4.5 Article

Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

The Emergence of SARS-CoV-2 Variants of Concern Is Driven by Acceleration of the Substitution Rate

John H. Tay et al.

Summary: The emergence of variants of concern (VOCs) in the ongoing SARS-CoV-2 pandemic can be attributed to an episodic increase in the substitution rate of the virus, which is around 4 times higher than the background rate estimate. This increase in substitution rate may have lasted for several weeks or months.

MOLECULAR BIOLOGY AND EVOLUTION (2022)

Article Medicine, General & Internal

Effectiveness of rAd26-rAd5, ChAdOx1 nCoV-19, and BBIBP-CorV vaccines for risk of infection with SARS-CoV-2 and death due to COVID-19 in people older than 60 years in Argentina: a test-negative, case-control, and retrospective longitudinal study

Analia Rearte et al.

Summary: The study conducted in Argentina demonstrated that the rAd26-rAd5, ChAdOx1 nCoV-19, and BBIBP-CorV vaccines, when administered to individuals aged 60 and above, effectively reduced the risk of SARS-CoV-2 infection and COVID-19 deaths.

LANCET (2022)

Article Virology

Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity

Alona Kuzmina et al.

Summary: This study assesses the impact of specific spike mutations carried by different viral variants on viral infectivity and neutralization sensitivity. The results show that individual mutations have no effect, but when combined with other mutations, viral infectivity and neutralization potential are enhanced or reduced. Similar analysis on the spike from Delta and Lota SARS-CoV-2 variants reveals different effects of specific RBD mutations on neutralization sensitivity and viral infectivity.

VIRUSES-BASEL (2022)

Article Multidisciplinary Sciences

Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7

Pengfei Wang et al.

Summary: The COVID-19 pandemic has had global repercussions, with promising vaccines and monoclonal antibody therapies. However, newly detected variants of SARS-CoV-2 present challenges to these treatment options.

NATURE (2021)

Article Microbiology

Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil

Paola Cristina Resende et al.

Summary: This study explores the origin and dissemination of the SARS-CoV-2 Brazilian lineage B.1.1.33, indicating that it may have emerged in Brazil in early February 2020 and subsequently evolved into a major circulating lineage. The lineage spread to various Brazilian regions and countries worldwide by March 2020, before air travel restrictions were implemented in Brazil. Public health interventions were partially effective in controlling the spread of lineage B.1.1.33, reducing its effective reproductive number by about 66% in Rio de Janeiro during March 2020, but failing to bring it below one. Continuous genomic surveillance of this lineage could provide valuable information on epidemic dynamics and the effectiveness of public health interventions in certain Brazilian states.

FRONTIERS IN MICROBIOLOGY (2021)

Article Virology

Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket

Anna Bertelli et al.

Summary: The Q675H spike mutation is a result of parallel evolution and enhances proteolytic exposure of the viral protein, promoting more efficient viral entry. This mutation is found in all variants of concern (VOCs) and suggests ongoing evolution of VOCs to improve viral fitness and adapt to the human host.

VIRUSES-BASEL (2021)

Article Biochemistry & Molecular Biology

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

Matthew McCallum et al.

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.
Review Biotechnology & Applied Microbiology

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Thomas P. Peacock et al.

Summary: SARS-CoV-2 virus is believed to have originated from animals and can cause a range of outcomes in humans, from asymptomatic cases to COVID-19. Over a year into the pandemic, the virus continues to mutate, driven by factors such as single nucleotide polymorphisms and insertions/deletions, which may impact its transmissibility and pathogenicity.

JOURNAL OF GENERAL VIROLOGY (2021)

Letter Microbiology

The Emergence of Sars-CoV-2 Variant Lambda (C.37) in South America

Pedro E. Romero et al.

MICROBIOLOGY SPECTRUM (2021)

Article Medicine, General & Internal

Cost-Effective Method to Perform SARS-CoV-2 Variant Surveillance: Detection of Alpha, Gamma, Lambda, Delta, Epsilon, and Zeta in Argentina

Carolina Torres et al.

Summary: Argentina conducted surveillance on SARS-CoV-2 variants, identifying Gamma and Lambda as the main variants, along with Alpha, Zeta, Epsilon, and more recently Delta. These variants predominated in different regions, with the emergence of Delta towards the end of the second wave, replacing Gamma and Lambda.

FRONTIERS IN MEDICINE (2021)

Article Multidisciplinary Sciences

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Nuno R. Faria et al.

Summary: A new variant of concern, P.1, with 17 mutations including three spike protein mutations associated with increased binding to human ACE2 receptors, emerged in Manaus, Brazil between November 2020 and January 2021. Molecular analysis suggests P.1 may be 1.7- to 2.4-fold more transmissible and that previous infection may provide 54 to 79% protection against P.1 infection compared to other lineages. Enhanced global genomic surveillance of such variants is crucial for pandemic response.

SCIENCE (2021)

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.
Article Biology

Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach

Reem Y. Aljindan et al.

Summary: COVID-19 is caused by the viral disease SARS-CoV-2, with mutations in the Spike-protein affecting the severity of infection. Understanding the interactions between viral proteins and host cells can provide insights into the pathological mechanisms of SARS-CoV-2 and aid in developing treatment strategies.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

Article Immunology

SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion

Isabella A. T. M. Ferreira et al.

Summary: The SARS-CoV-2 B.1.617 variant from India with key mutations L452R and E484Q shows reduced sensitivity to neutralizing antibodies elicited by the BNT162b2 mRNA vaccine, similar to the effect of L452R or E484Q mutations alone.

JOURNAL OF INFECTIOUS DISEASES (2021)

Article Cell Biology

Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection

Allison J. Greaney et al.

Summary: Vaccine-elicited antibodies have more focused neutralizing activity on the RBD of the SARS-CoV-2 spike protein, while infection-elicited antibodies have broader binding across epitopes; hence, single RBD mutations have less impact on neutralization by vaccine sera.

SCIENCE TRANSLATIONAL MEDICINE (2021)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

Qianqian Li et al.

Article Microbiology

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Andrew Rambaut et al.

NATURE MICROBIOLOGY (2020)

Article Multidisciplinary Sciences

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants

Bethany Dearlove et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biotechnology & Applied Microbiology

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

Michael R. Garvin et al.

GENOME BIOLOGY (2020)

Article Biochemical Research Methods

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics

Vladimir N. Minin et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemistry & Molecular Biology

Relaxed phylogenetics and dating with confidence

Alexei J. Drummond et al.

PLOS BIOLOGY (2006)