally and has evolved into different sublineages, with BA.4 and BA.5 dominating in South Africa. These sublineages show reduced neutralization by vaccine and naturally immune serum, indicating the possibility of repeat Omicron infections.
Article
Cell Biology
Yunlong Cao et al.
Summary: This study presents a rational approach for identifying broad-spectrum neutralizing antibody (NAbs) cocktails against fast-evolving SARS-CoV-2. By targeting non-immunodominant receptor-binding domain (RBD) epitopes and conserved sites associated with critical viral functions, the researchers identified a promising antibody cocktail with the potential to neutralize various sarbecoviruses, including the Omicron variant.
Article
Microbiology
Tyler N. Starr et al.
Summary: SARS-CoV-2 virus continues to undergo mutations in the spike receptor-binding domain, affecting biochemical properties related to ACE2 receptor binding, folding stability, and antibody recognition. This study investigates the effects of these mutations in the Omicron BA.1 and BA.2 variants, showing potential changes in function compared to the ancestral strain. The research highlights the importance of ongoing surveillance and understanding the mutational landscape for effective monitoring and control of the virus.
Article
Multidisciplinary Sciences
Qian Wang et al.
Summary: SARS-CoV-2 Omicron subvariants BA.2.12.1 and BA.4/5 have become dominant in the United States and South Africa, raising concerns about their ability to evade neutralizing antibodies and compromise the efficacy of COVID-19 vaccines and therapeutic monoclonals. A systematic antigenic analysis reveals that BA.2.12.1 and BA.4/5 have different levels of resistance to antibodies, with BA.2.12.1 being modestly resistant and BA.4/5 being substantially resistant. Certain mutations in the spike protein facilitate antibody escape, but compromise the spike affinity for the viral receptor. Only bebtelovimab retains full potency against both subvariants.
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
Multidisciplinary Sciences
Catherine J. Reynolds et al.
Summary: This study investigated the immune response of triple BioNTech BNT162b2 mRNA-vaccinated healthcare workers to the B.1.1.529 variant. It was found that individuals vaccinated with three doses showed enhanced immunity against previous variants, but reduced immune response to B.1.1.529. Individuals previously infected with other variants showed enhanced immunity against earlier variants, but reduced immune response to B.1.1.529.
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Multidisciplinary Sciences
Tyler N. Starr et al.
Summary: This study investigates the impact of mutations in the spike receptor-binding domain (RBD) of SARS-CoV-2 on its affinity for the ACE2 receptor and antibody recognition, as well as their implications for future evolution and interaction. The findings reveal that certain mutations cause shifts in the effects of mutations at other sites, shaping the evolutionary path of the virus.
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Multidisciplinary Sciences
Khadija Khan et al.
Summary: The SARS-CoV-2 Omicron sub-lineages BA.4 and BA.5, first identified in South Africa, have mutations in the spike receptor binding domain compared to BA.1. Experimental results show that BA.4 and BA.5 have reduced neutralization against BA.1 in unvaccinated individuals, but this effect is less pronounced in vaccinated individuals.
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Biochemistry & Molecular Biology
Izumi Kimura et al.
Summary: After the global spread of SARS-CoV-2 Omicron BA.2, several BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Statistical analysis showed that these BA.2 subvariants have higher effective reproduction numbers than the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments demonstrated that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, with BA.4/5 being more fusogenic. The study also provided the structure of the BA.4/5 spike receptor-binding domain and investigated the substitutions in the BA.4/5 spike that play a role in ACE2 binding and immune evasion. Additionally, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. The multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of the original BA.2.
Article
Microbiology
Akatsuki Saito et al.
Summary: The SARS-CoV-2 Omicron BA.2.75 variant, emerged in May 2022, demonstrates distinct virological properties compared to its ancestors BA.2 and BA.5. It exhibits higher effective reproduction number and sensitivity to antibodies, as well as greater affinity for the human receptor ACE2 and pathogenicity in hamsters.
CELL HOST & MICROBE
(2022)
Article
Microbiology
Yunlong Cao et al.
Summary: The newly emerged SARS-CoV-2 Omicron subvariant, BA.2.75, has shown a growth advantage over other circulating variants in India. This study reveals that BA.2.75 has a higher affinity for the host receptor ACE2 and exhibits increased low-pH-endosomal cell entry. It also demonstrates reduced evasion of humoral immunity from certain convalescent plasma, while showing a distinct neutralizing antibody escape pattern. These findings suggest that BA.2.75 may become the dominant variant following BA.4/BA.5.
CELL HOST & MICROBE
(2022)
Article
Microbiology
Qian Wang et al.
Summary: The newly emerged SARS-CoV-2 Omicron subvariant BA.2.75 exhibits moderate resistance to neutralization by sera from vaccinated/boosted individuals compared to the currently circulating BA.2, but is more sensitive than BA.4/5. BA.2.75 shows heightened resistance to class 1 and class 3 monoclonal antibodies targeting the spike-receptor-binding domain, while gaining sensitivity to class 2 antibodies. The resistance is mainly conferred by two mutations. BA.2.75 also shows slight resistance to a therapeutic antibody with potent activity against all Omicron subvariants. Additionally, BA.2.75 exhibits higher binding affinity to the host receptor ACE2 compared to other Omicron subvariants.
CELL HOST & MICROBE
(2022)
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Young-Jun Park et al.
Summary: SARS-CoV-2 Omicron sublineages have spike mutations that allow them to evade antibodies from previous infection or vaccination. Hybrid immunity or booster shots can generate neutralizing antibodies against Omicron variants, and breakthrough infections lead to the production of neutralizing antibodies in the nasal mucosa. Antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases show cross-reactivity with different receptor-binding domains, while primary Omicron infections elicit B cells with narrow specificity. A highly potent pan-variant-neutralizing antibody has been identified as a potential candidate for clinical development.
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Allison J. Greaney et al.
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Allison J. Greaney et al.
Summary: Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are key in neutralizing antibody responses, and a deep mutational scanning method was used to assess the impact of all amino-acid mutations in the RBD on antibody binding with 10 human monoclonal antibodies. The study identified the clustered escape mutations in different surfaces of the RBD that correspond to structurally defined antibody epitopes, showing that even antibodies targeting the same surface can have distinct escape mutations.
CELL HOST & MICROBE
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Allison J. Greaney et al.
Summary: The evolution of SARS-CoV-2 may impact the recognition of the virus by human antibody-mediated immunity, with mutations affecting antibody binding varying significantly among individuals and within the same individual over time. Despite this variability, mutations that greatly reduce antibody binding usually occur at specific sites in the RBD, with E484 being the most crucial. These findings can inform surveillance efforts for SARS-CoV-2 evolution in the future.
CELL HOST & MICROBE
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Summary: A study in Israel revealed that waning immunity after receiving two doses of the BNT162b2 vaccine led to an increase in the incidence of SARS-CoV-2 infection. Levels of spike-binding IgG and neutralizing antibodies decreased more significantly in men, individuals aged 65 or older, and immunosuppressed individuals in a longitudinal study involving nearly 4000 healthcare workers.
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Summary: The study identifies 41 human monoclonal antibodies that recognize the N-terminal domain of the SARS-CoV-2 spike protein and exhibit strong neutralizing activity. These antibodies inhibit cell-to-cell fusion, activate effector functions, and protect animals from virus challenge, highlighting the importance of NTD-specific neutralizing antibodies for protective immunity and vaccine development. Several SARS-CoV-2 variants with mutations in the NTD supersite suggest ongoing selective pressure on the virus.
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Summary: The emergence of the 501Y lineages of SARS-CoV-2 in 2020 coincided with a global shift in selective forces acting on various genes, leading to repeated convergent mutations at 35 genome sites known as the 501Y meta-signature. This meta-signature includes multiple mutation combinations that promote the persistence of diverse SARS-CoV-2 lineages in the face of increasing host immune recognition.
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