ArticleBriefings in bioinformatics2022
Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 24 citations in OpenAlex.
- The SARS-CoV-2 S2'-helix compared to stem helix confers higher genetic barrier to antibody resistance.PLoS pathogens · 2026Article
- From infected to recovered: the mediating role of sleep quality between self-compassion, social support and COVID-19 psychosomatic symptoms.BMC public health · 2024Article
- Impact of Missense Mutations on Spike Protein Stability and Binding Affinity in the Omicron Variant.Viruses · 2024Article
- Enhanced potency of an IgM-like nanobody targeting conserved epitope in SARS-CoV-2 spike N-terminal domain.Signal transduction and targeted therapy · 2024Article
- Efficacy and safety of GST-HG171 in adult patients with mild to moderate COVID-19: a randomised, double-blind, placebo-controlled phase 2/3 trial.EClinicalMedicine · 2024Article
- Trends and impacts of SARS-CoV-2 genome sharing: a comparative analysis of China and the global community, 2020-2023.Frontiers in public health · 2024Article
- Comparative genotyping of SARS-CoV-2 among Egyptian patients: near-full length genomic sequences versus selected spike and nucleocapsid regions.Medical microbiology and immunology · 2023Article
- Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph.Journal of mathematical biology · 2023Article
- Identifying featured indels associated with SARS-CoV-2 fitness.Microbiology spectrum · 2023Article
- BCEDB: a linear B-cell epitopes database for SARS-CoV-2.Database : the journal of biological databases and curation · 2023Article
- On the collection and integration of SARS-CoV-2 genome data.Biosafety and health · 2023Review
- Early warning of emerging infectious diseases based on multimodal data.Biosafety and health · 2023Review
- A Noncoding A-to-U Kozak Site Change Related to the High Transmissibility of Alpha, Delta, and Omicron VOCs.Molecular biology and evolution · 2023Article
- Mechanism of a rabbit monoclonal antibody broadly neutralizing SARS-CoV-2 variants.Communications biology · 2023Article
- PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries.BioMed research international · 2023Article
- CoV2-TCR: A web server for screening TCR CDR3 from TCR immune repertoire of COVID-19 patients and their recognized SARS-CoV-2 epitopes.Computational and structural biotechnology journal · 2023Article
- Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics.Zoological research · 2022Article
- COVID-19 Whole-Genome Resequencing with Redundant Tiling PCR and Subtract-Based Amplicon Normalization Successfully Characterized SARS-CoV-2 Variants in Clinical Specimens.Interdisciplinary perspectives on infectious diseases · 2022Article
- The Structure of Deviations From Maximum Parsimony for Densely-Sampled Data and Applications for Clade Support Estimation.IEEE transactions on computational biology and bioinformaticsArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors at 4 institutions in 1 country.
Funding
Abstract
Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a node-picking rendering strategy. In total, 1,002,739 high-quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, highly efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and ongoing positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB was written in Java and JavaScript. It not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.