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Article
Infectious Diseases
Wayne F. Leung et al.
Summary: This article reports a case of a 21-year-old woman with refractory B-cell acute lymphocytic leukaemia who had a long-lasting infection of SARS-CoV-2. The patient remained positive for the virus by viral culture for 78 days and by PCR for 97 days. Sequencing analysis showed a dynamic repertoire of mutations over time.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Virology
Yotam Bronstein et al.
Summary: Immunocompromised patients are at increased risk of persistent COVID-19 disease. Two patients with hematologic malignancies hospitalized for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection showed viral evolution, including new spike gene mutations, following treatment with anti-SARS-CoV-2 antibodies preparations. These cases demonstrate the potential evolution of antibody-resistant SARS-CoV-2 infections in immunocompromised patients.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mahan Ghafari et al.
Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Akatsuki Saito et al.
Summary: During the COVID-19 pandemic, the B.1.617.2/Delta variant has been found to be highly fusogenic and more pathogenic in infected hamsters compared to prototypic SARS-CoV-2. The P681R mutation in the spike protein of this variant enhances viral fusogenicity and pathogenicity.
Article
Microbiology
Kathryn E. Kistler et al.
Summary: This study quantifies the impact of adaptive evolution on the accumulation of mutations in the genome of SARS-CoV-2 and identifies spike S1 protein as the focus of adaptive evolution. The study also reveals positively selected mutations in other proteins that are shaping the evolutionary trajectory of SARS-CoV-2.
CELL HOST & MICROBE
(2022)
Review
Immunology
Monica Fung et al.
Summary: The COVID-19 pandemic caused by SARS-CoV-2 has led to significant morbidity and mortality globally. The impact of the disease on immunosuppressed patients, such as cancer patients and transplant recipients, remains unclear. Further research is needed to determine the risk of COVID-19 severity and death in immunocompromised patients.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Immunology
Ji Hoon Baang et al.
Summary: This case illustrates challenges in managing immunocompromised hosts with chronic COVID-19, who may act as persistent shedders and sources of transmission. The patient's lack of seroconversion and prolonged course highlight the importance of humoral immunity in resolving viral infections.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Arif Canakoglu et al.
Summary: ViruSurf is a large public database containing viral sequences and curated metadata from various sources, offering complex search functionalities. It includes harmful virus species to humans and enables faster responses to potential threats from new viruses in the future.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Allison J. Greaney et al.
Summary: Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are key in neutralizing antibody responses, and a deep mutational scanning method was used to assess the impact of all amino-acid mutations in the RBD on antibody binding with 10 human monoclonal antibodies. The study identified the clustered escape mutations in different surfaces of the RBD that correspond to structurally defined antibody epitopes, showing that even antibodies targeting the same surface can have distinct escape mutations.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
Changshuo Wei et al.
Summary: The study suggests that the rapid accumulation of mutations in the SARS-CoV-2 Omicron variant may have originated from humans jumping to mice and then back to humans, indicating an inter-species evolutionary trajectory.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Editorial Material
Infectious Diseases
Ed Moran et al.
LANCET INFECTIOUS DISEASES
(2021)
Article
Immunology
Hassan Tarhini et al.
Summary: This study describes the clinical evolutions and viral mutations of 3 deeply immunocompromised patients, revealing prolonged infectious viral shedding in some cases. Understanding the mechanisms and frequency of prolonged infectiousness is crucial for optimizing isolation policies.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Liping Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Bin Zhou et al.
Summary: Research has shown that the D614G substitution in the spike protein of SARS-CoV-2 leads to increased binding and replication potential in humans, as well as significantly higher replication and transmissibility in different animal models, providing an explanation for the global prevalence of this variant in the COVID-19 pandemic.
Article
Multidisciplinary Sciences
Steven A. Kemp et al.
Summary: Chronic infection with SARS-CoV-2 can lead to viral evolution and increased resistance to neutralizing antibodies in immunosuppressed individuals treated with convalescent plasma. During convalescent plasma therapy, there were significant shifts in the viral population structure and sensitivity, suggesting strong selection pressure on the virus during treatment.
Article
Biochemistry & Molecular Biology
Carole H. Sudre et al.
Summary: Reports on long-lasting COVID-19 symptoms, known as 'long COVID', are increasing. Analysis of data from over 4,000 COVID-19 cases revealed that long COVID is more common in older individuals, those with higher body mass index, and females. Experiencing more than five symptoms in the first week of illness was associated with long COVID. A simple model showed promise in distinguishing between short and long COVID cases early in the disease.
Article
Biochemistry & Molecular Biology
Rita E. Chen et al.
Summary: The study analyzed antibody neutralization activity against a panel of authentic isolates and chimeric SARS-CoV-2 variants, showing significantly reduced neutralizing activity against the B.1.351 variant first identified in South Africa. Antibodies targeting the receptor-binding domain and N-terminal domain, monoclonal antibodies, convalescent sera, and mRNA vaccine-induced immune sera exhibited decreased inhibitory activity against viruses with an E484K spike mutation, suggesting a need for updated monoclonal antibodies or vaccine adjustments to prevent loss of protection against emerging variants.
Article
Biochemistry & Molecular Biology
Oscar A. MacLean et al.
Summary: The study suggests that SARS-CoV-2 has undergone limited significant adaptation to humans, with evidence of moderate positive selection concentrated in the early phases of the pandemic. In contrast, bat Sarbecoviruses show evidence of significant positive selection and an adaptive depletion in CpG composition. This indicates that the progenitor of SARS-CoV-2 likely acquired efficient human-human transmission capabilities through evolutionary history in bats, leading to the emergence of a relatively generalist virus.
Article
Immunology
Suzy E. Meijer et al.
Summary: Whole-genome sequencing played a crucial role in investigating a nosocomial outbreak, revealing unexpected connections between cases and transmission dynamics, while refuting initial hypotheses.
OPEN FORUM INFECTIOUS DISEASES
(2021)
Article
Microbiology
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.
Article
Medicine, General & Internal
Thao T. Truong et al.
Summary: The study highlights the concern that persistent infection of SARS-CoV-2 in immunocompromised hosts may lead to mutation accumulation and emergence of strains that evade immune responses. There is a need to reassess infection control precautions and consider routine surveillance of mutations for their potential impact on viral transmission and immune escape.
Article
Multidisciplinary Sciences
Delphine Planas et al.
Summary: The SARS-CoV-2 B.1.617 Delta variant, first identified in India in 2020, has become dominant in some regions and is spreading to many countries. This variant shows resistance to certain monoclonal antibodies and antibodies in convalescent sera, as well as reduced neutralization by some COVID-19 vaccines. Administration of two doses of the vaccine is needed for a neutralizing response against the Delta variant.
Review
Genetics & Heredity
Kaiming Tao et al.
Summary: The emergence of multiple SARS-CoV-2 variants has significant impacts on the epidemiological and clinical aspects of the COVID-19 pandemic, including increased virus transmission rates, heightened risk of reinfection, and reduced effectiveness of neutralizing antibodies and vaccines. These variants have introduced new challenges to COVID-19 research, necessitating additional avenues of laboratory, epidemiological, and clinical studies.
NATURE REVIEWS GENETICS
(2021)
Review
Microbiology
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)
Editorial Material
Medicine, General & Internal
Lawrence Corey et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Article
Multidisciplinary Sciences
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)
Article
Microbiology
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.
Article
Biology
Michael Barton et al.
Summary: The study analyzed the effects of mutations in the Spike protein of SARS-CoV-2 on its interaction with ACE2, finding that most mutations increased affinity with ACE2. Two ACE2 mutations were also found to enhance binding with the Spike protein.
Article
Microbiology
Liang Chen et al.
Summary: The study documented the microevolution of SARS-CoV-2 in an immunosuppressed patient undergoing steroid and convalescent plasma therapy, showing multiple NTD and RBD mutations. This suggests that immunocompromised patients may serve as breeding grounds for immune escape mutants, highlighting the need for enhanced measures to reduce transmission.
Article
Microbiology
Vitor Borges et al.
Summary: This study reports a case of a immunocompromised patient with a persistent SARS-CoV-2 infection over at least 6 months, showing the accumulation of mutations during the infection, some of which may be associated with immune evasion and enhanced transmission. Monitoring the evolution of SARS-CoV-2 in immunocompromised individuals is crucial to identify novel adaptive mutations and mitigate the risk of introducing highly evolved variants into the community. Tracking the within-patient evolution of SARS-CoV-2 is key to understanding its adaptive traits and anticipating the emergence of variants of concern.
Article
Virology
Aine O'Toole et al.
Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.
Article
Biochemistry & Molecular Biology
Laura Perez-Lago et al.
Summary: This study investigates the clinical profiles of severely immunosuppressed patients with prolonged shedding of SARS-CoV-2, revealing acquired viral diversity and different evolutionary dynamics within patients.
Article
Medicine, General & Internal
Yaping Wang et al.
Summary: Infection with the Delta variant of concern (VOC) is characterized by a shorter incubation period, higher viral load, and longer duration of viral shedding, with an increased risk of critical illness for patients over the age of 60, calling for more intensive prevention and control measures.
Article
Multidisciplinary Sciences
Petra Mlcochova et al.
Summary: The B.1.617.2 (Delta) variant of SARS-CoV-2 has lower sensitivity to antibodies and higher replication efficiency compared to other lineages, which may contribute to its dominance and reduced vaccine effectiveness, highlighting the need for continued infection control measures post-vaccination.
Article
Health Care Sciences & Services
Bjoern Jensen et al.
Summary: The study indicates that treatment of SARS-CoV-2 with bamlanivimab in immunocompromised patients may result in the rapid development of immune escape variants, which could have significant implications for the effectiveness of vaccination and antibody-based therapies.
LANCET REGIONAL HEALTH-EUROPE
(2021)
Review
Infectious Diseases
Muge Cevik et al.
Summary: This study aimed to characterize the viral load dynamics, duration of viral shedding, and viable virus shedding of SARS-CoV-2 in various body fluids. The findings suggest that while SARS-CoV-2 RNA shedding can be prolonged in respiratory and stool samples, the duration of viable virus shedding is relatively short-lived.
Letter
Respiratory System
Yu Fu et al.
EUROPEAN RESPIRATORY JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Tyler N. Starr et al.
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Biochemistry & Molecular Biology
Victoria A. Avanzato et al.
Letter
Medicine, General & Internal
Bina Choi et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2020)
Article
Microbiology
Maoz Gelbart et al.
Article
Computer Science, Artificial Intelligence
Scott M. Lundberg et al.
NATURE MACHINE INTELLIGENCE
(2020)
Article
Biochemical Research Methods
Xiaolong Zhang et al.
BMC BIOINFORMATICS
(2019)
Article
Biochemical Research Methods
James Hadfield et al.
Article
Multidisciplinary Sciences
Stefan Elbe et al.
Article
Biochemistry & Molecular Biology
Jamie R. Flammer et al.
MOLECULAR AND CELLULAR BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
MM Reily et al.