Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

Article Multidisciplinary Sciences

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

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.

NATURE (2022)

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Article Multidisciplinary Sciences

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana et al.

Summary: The SARS-CoV-2 epidemic in southern Africa has experienced three distinct waves, driven by different variants. The recently identified Omicron variant has rapidly spread in South Africa and to numerous countries, raising global concern.

NATURE (2022)

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Article Biology

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e

Kathryn E. Kistler et al.

Summary: Seasonal coronaviruses, including OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein exposed to human immune response, potentially leading to reinfection. This adaptive change may require continual vaccine updates for effective protection against these viruses.

ELIFE (2021)

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Article Microbiology

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

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 (2021)

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Article Multidisciplinary Sciences

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Zijun Wang et al.

Summary: Volunteers who received the Moderna or Pfizer-BioNTech vaccine showed high levels of antibodies and memory B cell responses against SARS-CoV-2, with activity similar to individuals who had recovered from natural infection. However, their efficacy against specific SARS-CoV-2 variants was reduced, indicating a potential need for periodic updates to mRNA vaccines to maintain clinical efficacy.

NATURE (2021)

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Article Multidisciplinary Sciences

Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape

Kevin R. McCarthy et al.

Summary: The translation above discusses zoonotic pandemics caused by animal viruses spilling over into highly susceptible human populations, specifically focusing on the evolution of coronaviruses in human hosts and the impact of recurrent deletions in the spike glycoprotein on antibody epitopes. These studies help understand the antigenic evolution and adaptive evolution of SARS-CoV-2.

SCIENCE (2021)

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Article Multidisciplinary Sciences

A SARS-CoV-2 antibody curbs viral nucleocapsid protein-induced complement hyperactivation

Sisi Kang et al.

Summary: This study isolated and analyzed 32 N protein-specific monoclonal antibodies from a COVID-19 convalescent patient, shedding light on the response to the N protein. The complex structure of the mAb with the highest binding affinity revealed changes in epitopes and regulation of the antigen, affecting the N protein-induced complement hyperactivation.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

Irwin Jungreis et al.

Summary: Despite the clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. By comparing 44 Sarbecovirus genomes, a high-confidence protein-coding gene set is provided, characterizing protein-level and nucleotide-level evolutionary constraints, and prioritizing functional mutations from the ongoing COVID-19 pandemic.

NATURE COMMUNICATIONS (2021)

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Article Microbiology

A human coronavirus evolves antigenically to escape antibody immunity

Rachel T. Eguia et al.

Summary: This study investigates the evolution of human coronavirus 229E and finds that as the virus evolves, mutations in the spike protein can escape neutralization by antibodies in old human sera. The results suggest that viral evolution may impact immunity, highlighting the need for periodic updates to coronavirus vaccines.

PLOS PATHOGENS (2021)

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Article Biochemistry & Molecular Biology

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Darren P. Martin et al.

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.

CELL (2021)

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Article Multidisciplinary Sciences

Ongoing global and regional adaptive evolution of SARS-CoV-2

Nash D. Rochman et al.

Summary: The evolution of SARS-CoV-2 during the COVID-19 pandemic is primarily characterized by purifying selection, with a small number of sites evolving under positive selection. Variants in the spike protein's receptor-binding domain and the nucleocapsid protein region with NLS are enriched with positively selected amino acid replacements. These replacements form a connected network of apparent epistatic interactions and are indicators of major partitions in the SARS-CoV-2 phylogeny. The global virus diversity has been steadily increasing, with distinct periods based on phylogenetic distances and key mutations.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Editorial Material Microbiology

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Frank Konings et al.

Summary: A group convened and led by the Virus Evolution Working Group of the World Health Organization has announced a naming scheme to enable clear communication about SARS-CoV-2 variants of interest and concern.

NATURE MICROBIOLOGY (2021)

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Article Infectious Diseases