4.6 Review

Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking

Related references

Note: Only part of the references are listed.
Editorial Material Microbiology

SARS-CoV-2 Africa dashboard for real-time COVID-19 information

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Summary: The SARS-CoV-2 Africa dashboard is a customizable tool that provides visual representation of SARS-CoV-2 genomic information in African countries. It allows users to see the number of sequences deposited in each country and track the circulating variants. This dashboard enables real-time exploration of public data to assist policymakers, healthcare professionals, and the general public in understanding the ongoing pandemic.

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Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

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Summary: The hypothesis of chronic infection for the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is gaining credibility with the appearance of Omicron. In this study, we investigate the intrahost evolution and genetic diversity of lineage B.1.517 during a 471-day-long (and ongoing) SARS-CoV-2 chronic infection. We find an accelerated virus evolutionary rate within the host, resulting in the emergence and persistence of genetically distinct genotypes. Our findings highlight the role of untreated chronic infections in accelerating SARS-CoV-2 evolution and the emergence of genetically divergent variants.

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Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources

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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

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

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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.

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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

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Towards SARS-CoV-2 serotypes?

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Summary: This article discusses the immune evasion capabilities of Omicron and raises the question of whether it should be considered as a distinct SARS-CoV-2 serotype. It presents lines of evidence both supporting and against the concept of SARS-CoV-2 serotypes and discusses the implications of this classification.

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The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data

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Summary: The COVID-19 pandemic has led to widespread use of SARS-CoV-2 genome sequencing for epidemiological tracking and variant identification. The Ensembl COVID-19 browser, the first virus to be included in the Ensembl platform, provides multiple variant sets and annotations from relevant resources for SARS-CoV-2 research.

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VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes

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Summary: This research established an evaluation and prewarning system to monitor the genomic variation risks of SARS-CoV-2. It analyzed the effects of known and virtual variations on viral properties from the perspectives of genomics and structural biology, and verified the effectiveness of these characteristics for risk prediction using an artificial intelligence algorithm.

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Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California

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BMC PUBLIC HEALTH (2022)

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Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

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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.

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Where is the next SARS-CoV-2 variant of concern?

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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Darren P. Martin et al.

Summary: This study found 13 rare mutations among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene, which may impact important regions and functions of the S-gene. The mutations were predicted to decrease the fitness of the virus they occurred in prior to the emergence of Omicron. The study also suggests that the mutations in each cluster interact cooperatively to alter the function of Spike. Understanding how these complex and highly adaptive mutation constellations were assembled in the Omicron S-gene, and why they went undetected in the early stages, is crucial.

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Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

Philip L. Tzou et al.

Summary: The Stanford Coronavirus Resistance Database (CoV-RDB) collects and curates published data on the neutralizing susceptibility of SARS-CoV-2 variants and spike mutations to antibodies. The database provides an interactive interface for displaying neutralization data at different levels of granularity and offers a sequence analysis program to assist users in determining mutation-detection thresholds.

PLOS ONE (2022)

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Detecting Potentially Adaptive Mutations from the Parallel and Fixed Patterns in SARS-CoV-2 Evolution

Cheng-Yang Ji et al.

Summary: This article proposes a computational strategy to detect potentially adaptive mutations from the phylogenetic trajectory and identifies important sites that have experienced paraFix mutations in the dynamic evolution of SARS-CoV-2. These findings provide valuable clues for disease control and prevention.

VIRUSES-BASEL (2022)

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Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host

Sissy Therese Sonnleitner et al.

Summary: This study reports the occurrence of SARS-CoV-2 immune escape mutations in an immunocompromised patient with prolonged viral shedding. The results suggest that specific mutations may confer a fitness advantage to the virus and could be potential targets for future vaccine and therapeutic development for COVID-19.

NATURE COMMUNICATIONS (2022)

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The Evolution and Biology of SARS-CoV-2 Variants

Amalio Telenti et al.

Summary: The study of the genetics and evolution of the SARS-CoV-2 virus has played a crucial role in our understanding of the COVID-19 pandemic, providing real-time tracking of its global spread and adaptations to the human population. The virus has shown high transmissibility and has evolved new variants optimized for human-to-human transmission. Understanding the genetic makeup of the virus and its interactions with the human host is important for predicting and responding to new variants, as well as informing vaccine development.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2022)

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Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host

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.

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Taxonium, a web-based tool for exploring large phylogenetic trees

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Summary: The COVID-19 pandemic has generated an unprecedented amount of sequencing data for SARS-CoV-2, leading to the need for a scalable tool for exploring phylogenetic trees. Taxonium is a new tool that uses WebGL to enable the exploration of large trees with millions of nodes in the browser. This article describes the insights gained from analyzing a tree of five million sequences and provides a tool for exploring a public tree of over five million SARS-CoV-2 sequences.

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Context-specific emergence and growth of the SARS-CoV-2 Delta variant

John T. McCrone et al.

Summary: The globally spread SARS-CoV-2 Delta variant of concern has caused resurgences of COVID-19 worldwide. In England, the Delta variant was introduced through travel and social restrictions relaxation and spread through increased human activity. Hotel quarantine for travelers helped reduce importation transmission, but the Delta transmission chains were already established before travel restrictions were implemented. Increased inter-regional travel and local population mixing were key factors in the nationwide dissemination of Delta.

NATURE (2022)

Article Biochemistry & Molecular Biology

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

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.

NATURE MEDICINE (2022)

Article Biochemistry & Molecular Biology

Drivers of adaptive evolution during chronic SARS-CoV-2 infections

Sheri Harari et al.

Summary: In immunocompromised patients with chronic SARS-CoV-2 infection, adaptive evolution occurs and some mutations may lead to the emergence of variants of concern. However, certain mutations associated with global transmission are absent in chronic infections. The study also found a strong correlation between viral rebound and antibody evasion. The findings suggest a tradeoff between antibody evasion and transmissibility, highlighting the importance of monitoring chronic infections for understanding the emergence of variants of concern.

NATURE MEDICINE (2022)

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Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution

Tyler N. Starr et al.

Summary: This study investigates the impact of mutations in the spike receptor-binding domain (RBD) of SARS-CoV-2 on its affinity for the ACE2 receptor and antibody recognition, as well as their implications for future evolution and interaction. The findings reveal that certain mutations cause shifts in the effects of mutations at other sites, shaping the evolutionary path of the virus.

SCIENCE (2022)

Article Virology

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

William W. Hannon et al.

Summary: Using deep sequencing, researchers investigated the transmission of viral genetic variation among infected crew members during a SARS-CoV-2 outbreak. They found that the within-host viral diversity was low and occasional fixation of low-frequency mutations during transmission dominated viral evolution.

VIRUS EVOLUTION (2022)

Article Virology

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Sam A. J. Wilkinson et al.

Summary: Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. This study aims to rectify this and study the genomics of this patient group. Spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots, and numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally, a mutation in the envelope gene, T30I, was determined to be the second most frequent recurrently occurring mutation in persistent infections. Many recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimization.

VIRUS EVOLUTION (2022)

Article Virology

covSampler: A subsampling method with balanced genetic diversity for large-scale SARS-CoV-2 genome data sets

Yexiao Cheng et al.

Summary: A subsampling method named covSampler was developed for SARS-CoV-2 genome sequences, taking into account both their spatiotemporal distribution and genetic diversity. The method is efficient and stable, with customizable options for users. This work provides an easy-to-use tool and webserver for subsampling SARS-CoV-2 genome sequences.

VIRUS EVOLUTION (2022)

Letter Immunology

Highly Divergent SARS-CoV-2 Alpha Variant in Chronically Infected Immunocompromised Person

Bas B. Oude Munnink et al.

Summary: This study reports the detection of a highly divergent SARS-CoV-2 Alpha variant in an immunocompromised patient several months after the latest detection of the Alpha variant in the Netherlands. The patient remained infected for 42 weeks despite multiple treatment regimens and the disappearance of most clinical symptoms. Several potential immune escape mutations were identified in the spike protein.

EMERGING INFECTIOUS DISEASES (2022)

Article Virology

Contributions of adaptation and purifying selection to SARS-CoV-2 evolution

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.

VIRUS EVOLUTION (2022)

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The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

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.

VIRUS EVOLUTION (2022)

Article Virology

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

Mahan Ghafari et al.

Summary: The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Research suggests that these variants likely evolved within single individuals with long-term infections.

FRONTIERS IN VIROLOGY (2022)

Article Virology

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

Jakob McBroome et al.

Summary: This paper presents a fast and efficient heuristic method for phylogenetic analysis to identify newly introduced viral strains. It also introduces Cluster-Tracker, an interactive web-based tool for exploring and visualizing SARS-CoV-2 geographic data in the USA.

VIRUS EVOLUTION (2022)

Article Virology

An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain

Allison J. Greaney et al.

Summary: This study develops an "escape estimator" by aggregating deep mutational scanning data to predict the impact of viral mutations on antibody recognition and score the antigenic effect of mutation combinations. The scores from the estimator correlate with neutralization assays, highlighting the concerning antigenic properties of the Omicron variant.

VIRUS EVOLUTION (2022)

Article Virology

Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution

Daniele Ramazzotti et al.

Summary: This study shows that synonymous mutations in SARS-CoV-2 increase its adaptation to human codon usage, potentially improving its effectiveness in infecting humans.

VIRUS EVOLUTION (2022)

Review Biochemical Research Methods

Web tools to fight pandemics: the COVID-19 experience

Daniele Mercatelli et al.

Summary: The ongoing outbreak of COVID-19 has led to an unprecedented scientific response globally, resulting in a vast amount of publicly available epidemiological, biological, and clinical data. Bioinformatics scientists have swiftly developed online tools for non-computational users to analyze such data, with a focus on fields like epidemiology, genomics, interactomics, and pharmacology. This review catalogs the most popular web tools for COVID-19 research and analysis to provide a comprehensive overview of the current state of online resources for COVID-19.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Immunology

Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco

Gabriel Chamie et al.

Summary: During the shelter-in-place mandates in San Francisco, diverse lineages of SARS-CoV-2 infections continued circulating among low-income Latinx individuals who were unable to work from home and maintain income.

CLINICAL INFECTIOUS DISEASES (2021)

Review Biochemical Research Methods

A review on viral data sources and search systems for perspective mitigation of COVID-19

Anna Bernasconi et al.

Summary: With the outbreak of COVID-19, the research community is making unprecedented efforts to understand and mitigate the impact of the pandemic. Organizations are focusing on COVID-19 virus data and services, while new organizations and resources are emerging to lay the groundwork for future pandemic studies.

BRIEFINGS IN BIOINFORMATICS (2021)

Review Biochemical Research Methods

Bioinformatics resources for SARS-CoV-2 discovery and surveillance

Tao Hu et al.

Summary: In early 2020, the novel coronavirus responsible for the pneumonia outbreak in Wuhan was identified using NGS and bioinformatics pipelines. These technologies are now being used globally for genomic surveillance of SARS-CoV-2, tracking its spread, evolution, and global variation patterns, with a focus on technical advancements needed for future infectious disease outbreaks.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Microbiology

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

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)

Editorial Material Medicine, General & Internal

Genetic Variants of SARS-CoV-2-What Do They Mean?

Adam S. Lauring et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

Article Biochemistry & Molecular Biology

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Benoit Morel et al.

Summary: Inferring reliable phylogenies from virus sequence data is difficult due to the large number of sequences and low number of mutations; rooting the inferred phylogeny with external outgroups or applying novel computational methods is not credible; automatic classification of current sequences into subclasses for molecular species delimitation is also not possible due to sequences being too closely related.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Multidisciplinary Sciences

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Jacob E. Lemieux et al.

Summary: Analysis of 772 complete genomes of SARS-CoV-2 from early in the Boston-area epidemic shows multiple introductions of the virus, with two distinct superspreading events. One at a nursing facility resulted in rapid transmission and significant mortality, while the other at an international business conference led to sustained community transmission and widespread spread. The genetic variation generated by these events differed substantially, indicating varying transmission dynamics in superspreading events.

SCIENCE (2021)

Editorial Material Microbiology

One year of SARS-CoV-2 evolution

Aiping Wu et al.

Summary: Since the outbreak of the COVID-19 pandemic caused by SARS-CoV-2, the viral genome has undergone multiple mutations that may enhance transmission. One year later, continued analysis of emergent SARS-CoV-2 genome sequences aims to enhance understanding of the virus's evolution.

CELL HOST & MICROBE (2021)

Article Microbiology

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

Allison J. Greaney et al.

Summary: The evolution of SARS-CoV-2 may impact the recognition of the virus by human antibody-mediated immunity, with mutations affecting antibody binding varying significantly among individuals and within the same individual over time. Despite this variability, mutations that greatly reduce antibody binding usually occur at specific sites in the RBD, with E484 being the most crucial. These findings can inform surveillance efforts for SARS-CoV-2 evolution in the future.

CELL HOST & MICROBE (2021)

Editorial Material Multidisciplinary Sciences

Want to track pandemic variants faster? Fix the bioinformatics bottleneck Comment

Emma B. Hodcroft et al.

Summary: Researchers are in need of new approaches to control the pandemic as existing tools, rules, and incentives are struggling to cope with the flood of coronavirus genome sequences.

NATURE (2021)

Article Multidisciplinary Sciences

Detection of a SARS-CoV-2 variant of concern in South Africa

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.

NATURE (2021)

Article Multidisciplinary Sciences

SARS-CoV-2 within-host diversity and transmission

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.

SCIENCE (2021)

Article Genetics & Heredity

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients

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).

GENOME MEDICINE (2021)

Article Biology

COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

Albert Tian Chen et al.

Summary: COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations, lineages, and clades using the GISAID database. Users can query SNVs across different regions, mutations impacting diagnostic sensitivity, and the emergence of dominant lineages. The platform will be upgraded with new features to rapidly pinpoint mutations as the virus evolves and in response to interventions.

ELIFE (2021)

Article Multidisciplinary Sciences

Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants

Sebastian Weigang et al.

Summary: In a longitudinal case study, researchers demonstrate that SARS-CoV-2 variants with reduced sensitivity to neutralizing antibodies can evolve within persistently infected immunosuppressed patients. The study suggests that immunocompromised patients may serve as a potential source for the emergence of harmful variants, although immune control against these variants can still be achieved in some cases through the generation of neutralizing antibodies upon lowering immunosuppressive treatment.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Tara Alpert et al.

Summary: The study found that the SARS-CoV-2 B.1.1.7 variant primarily spread in the United States through ports of entry in New York, California, and Florida, with multiple independent establishments starting in early December 2020 and interstate spread by the end of the month. It is projected that B.1.1.7 will become the dominant lineage in many states by mid- to late March, highlighting the urgent need to enhance genomic surveillance.
Article Biochemistry & Molecular Biology

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Nicole L. Washington et al.

Summary: The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has been spreading in the United States with multiple introductions as early as late November 2020. The variant shows a logistic growth rate with roughly weekly doubling and increased transmission, requiring immediate action to minimize COVID-19 morbidity and mortality.
Article Biotechnology & Applied Microbiology

Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries

Rui Wang et al.

Summary: The study reveals many mutations on the RBD of the S protein, with the majority strengthening the binding between the RBD and host ACE2, indicating an evolution towards more infectious variants. Additionally, certain mutations found in different variants may weaken the binding between the RBD and antibodies, potentially compromising existing vaccines and antibody therapies. The study also identifies potential vaccine escape mutations that could pose a threat to current vaccines and antibody treatments.

GENOMICS (2021)

Article Public, Environmental & Occupational Health

Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster — Nebraska, November–December 2021

Lauren Jansen et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2021)

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)

Article Genetics & Heredity

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

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.

NATURE GENETICS (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 Biochemistry & Molecular Biology

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

Jakob McBroome et al.

Summary: A database of SARS-CoV-2 phylogenetic trees inferred with public sequences is presented, updated daily to include new sequences and encoded in MAT format. The researchers also introduce matUtils software for querying and manipulating the MATs efficiently.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Review Microbiology

Structural biology of SARS-CoV-2 and implications for therapeutic development

Haitao Yang et al.

Summary: The COVID-19 pandemic caused by SARS-CoV-2 has led to an unprecedented global health crisis, with limited therapeutic options available. Understanding the structure and function of the 29 proteins encoded by SARS-CoV-2 is crucial for developing novel therapeutics and treatment interventions. These proteins play various roles in the viral life cycle, from entry into host cells to genome replication and transcription, highlighting their potential as targets for therapeutic interventions.

NATURE REVIEWS MICROBIOLOGY (2021)

Editorial Material Medicine, General & Internal

SARS-CoV-2 Variants in Patients with Immunosuppression

Lawrence Corey et al.

NEW ENGLAND JOURNAL OF MEDICINE (2021)

Article Multidisciplinary Sciences

Ongoing global and regional adaptive evolution of SARS-CoV-2

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 Multidisciplinary Sciences

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

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.

SCIENCE (2021)

Article Microbiology

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

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.

PLOS PATHOGENS (2021)

Article Biology

Patterns of within-host genetic diversity in SARS-CoV-2

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.

ELIFE (2021)

Editorial Material Microbiology

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Frank Konings et al.

Summary: A group convened and led by the Virus Evolution Working Group of the World Health Organization has announced a naming scheme to enable clear communication about SARS-CoV-2 variants of interest and concern.

NATURE MICROBIOLOGY (2021)

Article Virology

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

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.

VIRUS EVOLUTION (2021)

Article Virology

CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

Roux-Cil Ferreira et al.

Summary: A new method utilizing Python has been developed to rapidly analyze and visualize a large number of SARS-CoV-2 genomes, allowing for quick assessment of virus variants. The use of weighted feature sets to generate distance matrices has enabled the construction of neighbor-joining trees for each lineage.

VIRUS EVOLUTION (2021)

Article Health Care Sciences & Services

Complementation of contact tracing by mass testing for successful containment of beta COVID-19 variant (SARS-CoV-2 VOC B.1.351) epidemic in Hong Kong

Vincent Chi-Chung Cheng et al.

Summary: This study successfully prevented local transmission of SARS-CoV-2 Variants of Concern (VOCs) in a densely populated city with low herd immunity for COVID-19 through contact tracing, quarantine, rapid genome sequencing complemented by mass testing. Systematic epidemic control measures are crucial in controlling virus transmission in densely populated areas.

LANCET REGIONAL HEALTH-WESTERN PACIFIC (2021)

Letter Immunology

SARS-CoV-2 Superspread in Fitness Center, Hong Kong, China, March 2021

Daniel K. W. Chu et al.

Summary: The study on a superspreading event at a fitness center in Hong Kong highlighted the risk of virus transmission in confined spaces with poor ventilation and limited public health interventions. Through genomic sequencing analysis, the research confirmed the importance of addressing these factors to prevent future outbreaks.

EMERGING INFECTIOUS DISEASES (2021)

Article Virology

Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa

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.

VIRUS EVOLUTION (2021)

Article Chemistry, Multidisciplinary

Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies

Jiahui Chen et al.

Summary: This study examines the impact of mutations on the spike protein of COVID-19, particularly on vaccines and antibody therapies. The research findings reveal that certain mutations may weaken the binding between the spike protein and antibodies, potentially reducing the efficacy of current treatments. Moreover, it is discovered that some mutations could enhance the binding between the spike protein and human angiotensin-converting enzyme 2 (ACE2), leading to more infectious variants of the virus.

CHEMICAL SCIENCE (2021)

Review Biochemical Research Methods

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Franziska Hufsky et al.

Summary: This review explores bioinformatics workflows and tools for the detection, analysis, tracking, evaluation, research, detection of drug targets, and development of therapeutic strategies related to SARS-CoV-2, providing valuable insights for the ongoing COVID-19 pandemic.

BRIEFINGS IN BIOINFORMATICS (2021)

Letter Immunology

Superspreading Event of SARS-CoV-2 Infection at a Bar, Ho Chi Minh City, Vietnam

Nguyen Van Vinh Chau et al.

Summary: This study reports a superspreading event of COVID-19 initiated at a bar in Vietnam, highlighting the risk of transmission in crowded indoor settings with poor ventilation.

EMERGING INFECTIOUS DISEASES (2021)

Article Virology

Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa

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.

VIRUS EVOLUTION (2021)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Multidisciplinary Sciences

A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2

Rui Shi et al.

NATURE (2020)

Article Multidisciplinary Sciences

Human neutralizing antibodies elicited by SARS-CoV-2 infection

Bin Ju et al.

NATURE (2020)

Article Infectious Diseases

Genetic diversity and evolution of SARS-CoV-2

Tung Phan

INFECTION GENETICS AND EVOLUTION (2020)

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

Potently neutralizing and protective human antibodies against SARS-CoV-2

Seth J. Zost et al.

NATURE (2020)

Article Infectious Diseases

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

Lucy van Dorp et al.

INFECTION GENETICS AND EVOLUTION (2020)

Article Genetics & Heredity

Exploring the coronavirus pandemic with the WashU Virus Genome Browser

Jennifer A. Flynn et al.

NATURE GENETICS (2020)

Article Genetics & Heredity

The UCSC SARS-CoV-2 Genome Browser

Jason D. Fernandes et al.

NATURE GENETICS (2020)

Article Multidisciplinary Sciences

Cryptic transmission of SARS-CoV-2 in Washington state

Trevor Bedford et al.

SCIENCE (2020)

Article Genetics & Heredity

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

Shuhui Song et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2020)

Letter Infectious Diseases

CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants

Intikhab Alam et al.

LANCET INFECTIOUS DISEASES (2020)

Article Biochemical Research Methods

Nextstrain: real-time tracking of pathogen evolution

James Hadfield et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Virus Variation Resource - improved response to emergent viral outbreaks

Eneida L. Hatcher et al.

NUCLEIC ACIDS RESEARCH (2017)

Editorial Material Infectious Diseases

GISAID: Global initiative on sharing all influenza data - from vision to reality

Yuelong Shu et al.

EUROSURVEILLANCE (2017)

Article Multidisciplinary Sciences

Data, disease and diplomacy: GISAID's innovative contribution to global health

Stefan Elbe et al.

GLOBAL CHALLENGES (2017)

Article Infectious Diseases

Eight challenges in phylodynamic inference

Simon D. W. Frost et al.

EPIDEMICS (2015)