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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.
Article
Immunology
Lu Lu et al.
Summary: Immune sera from BNT162b2 and Coronavac recipients showed reduced neutralizing antibody titers against the omicron variant. The presence of the spike R346K mutation did not affect the neutralization susceptibility.
CLINICAL INFECTIOUS DISEASES
(2022)
Letter
Microbiology
Tung Phan et al.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Letter
Medicine, General & Internal
Fabian Schmidt et al.
Summary: Neutralization assays showed much lower omicron neutralization compared to Wuhan-hu-1 after two doses of mRNA vaccine, but individuals who received a booster vaccine or were vaccinated after recovering from Covid-19 exhibited high levels of omicron neutralization.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Review
Immunology
Priyal Mistry et al.
Summary: The emergence of SARS-CoV-2 and the subsequent COVID-19 pandemic has led to the development of vaccines and investigation into the immune response to the virus. Variants of the virus have presented challenges to vaccine effectiveness. It is important to understand the immune memory response and continue to develop new antibody treatments and future vaccine approaches.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Virology
Kathleen Subramoney et al.
Summary: This study evaluated the ability to detect Omicron BA.1 using genotyping assays in the Gauteng province of South Africa. The results showed that genotyping assays for the detection of del69/70 and K417N mutations coupled with spike gene target failure (SGTF) can efficiently exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, there is still a need for assays to detect unique mutations for differentiation between other Omicron sublineages.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Biochemical Research Methods
Mandy Bloemen et al.
Summary: This article describes an easy, cheap and fast method for detecting mutations in the spike protein of SARS-CoV-2, particularly the Omicron variant.
JOURNAL OF VIROLOGICAL METHODS
(2022)
Editorial Material
Biochemical Research Methods
Sergey Knyazev et al.
Summary: During the COVID-19 pandemic, genomics and bioinformatics have become crucial tools in public health. They have been used to acquire genomic data that support global health responses, aid in the development of testing methods, and enable the timely tracking of novel SARS-CoV-2 variants. However, the rapid generation and analysis of genomic data present unique technical, scientific, and organizational challenges.
Article
Virology
Marco Gerdol et al.
Summary: Tracking the evolution of SARS-CoV-2 is crucial in the current pandemic situation. The virus acquires mutations at a slower rate compared to other RNA viruses, but the widespread circulation of SARS-CoV-2 in the human population has led to the emergence of several variants of concern. These variants carry multiple nonsynonymous mutations in the spike glycoprotein, potentially conferring resistance to neutralizing antibodies and affecting viral infectivity. In addition, some variants have deletion regions that overlap with antibody epitopes. This study highlights a recurrent insertion region in the N-terminal domain of the spike protein, which warrants further investigation into its effects on spike structure and viral infectivity.
Article
Genetics & Heredity
Arghavan Alisoltani et al.
Summary: This study focuses on the evolution of the SARS-CoV-2 genome and reveals a significant increase in the numbers and ratio of genomes with in-frame insertions and deletions (indels) among the variants of concern (VOCs). The co-occurrence of indels, especially deletions on spike N-terminal domain and non-structural protein 6 (NSP6), is a shared feature in several VOCs such as Alpha, Beta, Delta, and Omicron. The distribution of indels is correlated with spike mutations associated with immune escape, and the increasing population resistance due to vaccination and previous infections coincides with the growth of genomes with indels. Indels occur most frequently in the spike protein, but also in other proteins involved in host immune system interactions. Structural analysis suggests that indels remodel the surfaces of viral proteins at common epitopes and interaction interfaces, affecting the virus' interactions with host proteins. The study hypothesizes that the increased frequency, non-random distribution, and independent co-occurrence of indels in several VOCs is another response mechanism to elevated global population immunity.
FRONTIERS IN GENETICS
(2022)
Article
Virology
Philippe Corbisier et al.
Summary: A RT-PCR assay was developed for the specific detection of the SARS-CoV-2 Omicron Variant of Concern. The method demonstrated high specificity and sensitivity, allowing for rapid and accurate identification of the Omicron variant.
JOURNAL OF CLINICAL VIROLOGY
(2022)
Article
Environmental Sciences
Taxiarchis Chassalevris et al.
Summary: Wastewater-based variant surveillance provides valuable supplementary practice to conventional SARS-CoV-2 surveillance, offering timely and cost-effective information on virus prevalence.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Cell Biology
Sophie M-C Gobeil et al.
Summary: The study found that the mutation variant G614 of SARS-CoV-2 leads to significant changes in the protein structure, resulting in altered positioning ratio of RBD, which may have implications for vaccine design.
Article
Multidisciplinary Sciences
Helen Harper et al.
Summary: This study introduces a SNP identification pipeline that identifies 15 distinct genotypes from 50 sequenced SARS-CoV-2 samples, demonstrating the feasibility of using a genotyping panel for rapid, cost-effective, and reliable monitoring of SARS-CoV-2 variants.
Article
Multidisciplinary Sciences
Jun Zhang et al.
Summary: The Delta variant of SARS-CoV-2 is more efficient at fusing membranes at low levels of cellular receptor ACE2, possibly contributing to its heightened transmissibility. Each variant shows different rearrangement of the antigenic surface of the S protein, but only the changes in the RBD make it a better target for therapeutic antibodies.
Article
Biology
Sofya K. Garushyants et al.
Summary: The study reveals the presence of various insert sequences in the SARS-CoV-2 genome, which not only reflect virus variance but may also affect its pathogenicity and immune escape. The independent insertion mechanisms play a crucial role in the evolution of the novel coronavirus.
COMMUNICATIONS BIOLOGY
(2021)
Article
Medical Laboratory Technology
Daniel K. W. Chu et al.
CLINICAL CHEMISTRY
(2020)
Article
Biochemical Research Methods
Heng Li
Editorial Material
Infectious Diseases
Yuelong Shu et al.
Article
Virology
Donata Kalthoff et al.
Article
Biochemical Research Methods
Heng Li
Article
Biochemistry & Molecular Biology
Cornelis A. Albers et al.
