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Article
Public, Environmental & Occupational Health
Paul Elliott et al.
Summary: The REACT-1 Study funded by the Department of Health and Social Care in England aims to provide reliable data on the prevalence of SARS-CoV-2 infection over time and by location. The study collects data from random cross-sections of the population using the National Health Service list and disseminates the data through various channels. The study has important implications for public health, including providing real-time data on prevalence, vaccine effectiveness, symptom profiles, and the detection of new variants.
AMERICAN JOURNAL OF PUBLIC HEALTH
(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
Microbiology
Helen R. Fryer et al.
Summary: This study examines the impact of viral variation, age, and vaccine status on within-host viral burden based on a large, population-representative survey conducted in the UK. The findings show that viral burden increases with age, is reduced by vaccination, and is influenced by the interplay of vaccination status and viral variant. A novel method was also developed to account for bias in sampled viral burden.
Article
Biochemistry & Molecular Biology
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
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
Lennard Y. W. Lee et al.
Summary: The study found that the infectivity of SARS-CoV-2 varies with case viral load, contact event type, and age. Those with high viral loads are the most infectious. The B.1.1.7 variant increases transmission by 50%. The best performing LFDs can detect most infectious cases.
CLINICAL INFECTIOUS DISEASES
(2022)
Editorial Material
Biochemistry & Molecular Biology
Lorenzo Subissi et al.
Article
Multidisciplinary Sciences
Yun Lin et al.
Summary: Analysis of viral load data on confirmed cases can improve real-time estimation of the reproductive number, enabling more timely tracking of epidemic dynamics.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Houriiyah Tegally et al.
Summary: The genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth wave of the COVID-19 pandemic in South Africa, reveals their continued viral diversification and sheds light on the potential mechanisms that allow these new lineages to outcompete their predecessors. These new lineages, BA.4 and BA.5, share identical spike proteins with BA.2 but have certain differences such as the presence of the 69-70 deletion, L452R, F486V, and the wild-type amino acid at Q493. They can be identified by the S-gene target failure, a proxy marker associated with the 69-70 deletion. BA.4 and BA.5 have rapidly replaced BA.2 and have become the dominant lineages in South Africa.
Article
Virology
Richard A. Neher
Summary: Continued evolution and adaptation of SARS-CoV-2 has led to the emergence of more transmissible and immune evasive variants, with profound impact on the course of the pandemic. The evolution of the virus over 2.5 years since its emergence was analyzed, and the rates of synonymous and non-synonymous changes were estimated separately for evolution within clades and for the pandemic overall. The study found that the rate of synonymous mutations is around 6 changes per year, while the rate of non-synonymous mutations is estimated to be about 26 amino acid changes per year. This suggests that the evolutionary process of the different variants is qualitatively different from that in typical transmission chains and is likely dominated by adaptive evolution.
Article
Virology
Verity Hill et al.
Summary: The text discusses the origin and characteristics of the first designated variant of concern (VOC) of SARS-CoV-2, Alpha, and its rapid global spread. It explores the sampled sequences ancestral to Alpha and proposes explanations for how Alpha acquired numerous mutations while remaining largely undetected in a region with high genomic surveillance. The study also compares the ancestral branches and mutation profiles of other VOCs, highlighting the distinctiveness of the Delta variant.
Review
Virology
Vinicius Bonetti Franceschi et al.
Summary: Population-based prevalence surveys of Covid-19 from 37 studies in 19 countries revealed that most studies were from Europe and America, using antibody testing with highly variable sample sizes and prevalence estimates. Minority communities were disproportionately affected, and important risks of bias were detected in sample size, data analysis, standard measurements, and response rates. Few consistent patterns for high risk of bias were found, with intermediate risk related to American and European studies, municipal initiatives, blood samples, and prevalence above 1%. Low risk of bias was associated with Asian studies, nationwide initiatives, RT-PCR tests, and prevalence below 1%. Identifying methodological standards may assist in future population-based surveys.
REVIEWS IN MEDICAL VIROLOGY
(2021)
Article
Public, Environmental & Occupational Health
Koen B. Pouwels et al.
Summary: This study in England found significant changes in the number of individuals testing positive for SARS-CoV-2 and risk factors for positivity over time from April to November 2020. Important risk factors for testing positive varied between the first and second waves, with age being a key driver of increased positivity rates in the second wave. Continued monitoring for SARS-CoV-2 in the community will be important for managing the COVID-19 pandemic moving forwards.
LANCET PUBLIC HEALTH
(2021)
Article
Biochemistry & Molecular Biology
Emma C. Thomson et al.
Summary: SARS-CoV-2 virus can mutate and evade immunity, with mutations like N439K conferring resistance against neutralizing monoclonal antibodies and enhancing binding affinity to hACE2 receptor. Despite similar in vitro replication fitness and clinical outcomes compared to wild type, N439K mutation highlights the importance of ongoing molecular surveillance for guiding vaccine and therapeutic development and usage.
Article
Medicine, General & Internal
Raphael Sonabend et al.
Summary: The study assessed the UK Government's four-step process to easing lockdown restrictions in England, taking into account the impact of the Delta variant and other factors. The findings suggest that the risk of a large wave of COVID-19 hospital admissions resulting from lifting NPIs can be mitigated but there is substantial uncertainty in the epidemic trajectory due to the emergence of the Delta variant.
Article
Multidisciplinary Sciences
Harald S. Vohringer et al.
Summary: The study analyzed the dynamics of different lineages in English local authorities using real-time genomic data. The findings showed significant fluctuations in transmissibility and proportions of different variants over time, with Delta variant rapidly increasing in early summer 2021.
Letter
Medicine, General & Internal
Manoj Mohanan et al.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2021)
Article
Immunology
Michael Kidd et al.
Summary: Analysis of recent test data shows that samples containing the SARS-CoV-2 variant B1.1.7 with mutation Delta 69/70 exhibit S gene target failure (SGTF) in ThermoFisher TaqPath RT-qPCR. Samples with SGTF profile are more likely to have higher viral loads, indicating higher infectivity and rapid spread of this variant.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Nicholas G. Davies et al.
Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.
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
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.
Article
Multidisciplinary Sciences
Nicholas G. Davies et al.
Summary: Studies have shown that the SARS-CoV-2 B.1.1.7 lineage is more transmissible and may cause more severe illness compared to pre-existing variants.
Article
Multidisciplinary Sciences
Erik Volz et al.
Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.
Article
Genetics & Heredity
Yatish Turakhia et al.
Summary: UShER is an efficient method that aids in real-time analysis of viral evolution during the COVID-19 pandemic by facilitating the addition of new SARS-CoV-2 genome sequences onto the existing phylogeny. The unprecedented accumulation of viral genome sequences is leading to a new era of 'genomic contact tracing' using viral genomes to trace local transmission dynamics. UShER addresses the challenge of placing new sequences onto the already large viral phylogeny, thus improving the speed of phylogenetic placement and data visualization for real-time contact tracing.
Article
Biochemistry & Molecular Biology
Chantal B. F. Vogels et al.
Summary: With the emergence of SARS-CoV-2 variants with increased transmissibility and immune escape, targeted surveillance is urgently needed. The B.1.1.7 variant can be detected by a specific deletion in the spike gene, but other variants like B.1.351 and P.1 cannot. An open-source PCR assay targeting a deletion in the ORF1a gene has been designed and validated to enhance surveillance for these variants.
Article
Multidisciplinary Sciences
Philippe Lemey et al.
Summary: In late summer 2020, more than half of the SARS-CoV-2 lineages circulating in many European countries resulted from new introductions, and the success in onward transmission of these newly introduced lineages was negatively associated with the local incidence of COVID-19. The widespread dissemination of variants in summer 2020 highlights the threat of viral spread when restrictions are lifted.
Article
Multidisciplinary Sciences
Emma B. Hodcroft et al.
Summary: A variant of SARS-CoV-2, 20E (EU1), was identified in Spain in early summer 2020 and later spread across Europe. Despite not showing increased transmissibility, the variant's success can be attributed to rising incidence in Spain, resumption of travel, and lack of effective screening and containment measures. Travel played a significant role in introducing the variant multiple times to European countries during the summer, undermining local efforts to prevent SARS-CoV-2 infection.
Review
Biochemistry & Molecular Biology
Bas B. Oude Munnink et al.
Summary: This review summarizes the current knowledge on key viral mutations and variants, emphasizing the need for a systematic approach to link global genomic surveillance with timely assessment of the phenotypic characteristics of novel variants in preparation for the next phase of the pandemic.
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)
Review
Multidisciplinary Sciences
Pratha Sah et al.
Summary: Quantification of asymptomatic infections is crucial for effective public health responses to the COVID-19 pandemic. Analyzing over 350 studies, it was estimated that 35.1% of infections never developed clinical symptoms and were truly asymptomatic. At the time of testing, 42.8% of cases showed no symptoms, including both asymptomatic and presymptomatic infections.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Moritz U. G. Kraemer et al.
Summary: Understanding the spatial invasion dynamics of the B.1.1.7 lineage, researchers found a multistage process with early growth rates linked to human mobility and asymmetric lineage export from dominant source locations. Additionally, they explored how the spread of B.1.1.7 was influenced by nonpharmaceutical interventions and spatial variation in previous attack rates. The study emphasizes the importance of considering behavioral and epidemiological contexts in accurately interpreting the growth rates of emerging variants of concern.
Article
Multidisciplinary Sciences
James A. Hay et al.
Summary: Population distribution of viral loads changes during an epidemic, and Ct values from random samples can improve estimates of an epidemic's trajectory. Combining data from multiple samples enhances the precision and robustness of estimation. These methods can be applied to real-time estimates of epidemic trajectories for outbreak management and response.
Article
Cell Biology
Bo Meng et al.
Summary: The Delta H69N70 mutation in SARS-CoV-2 spike protein increases infectivity and partially rescues immune escape mutations that impair infectivity. Continued surveillance and research on deletions with functional effects are necessary.
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
Bui Quang Minh et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Microbiology
Andrew Rambaut et al.
NATURE MICROBIOLOGY
(2020)
Article
Microbiology
David Bonsall et al.
JOURNAL OF CLINICAL MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Sean L. Wu et al.
NATURE COMMUNICATIONS
(2020)
Review
Public, Environmental & Occupational Health
M. U. G. Kraemer et al.
EPIDEMIOLOGY AND INFECTION
(2019)
Article
Virology
Lei Zhao et al.
Article
Virology
Chris Wymant et al.
Article
Virology
Pavel Sagulenko et al.
Article
Ecology
Guangchuang Yu et al.
METHODS IN ECOLOGY AND EVOLUTION
(2017)
Article
Biochemistry & Molecular Biology
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION
(2013)
