4.6 Article

Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture

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 Virology

Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs

Amit K. Maiti

Summary: SARS-CoV2 virus is believed to have originated from the closely related bat Coronavirus RaTG13 lineage, using its key entry-point residues in the S1 protein to attach to the human ACE2 receptor. Genetic data suggests that SARS-CoV2 had already originated long before its appearance in humans in 2019, and it has undergone mutations during human transmission.

VIRUS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Structure-Based Development of SARS-CoV-2 Spike Interactors

Flavia Squeglia et al.

Summary: The study engineered stable S-plug molecules through a computational approach to potentially inhibit viral entry by interfering with the interaction between SARS-CoV-2 spike protein and ACE2. These molecules have high stability and affinity to the spike protein, providing a solid foundation for the development of therapeutic and diagnostic tools against ACE2-accessing coronaviruses.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Review Microbiology

Molecular Virology of SARS-CoV-2 and Related Coronaviruses

Yu-An Kung et al.

Summary: This review discusses the molecular mechanisms of SARS-CoV-2 and related coronaviruses, with a focus on host factors or pathways identified through genome-wide CRISPR screening that can be targeted for the development of effective antiviral agents.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2022)

Article Microbiology

Profiling of SARS-CoV-2 Subgenomic RNAs in Clinical Specimens

Zigui Chen et al.

Summary: The expression profile of subgenomic RNAs (sgRNAs) of SARS-CoV-2 is associated with viral load, time of specimen collection after onset, age of the patient, and mutation. Using sgRNA as a biomarker may be an effective method for monitoring viral activity and the progression of COVID-19 infection.

MICROBIOLOGY SPECTRUM (2022)

Review Virology

SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis

Diego Menezes et al.

Summary: This study systematically reviewed and conducted a scientometric analysis of SARS-CoV-2 genomic surveillance studies in Brazil. The findings revealed 96 different strains, with VOC gamma, VOC delta, and VOI zeta being the most common. The states with the highest number of samples in published articles were Sao Paulo, Rio de Janeiro, and Minas Gerais. The study also discovered cases of co-infection, re-infection, and vaccine breakthrough.

VIRUSES-BASEL (2022)

Article Virology

Dynamics and Determinants of SARS-CoV-2 RT-PCR Testing on Symptomatic Individuals Attending Healthcare Centers during 2020 in Bahia, Brazil

Felicidade Mota Pereira et al.

Summary: This study used RT-PCR testing data to explore regional and individual determinants of test positivity in COVID-19 patients in the state of Bahia, Brazil. The study found that age and male gender were the most significant determinants of test positivity. There were differences in positivity rates among different socio-demographic strata, with higher rates in areas with low education levels during the first wave and in areas with higher education levels during the second wave. The positivity rates generally aligned with the state-level reported cases.

VIRUSES-BASEL (2022)

Article Virology

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Svetoslav Nanev Slavov et al.

Summary: Brazil, with one of the highest rates of COVID-19 infections and deaths, has implemented a successful vaccination program that reduced mortality and morbidity. The study conducted in the town of Serrana revealed that the vaccine campaign significantly reduced deaths and morbidity during the Gamma and Delta variants of concern (VOC). However, the Omicron VOC showed rapid substitution and morbidity rates despite vaccination.

VIRUSES-BASEL (2022)

Article Virology

Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil

Anna Carolina S. Dantas et al.

Summary: This study aimed to identify risk factors for mortality from SARS-CoV-2 infection, evaluate gene expression patterns of immune response pathways in COVID-19 patients, and identify circulating SARS-CoV-2 variants in a medium-sized city in Northeast Brazil. The study found that pre-existing comorbidity, male gender, cardiovascular disease, diabetes, chronic obstructive pulmonary disease, and PCR cycle threshold values under 22 were identified as risk factors for mortality. Furthermore, the study demonstrated that the severity of infection was associated with increased activation of inflammatory pathways, and multiple lineages of the virus were circulating.

VIRUSES-BASEL (2022)

Article Microbiology

Ubiquitination of SARS-CoV-2 ORF7a Prevents Cell Death Induced by Recruiting BclXL To Activate ER Stress

Zhixin Liu et al.

Summary: This study reveals that the ORF7a protein of SARS-CoV-2 induces cell apoptosis and endoplasmic reticulum stress by recruiting BclXL and utilizing the ubiquitin system. Understanding the mechanism of ORF7a's interaction with host cells provides a promising target for developing strategies to minimize the COVID-19 pandemic.

MICROBIOLOGY SPECTRUM (2022)

Article Immunology

Emergence of a Severe Acute Respiratory Syndrome Coronavirus 2 Virus Variant With Novel Genomic Architecture in Hong Kong

Herman Tse et al.

Summary: During the COVID-19 pandemic, various SARS-CoV-2 lineages have continuously evolved, with one variant being reported to have a unique genomic architecture characterized by missing genes and a new protein product due to partial duplication and transposition within the 5'-UTR.

CLINICAL INFECTIOUS DISEASES (2021)

Letter Virology

Genomic Characterization of a Novel SARS-CoV-2 Lineage from Rio de Janeiro, Brazil

Carolina M. Voloch et al.

JOURNAL OF VIROLOGY (2021)

Article Biochemistry & Molecular Biology

The SARS-CoV-2 subgenome landscape and its novel regulatory features

Dehe Wang et al.

Summary: Through next-generation sequencing, it was found that SARS-CoV-2 can generate diverse subgenomes through template switching. The majority of template switches result from RNA-RNA interactions, with terminal pairing status playing a key role.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

Analysis of SARS-CoV-2 infection dynamic in vivo using reporter-expressing viruses

Chengjin Ye et al.

Summary: The study presents a novel strategy placing reporter genes upstream of the highly expressed viral nucleocapsid gene to efficiently visualize SARS-CoV-2 in infected cells and organisms. Real-time viral infection can be tracked noninvasively using an in vivo imaging system, helping to identify neutralizing antibodies. The reporter-expressing rSARS-CoV-2 maintained pathogenicity and stability, supporting their use for investigating viral infection, dissemination, pathogenesis, and therapeutic interventions in vivo.

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

Article Infectious Diseases

A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay

Yanina Panzera et al.

Summary: The emergence of the Delta 12 variant with a 12-nucleotide deletion in ORF7a, resulting in a loss of 4 amino acids, is reported in this study. This variant was identified in a South American outbreak and phylogenetic analysis showed significant separation from other Uruguayan strains. The presence of molecular markers like this deletion is useful for tracking outbreaks and highlights the virus's ability to maintain functionality despite genetic material loss.

TRANSBOUNDARY AND EMERGING DISEASES (2021)

Article Multidisciplinary Sciences

Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14+ monocytes

Ziliang Zhou et al.

Summary: SARS-CoV-2 ORF7a interacts efficiently with human CD14(+) monocytes, triggering inflammatory responses such as decreased HLA expression and increased production of proinflammatory cytokines. This suggests that ORF7a may be a key immunomodulating factor in the severe immune response seen in COVID-19 patients.

ISCIENCE (2021)

Article Multidisciplinary Sciences

Characterization of an attenuated SARS-CoV-2 variant with a deletion at the S1/S2 junction of the spike protein

Pui Wang et al.

Summary: The study demonstrates that the cell-adapted SARS-CoV-2 variant Ca-DelMut replicates more efficiently than the wild-type virus and induces a strong neutralizing antibody and T cell response in hamsters, while causing no apparent pathological changes. Animals immunized with Ca-DelMut are fully protected with sterilizing immunity against subsequent wild-type SARS-CoV-2 challenge.

NATURE COMMUNICATIONS (2021)

Article Cell Biology

SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7a that limits immune suppression

Artem Nemudryi et al.

Summary: Over 950,000 whole-genome sequences of SARS-CoV-2 have been determined globally, providing crucial insights into the virus's transmission and evolution. Mutations in ORF7a have been found to affect the virus's ability to suppress the immune response, highlighting the importance of understanding viral mechanisms in combating COVID-19.

CELL REPORTS (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Virology

Replication Kinetics of B.1.351 and B.1.1.7 SARS-CoV-2 Variants of Concern Including Assessment of a B.1.1.7 Mutant Carrying a Defective ORF7a Gene

Alyssa T. Pyke et al.

Summary: The emergence of SARS-CoV-2 variants poses challenges to public health disease management, and the replication and evolutionary dynamics of the virus have important implications for the development of vaccines, antiviral therapies, and epidemiological control strategies for COVID-19.

VIRUSES-BASEL (2021)

Review Biochemistry & Molecular Biology

SARS-CoV-2: from its discovery to genome structure, transcription, and replication

Ayslan Castro Brant et al.

Summary: SARS-CoV-2 is a highly contagious respiratory virus causing adult atypical pneumonia COVID-19 with severe acute respiratory syndrome (SARS). This virus enters susceptible cells and directly translates polyproteins to initiate viral genome replication and transcription.

CELL AND BIOSCIENCE (2021)

Article Microbiology

Meta-Analysis and Structural Dynamics of the Emergence of Genetic Variants of SARS-CoV-2

Nicolas Castonguay et al.

Summary: This study analyzed the appearance and prevalence trajectory of mutations in all SARS-CoV-2 genes from December 2019 to April 2021. The goal was to identify the most frequent genetic modifications, study the dynamics of their propagation, incorporation into the consensus sequence, and their impact on virus biology. Additionally, the study analyzed the structural properties of spike glycoprotein of the B.1.1.7, B.1.351, and P.1 variants for their binding to the host receptor ACE2, offering insights into the impact of these mutations on neutralizing antibody therapeutics and vaccines.

FRONTIERS IN MICROBIOLOGY (2021)

Article Microbiology

Genome Sequences of Three SARS-CoV-2 ORF7a Deletion Variants Obtained from Patients in Hong Kong

Herman Tse et al.

Summary: The genome sequences of SARS-CoV-2 strains from three COVID-19 patients in Hong Kong displayed a shared 370-nucleotide deletion, leading to the complete loss of the ORF7a gene.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2021)

Article Medicine, Research & Experimental

Reduced subgenomic RNA expression is a molecular indicator of asymptomatic SARS-CoV-2 infection

Chee Hong Wong et al.

Summary: The study examined SARS-CoV-2 subgenomic RNAs (sgRNAs) in diagnostic samples from symptomatic and asymptomatic COVID-19 patients. Results showed a distinct pattern of sgRNA expression in symptomatic vs asymptomatic infections, as well as unique structural deletions in viral RNA from symptomatic individuals. These findings suggest that sgRNA expression and structural variations are correlated with the severity of clinical symptoms in SARS-CoV-2 infection and could potentially guide treatment responses, testing strategies, and vaccine development.

COMMUNICATIONS MEDICINE (2021)

Article Immunology

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao et al.

Summary: The study utilized deep meta-transcriptomic sequencing to identify SNP types and dynamics of SARS-CoV-2 mutations, revealing viral evolution during infection and independent compartmentalization of populations in different respiratory tissues. Positive selection amino acids and high-frequency alternate allele variants were observed in the virus genome.

VIRULENCE (2021)

Review Microbiology

Coronavirus biology and replication: implications for SARS-CoV-2

Philip V'kovski et al.

Summary: This review discusses key aspects of coronavirus biology and their implications for SARS-CoV-2 infections, treatment, and prevention strategies. Understanding virus-host interactions at the molecular level is crucial for developing effective intervention strategies. Summarizing the discoveries of SARS-CoV-2 infection and comparing it with other coronaviruses will support future preparedness and combat strategies.

NATURE REVIEWS MICROBIOLOGY (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 Architecture of SARS-CoV-2 Transcriptome

Dongwan Kim et al.

Editorial Material Multidisciplinary Sciences

Pathogenic T-cells and inflammatory monocytes incite inflammatory storms in severe COVID-19 patients

Yonggang Zhou et al.

NATIONAL SCIENCE REVIEW (2020)

Article Multidisciplinary Sciences

Structure of replicating SARS-CoV-2 polymerase

Hauke S. Hillen et al.

NATURE (2020)

Article Multidisciplinary Sciences

Virological assessment of hospitalized patients with COVID-2019

Roman Woelfel et al.

NATURE (2020)

Article Public, Environmental & Occupational Health

Variant analysis of SARS-CoV-2 genomes

Takahiko Koyama et al.

BULLETIN OF THE WORLD HEALTH ORGANIZATION (2020)

Article Multidisciplinary Sciences

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Darlan S. Candido et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

Omer Ziv et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication

Soren Alexandersen et al.

NATURE COMMUNICATIONS (2020)

Article Immunology

Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction

Siu-Ying Lau et al.

EMERGING MICROBES & INFECTIONS (2020)

Article Biochemical Research Methods

Parallelization of MAFFT for large-scale multiple sequence alignments

Tsukasa Nakamura et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

Nextstrain: real-time tracking of pathogen evolution

James Hadfield et al.

BIOINFORMATICS (2018)

Article Nursing

Middle East Respiratory Syndrome Coronavirus

Louise C. O'Keefe

WORKPLACE HEALTH & SAFETY (2016)

Article Virology

Continuous and Discontinuous RNA Synthesis in Coronaviruses

Isabel Sola et al.

ANNUAL REVIEW OF VIROLOGY, VOL 2 (2015)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Medicine, General & Internal

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

Ali Moh Zaki et al.

NEW ENGLAND JOURNAL OF MEDICINE (2012)

Letter Biotechnology & Applied Microbiology

Integrative genomics viewer

James T. Robinson et al.

NATURE BIOTECHNOLOGY (2011)

Article Biochemistry & Molecular Biology

Tetherin Inhibits HIV-1 Release by Directly Tethering Virions to Cells

David Perez-Caballero et al.

Article Biochemistry & Molecular Biology

SARS-CoV accessory protein 7a directly interacts with human LFA-1

Karen Haenel et al.

BIOLOGICAL CHEMISTRY (2007)

Article Biochemistry & Molecular Biology

Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein

CA Nelson et al.

STRUCTURE (2005)

Review Biochemistry & Molecular Biology

Severe acute respiratory syndrome

JSM Peiris et al.

NATURE MEDICINE (2004)

Article Respiratory System

SARS: Epidemiology

M Chan-Yeung et al.

RESPIROLOGY (2003)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)