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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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A new coronavirus associated with human respiratory disease in China

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An interactive web-based dashboard to track COVID-19 in real time

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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

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Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

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

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Amino Acid Difference Formula to Help Explain Protein Evolution

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Nidovirales: Evolving the largest RNA virus genome

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A single amino acid in the PB2 gene of influenza A virus is a determinant of host range

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Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020

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A Rapid, Whole Genome Sequencing Assay for Detection and Characterization of Novel Coronavirus (SARS-CoV-2) Clinical Specimens Using Nanopore Sequencing

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Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiologyPreprint

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VirusLab: A Tool for Customized SARS-CoV-2 Data Analysis

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AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution

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IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution

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Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France

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A SARS-CoV-2 Delta Variant Containing Mutation in the Probe Binding Region Used for qRT-PCR Test in Japan Exhibited Atypical PCR Amplification and Might Induce False Negative Result

Rajib, S. A., Ogi, Y., Hossain, M. B., Ikeda, T., Tanaka, E., Kawaguchi, T., & Satou, Y. (2021) · Journal of Infection and Chemotherapy · doi:10.1016/j.jiac.2022.01.019 · Cited by 8

Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes

Panzera, Y., Calleros, L., Goñi, N., Marandino, A. E., Techera, C., Grecco, S., Ramos, N., Frabasile, S., Tomás, G., Condon, E., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0263563 · Cited by 8

Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru

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The Effect of Select SARS-CoV-2 N-Linked Glycan and Variant of Concern Spike Protein Mutations on C-Type Lectin-Receptor-Mediated Infection

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Covariant Fitness Clusters Reveal Structural Evolution of SARS-CoV-2 Polymerase Across the Human PopulationPreprint

Wang, C., Elghobashi‐Meinhardt, N., & Balch, W. E. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.07.475295 · Cited by 9

Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion

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Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania

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Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoringPreprint

Garushyants, S. K., Rogozin, I. B., & Koonin, E. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.23.441209 · Cited by 8

An integrated multiscale computational framework deciphers SARS-CoV-2 resistance to sotrovimab

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Molecular dynamics and intrinsic disorder analysis of the SARS-CoV-2 Nsp1 structural changes caused by substitution and deletion mutations

Rezaei, S., Pereira, F., Uversky, V. N., & Sefidbakht, Y. (2022) · Molecular Simulation · doi:10.1080/08927022.2022.2075546 · Cited by 6

Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

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COVID Variants, Villain and Victory: A Bioinformatics Perspective

Shukla, N., Srivastava, N., Gupta, R., Srivastava, P., & Narayan, J. (2023) · Microorganisms · doi:10.3390/microorganisms11082039 · Cited by 6

A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions

Soliman, M. S., AbdelFattah, M., Aman, S. M. N., Ibrahim, L. M., & Aziz, R. K. (2020) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2020.0194 · Cited by 6

High-throughput design of symmetrical dimeric SARS-CoV-2 main protease: structural and physical insights into hotspots for adaptation and therapeutics

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CoVigator—A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

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Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

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Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2

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ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes

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Coordinating SARS-CoV-2 genomic surveillance in the United States

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Recombinant Decoy Exhibits Broad Protection against Omicron and Resistance Potential to Future Variants

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Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concernPreprint

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The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

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UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example

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Biochemical characterization of naturally occurring mutations in SARS ‐ CoV ‐2 RNA ‐dependent RNA polymerase

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Spike Protein and the Various Cell-Surface Carbohydrates: An Interaction Study

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Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreakPreprint

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Transmission of SARS-CoV-2 Delta Variant Among Vaccinated Healthcare Workers, VietnamPreprint

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Predicted binding interface between coronavirus nsp3 and nsp4Preprint

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Bioinformatics for the Origin and Evolution of Viruses

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CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance

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Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

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Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates

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Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh

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SAS: A Platform of Spike Antigenicity for SARS-CoV-2

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Covidex: an ultrafast and accurate tool for virus subtypingPreprint

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Role of FYVE and Coiled-Coil Domain Autophagy Adaptor 1 in severity of COVID-19 infectionPreprint

Smieszek, S. P., Przychodzen, B. P., Polymeropoulos, C. M., Polymeropoulos, V. M., & Polymeropoulos, M. H. (2021) · medRxiv · doi:10.1101/2021.01.22.21250070 · Cited by 3

In silico tracking of SARS-CoV-2 Nsp1 structural variants in helix-turn-helix motifPreprint

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Vaccine development strategies and impact

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Diagnostic Applications for RNA-Seq Technology and Transcriptome Analyses in Human Diseases Caused by RNA Viruses

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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillancePreprint

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Localised community circulation of SARS-CoV-2 viruses with an increased accumulation of single nucleotide polymorphisms that adversely affect the sensitivity of real-time reverse transcription assays targeting Nucleocapsid proteinPreprint

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Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirusPreprint

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Identifying stable-against-mutations viral epitopes in SARS-CoV-2Preprint

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Recombinant SARS-CoV-2 lacking initiating and internal methionine codons within ORF10 is attenuated in vivoPreprint

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Molecular Epidemiology of SARS-CoV-2 Variants in Vaccinated and Non-Vaccinated Patients of Erbil Province, Kurdistan Region-Iraq

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Predicting the trend of SARS-CoV-2 mutation frequencies using historical data

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Databases, DrugBank, and virtual screening platforms for therapeutic development

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Development and application of EpitopeScan, a Python3 toolset for mutation tracking in SARS-CoV-2 immunogenic epitopes

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Cross-Species Susceptibility of Emerging Variants of SARS-CoV-2 Spike

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In silico framework for genome analysis

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VITALdb: to select the best viroinformatics tools for a desired virus or application

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Update on the First Year of COVID-19 (First Year of COVID-19)?

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Molecular Dynamics of SARS-CoV-2 Nsp1 Structural Changes Associated with Variant MutationsPreprint

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Systems biology in COVID-19

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Publicly available resources in COVID-19 research and their applications

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Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeuticsPreprint

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Conceptual Modeling for Bioinformatics

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Computational insights into SARS-CoV-2: mutation detection, therapeutic discovery, and vaccine development

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Analyse du cycle du SARS-CoV-2 en modèle cellulaire par microscopie électronique à transmission

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FAIRsharing record for: ViruSurf

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CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study

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VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants

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Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond

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Coronapp : A web application to annotate and monitor SARS‐CoV‐2 mutations

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Viral Instant Mutation Viewer (VIMVer): a tool to speed up the identification and analysis of new SARS-CoV2 emerging variant

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