Related references
Note: Only part of the references are listed.
Article
Multidisciplinary Sciences
Emily E. Bendall et al.
Summary: Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of selection along a transmission chain. The transmission bottlenecks of non-VOC SARS-CoV-2 lineages and Alpha, Delta, and Omicron variants are similar, indicating that these tight bottlenecks will limit the spread of new mutations.
NATURE COMMUNICATIONS
(2023)
Letter
Virology
Serena Messali et al.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Review
Microbiology
Peter V. Markov et al.
Summary: In this Review, the evolution of SARS-CoV-2, the phases of the COVID-19 pandemic, factors driving virus evolution, and potential future scenarios and their health repercussions are explored. The mechanisms generating genetic variation in SARS-CoV-2 and the selective forces driving its evolution are examined. Uncertainties are evaluated and scenarios for the future evolutionary trajectories of SARS-CoV-2 are outlined.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
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.
Article
Immunology
Masaud Shah et al.
Summary: The new SARS-CoV-2 variant Omicron has enhanced transmissibility and multiple mutations that may weaken the effectiveness of therapeutic antibodies. Computational studies have shown that Omicron binds to ACE2 with a higher strength and specific mutations contribute significantly to the binding energies. These mutations also result in a drop in the electrostatic potential between RBDOmic and monoclonal antibodies, particularly etesevimab, bamlanivimab, and CT-p59. Sotrovimab, which targets a conserved epitope on the Spike protein, could be used as a cocktail therapy for Omicron-driven COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Public, Environmental & Occupational Health
Azfar D. Hossain et al.
Summary: Provider-initiated contact tracing can be an effective public health tool for controlling infectious diseases. However, the heterogeneity in contact tracing methods, scarcity of quantitative evidence on its effectiveness, and lack of specificity in tracing parameters important for disease control may limit authorities' ability to make informed decisions regarding its deployment.
LANCET PUBLIC HEALTH
(2022)
Article
Virology
Pilar Gallego-Garcia et al.
Summary: Understanding the transmission of SARS-CoV-2 is crucial for effective prevention measures. This study investigated the effectiveness of genomic sequencing in inferring transmission events. The research found that intrahost genomic variation in SARS-CoV-2 is limited, making it difficult to identify direct transmission events. The slow mutation rate, convergent events, and technical artifacts hinder the reliable reconstruction of transmission based solely on genomic data. Detailed contact tracing is essential for studying SARS-CoV-2 transmission at a high resolution.
Article
Virology
Serena Messali et al.
Summary: The first outbreak of SARS-CoV-2 B.1.1.7 lineage in Italy in January 2021 was characterized by high transmissibility and rapid dominance. Containment measures led to a decreasing epidemic curve, highlighting the importance of appropriate control and surveillance for restraining virus spread.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Virology
Francesca Caccuri et al.
Summary: A study found that there is a dynamic interplay between major and minor variants of the novel coronavirus in immunocompromised patients, with minor variants gradually replacing the major variant during infection and using different entry mechanisms into host cells. Minor variants may have a faster replication activity and induce specific viral RNA-sensing mechanisms, leading to increased interferon production. This finding may explain the rapid global spread of SARS-CoV-2 variants.
Article
Biochemical Research Methods
Niema Moshiri
Summary: ViralMSA is a user-friendly reference-guided MSA tool that allows for the alignment of large viral genome datasets efficiently, but it omits insertions with respect to the reference genome.
Article
Multidisciplinary Sciences
Claudia Alteri et al.
Summary: The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Using whole genome sequencing, researchers found multiple virus introductions into the region with transmission occurring before the first case was detected.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Houriiyah Tegally et al.
Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.
Article
Multidisciplinary Sciences
Mahesh S. Dhar et al.
Summary: Delhi experienced multiple severe outbreaks in 2020, reaching a seropositivity rate of >50% by 2021. The Delta variant's high transmissibility and immune evasion led to a surge in cases in Delhi.
Article
Multidisciplinary Sciences
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.
Article
Multidisciplinary Sciences
Daniel Butler et al.
Summary: By utilizing a fast colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling, the authors provide insights into the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Yanqun Wang et al.
Summary: The study investigates the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomical sites, revealing the co-existence of different genotypes within the same patient and a clear genetic differentiation between populations in the respiratory tract (RT) and gastrointestinal tract (GIT).
Article
Multidisciplinary Sciences
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.
Review
Medicine, Research & Experimental
Elmira Mohammadi et al.
Summary: Understanding the genetic diversity and mutations of SARS-CoV-2 can provide valuable insights for DNA-based diagnosis, antiviral drugs, and vaccine development for COVID-19.
BIOMEDICINE & PHARMACOTHERAPY
(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
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.
Article
Microbiology
Fengming Sun et al.
Summary: The study used single-molecule real-time technology to sequence the haplotypes of spike gene from 9 confirmed SARS-CoV-2 patients, revealing stable quasispecies structures and potential evolutionary advantages of minor mutants. The findings suggest that virus populations in different tissues/organs may replicate independently, and the quasispecies complexity of sputum samples is significantly lower than that of nasopharyngeal swabs.
MICROBIOLOGY SPECTRUM
(2021)
Article
Virology
James E. San et al.
Summary: The study demonstrates the importance of combining within-host diversity and bottleneck analysis for understanding transmission events in SARS-CoV-2 outbreaks. It provides insights into the maintenance of viral genetic diversity, identifies potential targets for positive selection, and shows that within-host variants can be transferred between patients. These findings will aid in developing strategies to comprehend transmission events and curb the spread of SARS-CoV-2.
Article
Virology
James E. San et al.
Summary: This study used high-throughput sequencing data and bottleneck analysis to trace the transmission pathways of the SARS-CoV-2 virus in two nosocomial outbreaks. The findings suggest that certain within-host variants may have been transmitted upon infection rather than arising de novo independently. By examining the mutational landscape, selection pressure, and diversity, new insights were provided into the transmission events of SARS-CoV-2 outbreaks.
Article
Biochemistry & Molecular Biology
Bui Quang Minh et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Fan Wu et al.
Article
Multidisciplinary Sciences
Xiaolu Tang et al.
NATIONAL SCIENCE REVIEW
(2020)
Article
Infectious Diseases
Tung Phan
INFECTION GENETICS AND EVOLUTION
(2020)
Editorial Material
Microbiology
Stephanie W. Lo et al.
NATURE REVIEWS MICROBIOLOGY
(2020)
Editorial Material
Multidisciplinary Sciences
Elizabeth C. Lee et al.
Article
Virology
Pavel Sagulenko et al.
Article
Virology
Ashley Sobel Leonard et al.
JOURNAL OF VIROLOGY
(2017)
Article
Medicine, Research & Experimental
Donghyun Park et al.
COLD SPRING HARBOR MOLECULAR CASE STUDIES
(2016)
Article
Virology
Mark P. Zwart et al.
ANNUAL REVIEW OF VIROLOGY, VOL 2
(2015)
Article
Biochemical Research Methods
Pablo A. Jaskowiak et al.
BMC BIOINFORMATICS
(2014)
Review
Microbiology
Esteban Domingo et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2012)
Article
Biochemical Research Methods
Mattia C. F. Prosperi et al.
BMC BIOINFORMATICS
(2011)
Article
Multidisciplinary Sciences
E Minskaia et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2006)
Letter
Medicine, General & Internal
DP Xu et al.
NEW ENGLAND JOURNAL OF MEDICINE
(2004)