SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion

Review Immunology

Broadly neutralizing antibodies to SARS-CoV-2 and other human coronaviruses

Yanjia Chen et al.

Summary: This article summarizes neutralizing antibodies targeting four key regions of the SARS-CoV-2 spike protein, which are important for developing antibody therapeutics and designing next-generation vaccines.

NATURE REVIEWS IMMUNOLOGY (2023)

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Review Virology

Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines

Yusha Araf et al.

Summary: The Omicron variant of SARS-CoV-2 is a heavily mutated virus with a high risk of infection. Limited information is available regarding the genomics, transmissibility, and effectiveness of vaccines against this variant, emphasizing the need for further investigation.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Biochemistry & Molecular Biology

The Slowing Rate of CpG Depletion in SARS-CoV-2 Genomes Is Consistent with Adaptations to the Human Host

Akhil Kumar et al.

Summary: This study reveals that the depletion of CpG dinucleotides in SARS-CoV-2 genomes is not uniform and varies over time. The rate of CpG depletion is highest during early evolution in humans and gradually reaches an equilibrium. The study also shows that CpG depletion occurs mainly at specific positions within codons and SARS-CoV-2 genomes selectively lose CpGs-motifs from a U-rich context.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

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Article Biochemistry & Molecular Biology

Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes

Ankit K. Pathak et al.

Summary: During the COVID-19 pandemic, genome sequencing of SARS-CoV-2 has been valuable for tracking its spread and identifying variants of concern. Intra-host single nucleotide variations (iSNVs) can capture variability within a host, and some variations have been found to become fixed in the population. Mutations in the Spike protein may affect antigenicity and immune escape. Therefore, tracking and studying iSNVs in ongoing genome surveillance programs is important for early identification of potential variants of concern.

NUCLEIC ACIDS RESEARCH (2022)

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Review Genetics & Heredity

Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination

Riccardo Pecori et al.

Summary: The AID/APOBEC polynucleotide cytidine deaminases have diverse functions as both DNA mutators and RNA editors, and their strict functional classification needs to be reconsidered. Understanding the structural differences and similarities between these enzymes will contribute to improving the design of programmable base editors for therapeutic purposes.

NATURE REVIEWS GENETICS (2022)

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Article Virology

Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2

Binbin Xi et al.

Summary: The study examines the molecular and evolutionary characteristics of SARS-CoV-2 to better understand and respond to the ongoing outbreaks. The analysis of genomic data reveals significant variations in haplotype subtypes across different regions and highlights the lack of early SARS-CoV-2 genomic data. The virus has undergone dynamic selection and may have enhanced transmissibility and immune escape capabilities over time.

VIRUSES-BASEL (2022)

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Review Virology

The Deltacron conundrum: Its origin and potential health risks

Saria Farheen et al.

Summary: This article discusses the potential mutations, risk factors, and therapeutic options related to the newly emerged Deltacron variant. Although there was controversy about the variant potentially being a product of lab contamination, it has been proven otherwise. Experts are actively researching the epidemiological characteristics of this variant to control potential outbreaks.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Biochemistry & Molecular Biology

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Erik Volz et al.

Summary: The study suggests a positive selection for the SARS-CoV-2 spike protein variant D614G in the UK, but no evidence of differences in COVID-19 mortality or clinical severity in patients infected with this variant. 614G is associated with higher viral load and younger age of patients compared to 614D.

CELL (2021)

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Article Multidisciplinary Sciences

Learning the language of viral evolution and escape

Brian Hie et al.

Summary: Researchers used machine learning algorithms to model viral escape and identified patterns in escape mutations, showing that language models can accurately predict viral escape patterns similar to how words can change the meaning of a sentence. This study represents a promising conceptual bridge between natural language and viral evolution.

SCIENCE (2021)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape

Qianqian Li et al.

Summary: The 501Y.V2 variants of SARS-CoV-2 with multiple mutations are rapidly spreading from South Africa to other countries, showing reduced susceptibility to neutralizing antibodies and potential compromise of monoclonal antibodies and vaccines. Enhanced infectivity in murine ACE2-overexpressing cells suggests the possibility of transmission to mice.

CELL (2021)

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Article Biochemistry & Molecular Biology

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

Wilfredo F. Garcia-Beltran et al.

Summary: New variants of SARS-CoV-2 show high resistance to vaccine neutralization, with some able to escape vaccine responses with just a few mutations, highlighting the importance of developing broadly protective measures against variants.

CELL (2021)

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Article Biochemistry & Molecular Biology

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera

Daming Zhou et al.

Summary: The race to develop vaccines against SARS-CoV-2 variants, such as B.1.1.7, B.1.351, and P.1, is ongoing as these variants have mutations in the spike protein, potentially leading to immune escape. A structure-function analysis of B.1.351 revealed tighter ACE2 binding and widespread evasion from monoclonal antibody neutralization, particularly driven by the E484K mutation.

CELL (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 within-host diversity and transmission

Katrina A. Lythgoe et al.

Summary: The study found that SARS-CoV-2 infections in clinical samples in the UK are characterized by low levels of within-host diversity and a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with shared diversity not persisting.

SCIENCE (2021)

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Article Virology

The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense

Cem Azgari et al.

Summary: Understanding the evolution of SARS-CoV-2 is crucial in managing the COVID-19 pandemic, with mutagenesis and selection being key mechanisms. This study used a phylogenetic approach to reveal the contribution of mutagenesis and selection to the genetic diversity of SARS-CoV-2 genomes, showing that mutation patterns are influenced by host antiviral mechanisms and potential adaptive responses.

VIRUSES-BASEL (2021)

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Article Evolutionary Biology

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2

Nicola De Maio et al.

Summary: The COVID-19 pandemic has prompted an unprecedented response from the sequencing community, leading to a study of mutation rates and selective pressures using sequence data from over 140,000 SARS-CoV-2 genomes. Two specific mutation rates, G -> U and C -> U, were found to be significantly higher than others, possibly attributed to APOBEC and ROS activity. Genomic context does have an effect on mutation rates, but its impact is limited.

GENOME BIOLOGY AND EVOLUTION (2021)

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Article Microbiology

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

Andrew L. Valesano et al.

Summary: This study found that the within-host genetic diversity of SARS-CoV-2 is low and does not vary over time. While shared variation across individuals is generally limited, there are instances of intrahost variants shared among individuals who are unlikely to be related by transmission, indicating limited utility for predicting future lineages.

PLOS PATHOGENS (2021)

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Review Microbiology

SARS-CoV-2 variants, spike mutations and immune escape

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)

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Article Microbiology

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Katarina M. Braun et al.

Summary: The study shows that within-host diversity of SARS-CoV-2 is low and transmission bottlenecks are narrow, with most infections founded by very few viruses. Within-host variants are rarely transmitted, even within the same household, and are seldom detected along phylogenetically linked infections within the broader community. This suggests that most variation generated within-host is lost during transmission.

PLOS PATHOGENS (2021)

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Article Biology

Patterns of within-host genetic diversity in SARS-CoV-2

Gerry Tonkin-Hill et al.

Summary: The study examines within-host diversity in 1181 samples of SARS-CoV-2, finding detectable within-host mutations in 95.1% of the samples. Analysis of the mutational spectra reveals strong strand asymmetries, suggesting that damage or RNA editing may dominate the accumulation of mutations during the SARS-CoV-2 pandemic.

ELIFE (2021)

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Article Biochemistry & Molecular Biology

AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus

Binbin Xi et al.

Summary: Researchers developed a flexible automated tool, AutoVEM2, for analyzing candidate key mutations and epidemic trends. Analyzing multiple viruses demonstrated the functions and effectiveness of AutoVEM2.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

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Article Biochemistry & Molecular Biology

AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution

Binbin Xi et al.

Summary: With the global epidemic of SARS-CoV-2, monitoring the variation and key mutations of the virus is crucial for vaccine development and treatment updates. The AutoVEM tool efficiently analyzed over 131,576 genome sequences to reveal important mutation sites and discover potential new mutations related to infectivity and pathogenicity.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

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Article Biochemistry & Molecular Biology

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

Wael Kamel et al.

Summary: This study systematically identified the cellular and viral RNA-binding proteins involved in SARS-CoV-2 infection, revealing significant remodeling of the cellular RNA-bound proteome and potential new antiviral therapy targets. The research uncovered the regulatory role of tRNA ligase complex components in SARS-CoV-2 infection and demonstrated the inhibitory effect of drugs targeting host RBPs interacting with SARS-CoV-2 RNA on viral infection.

MOLECULAR CELL (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 Medicine, General & Internal