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

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Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanoporePreprint

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The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology

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Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

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One year update on the COVID-19 pandemic: Where are we now?

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In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2

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Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants

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Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene

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Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

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PDBsum extras: SARS‐CoV ‐2 and AlphaFold models

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

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Using artificial intelligence techniques for COVID-19 genome analysis

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Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes

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

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An observational study of breakthrough SARS-CoV-2 Delta variant infections among vaccinated healthcare workers in Vietnam

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Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities

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Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

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A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants

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Nucleic Acid Testing of SARS-CoV-2

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Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp14 RNA cap methyltransferase

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SARS-CoV-2 E Gene Variant Alters Analytical Sensitivity Characteristics of Viral Detection Using a Commercial Reverse Transcription-PCR Assay

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SARS-CoV-2 variants reveal features critical for replication in primary human cells

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An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms

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ViruSurf: an integrated database to investigate viral sequences

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Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations

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Comprehensive literature review on COVID-19 vaccines and role of SARS-CoV-2 variants in the pandemic

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Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring

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Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes

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Web tools to fight pandemics: the COVID-19 experience

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SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia

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Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic

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SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring

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High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples

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

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Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

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HLA-A∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses

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Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae )

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Genomic characterization of SARS‐CoV‐2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins

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Interface‐based design of the favipiravir‐binding site in SARS‐CoV‐2 RNA‐dependent RNA polymerase reveals mutations conferring resistance to chain termination

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A deletion in SARS‐CoV‐2 ORF7 identified in COVID‐19 outbreak in Uruguay

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First detection and molecular analysis of SARS-CoV-2 from a naturally infected cat from Argentina

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SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions

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SARS‐CoV‐2 worldwide replication drives rapid rise and selection of mutations across the viral genome: a time‐course study – potential challenge for vaccines and therapies

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

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Toxin-like peptides in plasma, urine and faecal samples from COVID-19 patients

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SARS-CoV-2 transmission routes from genetic data: A Danish case study

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Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka

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SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave

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Targeted design of drug binding sites in the main protease of SARS-CoV-2 reveals potential signatures of adaptation

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SARS‐CoV‐2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions

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Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design

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Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD

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Analysis of SARS-CoV-2 Genomes from West Java, Indonesia

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The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro

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Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein

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Multifaceted Assessment of Wastewater-Based Epidemiology for SARS-CoV-2 in Selected Urban Communities in Davao City, Philippines: A Pilot Study

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Empowering Virus Sequence Research Through Conceptual Modeling

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Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India

Shastri, J. S., Parikh, S., Agrawal, S. R., Chatterjee, N., Pathak, M., Chaudhary, S., Sharma, C., Kanakan, A., Vivekanand, A., Vasudevan, J. S., et al. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.631769 · Cited by 23

Identification of Highly Conserved SARS-CoV-2 Antigenic Epitopes with Wide Coverage Using Reverse Vaccinology Approach

Hisham, Y., Ashhab, Y., Hwang, S., & Kim, D. (2021) · Viruses · doi:10.3390/v13050787 · Cited by 22

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

Pattabiraman, C., Prasad, P., George, A. K., Sreenivas, D., Rasheed, R., Reddy, N. V. K., Desai, A. S., & Ravi, V. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16768.1 · Cited by 21

COV2Var, a function annotation database of SARS-CoV-2 genetic variation

Feng, Y., Yi, J., Yang, L., Wang, Y., Wen, J., Zhao, W., Kim, P., & Zhou, X. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad958 · Cited by 26

Emergence of new subgenomic mRNAs in SARS-CoV-2Preprint

Mears, H. V., Young, G. R., Sanderson, T., Harvey, R., Crawford, M. R., Snell, D. M., Fowler, A. S., Hussain, S., Nicod, J., Peacock, T. P., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.20.488895 · Cited by 22

Accurate and fast clade assignment via deep learning and frequency chaos game representation

Cartes, J. A., Anand, S. K., Ciccolella, S., Bonizzoni, P., & Vedova, G. D. (2022) · GigaScience · doi:10.1093/gigascience/giac119 · Cited by 19

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2Preprint

Richard, D., Shaw, L. P., Lanfear, R., Corbett-Detig, R. B., Hinrichs, A. S., McBroome, J., Turakhia, Y., Acman, M., Owen, C. J., Tan, C. C. S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.06.442903 · Cited by 20

Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples

Napit, R., Manandhar, P., Chaudhary, A., Shrestha, B., Poudel, A., Raut, R., Pradhan, S. M., Raut, S., Rajbhandari, P. G., Gurung, A., et al. (2023) · PLoS ONE · doi:10.1371/journal.pone.0283664 · Cited by 19

Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries

Masoudi‐Sobhanzadeh, Y., Salemi, A., Pourseif, M. M., Jafari, B., Omidi, Y., & Masoudi‐Nejad, A. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab113 · Cited by 18

Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave

Tan, K., Tan, J.-Y., Wong, J.-E., Teoh, B., Tiong, V., Abd‐Jamil, J., Nor’e, S.-S., Khor, C., Johari, J., Yaacob, C., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-01223-4 · Cited by 20

Applying the digital data and the bioinformatics tools in SARS-CoV-2 research

Tan, M., Xia, J., Luo, H., Meng, G., & Zhu, Z. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.044 · Cited by 18

Kinetic comparison of all eleven viral polyprotein cleavage site processing events by SARS-CoV-2 main protease using a linked protein FRET platform

Kenward, C., Vuckovic, M., Paetzel, M., & Strynadka, N. C. J. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107367 · Cited by 18

Chronic SARS-CoV-2 infection and viral evolution in a hypogammaglobulinaemic individualPreprint

Williamson, M. K., Hamilton, F., Hutchings, S., Pymont, H. M., Hackett, M., Arnold, D., Maskell, N. A., MacGowan, A. P., Albur, M., Jenkins, M. H., et al. (2021) · medRxiv · doi:10.1101/2021.05.31.21257591 · Cited by 17

Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic

Surleac, M. D., Bănică, L. M., Casangiu, C., Cotic, M., Florea, D., Săndulescu, O., Milu, P., Streinu‐Cercel, A., Vlaicu, O., Paraskevis, D. N., et al. (2020) · Life · doi:10.3390/life10080152 · Cited by 18

Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota

Petrillo, M., Querci, M., Brogna, C., Ponti, J., Cristoni, S., Markov, P. V., Valsesia, A., Leoni, G., Benedetti, A., Wiss, T., et al. (2022) · F1000Research · doi:10.12688/f1000research.109236.1 · Cited by 24

COVID-19 relapse associated with SARS-CoV-2 evasion from CD4+ T-cell recognition in an agammaglobulinemia patient

Morita, R., Kubota‐Koketsu, R., Lu, X., Sasaki, T., Nakayama, E. E., Liu, Y., Okuzaki, D., Motooka, D., Wing, J. B., Fujikawa, Y., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106685 · Cited by 15

IgV somatic mutation of human anti–SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity

de Mattos Barbosa, M. G., Liu, H., Huynh, D., Shelley, G., Keller, E. T., Emmer, B. T., Sherman, E., Ginsburg, D., Kennedy, A. A., Tai, A. W., et al. (2021) · JCI Insight · doi:10.1172/jci.insight.147386 · Cited by 14

Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak

Lobiuc, A., Dimian, M., Gheorghita, R. E., Căliman-Sturdza, O. A., & Covașă, M. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.654417 · Cited by 14

SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolutionPreprint

Siqueira, J. D., Goes, L. R., Alves, B. M., de Carvalho, P. S., Cicala, C., Arthos, J. A., Viola, J. P. B., de Melo, A. C., Soares, M. A., & on behalf of the INCA COVID-19 Task Force (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.26.267831 · Cited by 14

Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant

Hallak, K. L., & Rosset, S. (2022) · Communications Biology · doi:10.1038/s42003-022-03198-y · Cited by 13

SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing

Mannsverk, S., Bergholm, J., Palanisamy, N., Ellström, P., Kaden, R., Lindh, J. G., & Lennerstrand, J. (2022) · Virology Journal · doi:10.1186/s12985-022-01896-x · Cited by 16

Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samplesPreprint

Napit, R., Manandhar, P., Chaudhary, A., Shrestha, B., Poudel, A., Raut, R., Pradhan, S. M., Raut, S., Mathema, S., Rajbhandari, R. M., et al. (2021) · medRxiv · doi:10.1101/2021.03.29.21254053 · Cited by 13

Genome Sequences of the Delta Variant (B.1.617.2) and the Kappa Variant (B.1.617.1) Detected in Morocco

Melloul, M., Chouati, T., Hemlali, M., Amine, S. A., Touil, N., Elannaz, H., Ennibi, K., Youbi, M., Merabet, M., Bellefquih, A. M., et al. (2021) · Microbiology Resource Announcements · doi:10.1128/mra.00727-21 · Cited by 12

A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19

Lobiuc, A., Șterbuleac, D., Căliman-Sturdza, O. A., Dimian, M., & Covașă, M. (2021) · Biology · doi:10.3390/biology10121276 · Cited by 12

Exploration of potential inhibitors for SARS‐CoV‐2 Mpro considering its mutants via structure‐based drug design, molecular docking, MD simulations, MM/PBSA, and DFT calculations

Ghasemlou, A., Uskoković, V., & Sefidbakht, Y. (2022) · Biotechnology and Applied Biochemistry · doi:10.1002/bab.2369 · Cited by 12

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

Abdullaev, A. A., Abdurakhimov, A., Mirakbarova, Z., Ibragimova, S., Tsoy, V., Nuriddinov, S., Akbarovna, D. D., Turdikulova, S. U., & Abdurakhmonov, I. Y. (2022) · PLoS ONE · doi:10.1371/journal.pone.0270314 · Cited by 13

SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database

Rahimian, K., Arefian, E., Mahdavi, B., Mahmanzar, M., Kuehu, D. L., & Deng, Y. (2023) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqad037 · Cited by 12

Looking for SARS-CoV-2 Therapeutics Through Computational Approaches

Vincenzi, M., Mercurio, F. A., & Leone, M. (2022) · Current Medicinal Chemistry · doi:10.2174/0929867329666221004104430 · Cited by 13

Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development

Gruca, A., Ziemska-Legięcka, J., Jarnot, P., Sarnowska, E. A., Sarnowski, T. J., & Grynberg, M. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04017-7 · Cited by 11

Molecular epidemiology of SARS-CoV-2 in Cyprus

Richter, J., Fanis, P., Tryfonos, C., Koptides, D., Krashias, G., Bashiardes, S., Hadjisavvas, A., Loizidou, M. A., Oulas, A., Alexandrou, D., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0248792 · Cited by 11

Generation and Effect Testing of a SARS-CoV-2 RBD-Targeted Polyclonal Therapeutic Antibody Based on a 2-D Airway Organoid Screening System

He, Y., Qu, J. T., Wei, L., Liao, S., Zheng, N., Liu, Y., Wang, X., Jing, Y., Shen, C. K.-F., Ji, C., et al. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.689065 · Cited by 11

Molecular Analysis of SARS-CoV-2 Lineages in Armenia

Avetyan, D., Hakobyan, S., Nikogհosyan, M., Ghukasyan, L., Khachatryan, G., Sirunyan, T., Muradyan, N., Zakharyan, R., Chavushyan, A., Hayrapetyan, V., et al. (2022) · Viruses · doi:10.3390/v14051074 · Cited by 10

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

Liu, B., Liu, K., Zhang, H., Zhang, L., Bian, Y., & Huang, L. (2020) · Journal of Medical Internet Research · doi:10.2196/22299 · Cited by 31

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

Bernasconi, A., Gulino, A., Alfonsi, T., Canakoglu, A., Pinoli, P., Sandionigi, A., & Ceri, S. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab478 · Cited by 27

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

Wilde, V., Canard, B., & Ferrón, F. (2023) · Viruses · doi:10.3390/v15081628

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

Mercatelli, D., Triboli, L., Fornasari, E., Ray, F., & Giorgi, F. M. (2020) · Journal of Medical Virology · doi:10.1002/jmv.26678 · Cited by 91

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

Wilde, V., Canard, B., & Ferrón, F. (2022) · HAL AMU