Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2

Article Biochemistry & Molecular Biology

CoV3D: a database of high resolution coronavirus protein structures

Ragul Gowthaman et al.

Summary: CoV3D is a database and resource for coronavirus protein structures, updated weekly, providing users with comprehensive sets of coronavirus protein structures and complexes, with integrated molecular viewers for visualization.

NUCLEIC ACIDS RESEARCH (2021)

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News Item Multidisciplinary Sciences

FAST-SPREADING COVID VARIANT CAN ELUDE IMMUNE RESPONSES

Ewen Callaway

NATURE (2021)

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Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Nicholas G. Davies et al.

Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.

SCIENCE (2021)

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Article Cell Biology

Linear epitope landscape of the SARS-CoV-2 Spike protein constructed from 1,051 COVID-19 patients

Yang Li et al.

Summary: By analyzing the serum IgG response of 1,051 COVID-19 patients, researchers identified linear epitopes of the SARS-CoV-2 Spike protein, revealing two regions rich in linear epitopes and identifying variable peptide responses associated with disease severity. Antibodies obtained from immunizing mice with linear epitopes did not show significant neutralizing activity against the virus, suggesting the importance of understanding humoral responses for vaccine refinement.

CELL REPORTS (2021)

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Article Multidisciplinary Sciences

Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

Alex Graudenzi et al.

Summary: This study conducted a large-scale analysis of intra-host genomic diversity of SARS-CoV-2, revealing interactions between host-related mutational processes and transmission dynamics, as well as identifying mutational signatures related to nucleotide substitutions. The study also demonstrated the impact of purifying selection on these mutational processes, while some mutations transition towards clonality, increasing overall genomic diversity. Additionally, phylogenomic analysis supported the hypothesis of transmission of minor variants, paving the way for integrated analysis of intra-host genomic diversity and clinical outcomes of SARS-CoV-2 infections.

ISCIENCE (2021)

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Article Biochemistry & Molecular Biology

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Sergey Knyazev et al.

Summary: Minority viral haplotypes, which can become dominant if drug-resistant or evade the immune system better, are crucial in disease treatment. A new method, CliqueSNV, has been proposed to reduce sequencing noise and accurately identify minority haplotypes with frequencies below the sequencing error rate. This method shows consistent performance across different sequencing platforms.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

Host-directed editing of the SARS-CoV-2 genome

Tobias Mourier et al.

Summary: The extensive sequence data from SARS-CoV-2 in 2020 pandemic has facilitated the study of viral genome evolution, revealing instances of directional mutation pressures exerted on the genome by host antiviral defense systems. It discusses three human defense mechanisms – APOBEC, ADAR, and ROS – and their potential implications on SARS-CoV-2 evolution.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2021)

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Article Biochemistry & Molecular Biology

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Sergey Knyazev et al.

Summary: Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. The CliqueSNV technology effectively reduces sequencing noise and enables accurate identification of low-frequency viral haplotypes.

NUCLEIC ACIDS RESEARCH (2021)

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Article Immunology