SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

Features and development of Coot

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SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

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A new coronavirus associated with human respiratory disease in China

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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

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Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

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Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein

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Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation

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Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation

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COVID-19: Recent Developments in Therapeutic Approaches

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Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification

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Effective virus-neutralizing activities in antisera from the first wave of survivors of severe COVID-19

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Structural insights into SARS-CoV-2 infection and therapeutics development

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SARS-CoV-2 gained a novel spike protein S1–N-Terminal Domain (S1-NTD)

Desingu, P. A., Nagarajan, K., & Dhama, K. (2022) · Environmental Research · doi:10.1016/j.envres.2022.113047 · Cited by 11

Recurrent independent emergence and transmission of SARS-CoV-2 Spike amino acid H69/V70 deletionsPreprint

Gupta, R. K., Kemp, S. A., Harvey, W. T., Lytras, S., Carabelli, A. M., & Robertson, D. L. (2021) · Research Square · doi:10.21203/rs.3.rs-136937/v1 · Cited by 12

Differential Ability of Spike Protein of SARS-CoV-2 Variants to Downregulate ACE2

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Stabilization of the Metastable Pre-Fusion Conformation of the SARS-CoV-2 Spike Glycoprotein through N-Linked Glycosylation of the S2 Subunit

Zan, F., Zhou, Y., Chen, T., Chen, Y., Mu, Z., Qian, Z., & Ou, X. (2024) · Viruses · doi:10.3390/v16020223 · Cited by 9

SARS-CoV-2 S protein harbors furin cleavage site located in a short loop between antiparallel β-strand

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Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses

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Distinct pathways for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses

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Dynamical nonequilibrium molecular dynamics simulations reveal allosteric networks, signal transduction mechanisms, and sites associated with drug resistance in biomolecular systems

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Computational Chemistry to Repurposing Drugs for the Control of COVID-19

Hassanzadeganroudsari, M., Ahmadi, A., Rashidi, N., Hossain, M. M., Habib, A., & Apostolopoulos, V. (2021) · Biologics · doi:10.3390/biologics1020007 · Cited by 10

Natural Bioactive Molecules as Potential Agents Against SARS-CoV-2

Chen, W., Wang, Z., Wang, Y., & Li, Y. (2021) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.702472 · Cited by 11

Structural heterogeneity and precision of implications drawn from cryo-electron microscopy structures: SARS-CoV-2 spike-protein mutations as a test case

Mehra, R., & Kepp, K. P. (2022) · European Biophysics Journal · doi:10.1007/s00249-022-01619-8 · Cited by 10

Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations

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Cryo-EM and cryo-ET of the spike, virion, and antibody neutralization of SARS-CoV-2 and VOCs

Xu, C., Han, W., & Cong, Y. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102664 · Cited by 9

Automated pipelines for rapid evaluation during cryoEM data acquisition

Mendez, J. H., Chua, E. Y. D., Paraan, M., Potter, C. S., & Carragher, B. O. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102729 · Cited by 10

Structural basis of severe acute respiratory syndrome coronavirus 2 infection

Ge, J., Zhang, S., Zhang, L., & Wang, X. (2020) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000658 · Cited by 10

The Possible Role of Microbial Proteases in Facilitating SARS-CoV-2 Brain Invasion

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Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike

Li, Y., Zheng, P., Liu, T., Shi, C., Wang, B., Xu, Y., & Jin, T. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.930931 · Cited by 9

Architects of infection: A structural overview of SARS-related coronavirus spike glycoproteins

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SARS-CoV-2–host cell surface interactions and potential antiviral therapies

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Multifaceted membrane binding head of the SARS-CoV-2 spike protein

Tran, A., Kervin, T. A., & Overduin, M. (2022) · Current Research in Structural Biology · doi:10.1016/j.crstbi.2022.05.001 · Cited by 8

Through an ecological lens

Petrone, M. E., Holmes, E. C., & Harvey, E. (2023) · EMBO Reports · doi:10.15252/embr.202256578 · Cited by 9

Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater

Conway, M. J., Yang, H., Revord, L. A., Novay, M. P., Lee, R. J., Ward, A. S., Abel, J. D., Williams, M. R., Uzarski, R. L., & Alm, E. W. (2024) · BMC Genomics · doi:10.1186/s12864-024-09977-7 · Cited by 9

Neuropilin-1 Protein May Serve as a Receptor for SARS-CoV-2 Infection: Evidence from Molecular Dynamics Simulations

Nguyen, H. L., Hieu, H. K., Nguyen, T. Q., Nhung, N. T. A., & Li, M. S. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c03119 · Cited by 8

Jumping a Moving Train: SARS-CoV-2 Evolution in Real Time

Moustafa, A. M., & Planet, P. J. (2021) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piab051 · Cited by 8

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

Colson, P., Delerce, J., Burel, E., Beye, M., Fournier, P., Levasseur, A., Lagier, J., & Raoult, D. (2021) · Virus Genes · doi:10.1007/s11262-021-01877-2 · Cited by 9

Subgenomic RNA profiling suggests novel mechanism in coronavirus gene regulation and host adaption

Lyu, L., Feng, R., Zhang, M., Xie, X., Liao, Y., Zhou, Y., Guo, X., Su, B., Dorsett, Y., & Chen, L. (2022) · Life Science Alliance · doi:10.26508/lsa.202101347 · Cited by 8

Comparison of Insertion, Deletion, and Point Mutations in the Genomes of Human Adenovirus HAdvC-2 and SARS-CoV-2

Akaishi, T. (2022) · The Tohoku Journal of Experimental Medicine · doi:10.1620/tjem.2022.j049 · Cited by 8

The Local Topological Free Energy of the SARS-CoV-2 Spike Protein

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COVID-19 Spotlights Connections between Disease and Multiple Lifestyle Factors

Enichen, E. J., Harvey, C., & Demmig‐Adams, B. (2022) · American Journal of Lifestyle Medicine · doi:10.1177/15598276221123005 · Cited by 10

Effect of the Graphene Nanosheet on Bio-Functions of the Spike Protein at Open and Closed States: The Comparison Between SARS-CoV-2 WT and Omicron Variant

Yan, Z., Li, X., Ma, Y., & Ding, H. (2022) · Langmuir · doi:10.1021/acs.langmuir.2c02316 · Cited by 8

Combinatorial Approach with Mass Spectrometry and Lectin Microarray Dissected Site-Specific Glycostem and Glycoleaf Features of the Virion-Derived Spike Protein of Ancestral and γ Variant SARS-CoV-2 Strains

Hiono, T., Sakaue, H., Tomioka, A., Kaji, H., Sasaki, M., Orba, Y., Sawa, H., & Kuno, A. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00874 · Cited by 8

Insights into SARS-CoV-2: Medicinal Chemistry Approaches to Combat Its Structural and Functional Biology

Zhuo, L., Wang, M., Yang, J., Xu, H.-C., Huang, W., Shang, L., & Yang, G. (2021) · Topics in Current Chemistry · doi:10.1007/s41061-021-00335-9 · Cited by 8

Up, up, down, down: the structural biology of the SARS-CoV-2 spike protein and how it cheats the immune system

Stäb, S., Pearce, N. M., Tronrud, D. E., Ginn, H. M., Fadda, E., Santoni, G., & Thorn, A. (2024) · Crystallography Reviews · doi:10.1080/0889311x.2024.2363756 · Cited by 7

Potential Effects of Hyperglycemia on SARS-CoV-2 Entry Mechanisms in Pancreatic Beta Cells

Michaels, T. M., Essop, M. F., & Joseph, D. E. (2024) · Viruses · doi:10.3390/v16081243 · Cited by 12

D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes

Kearns, F. L., Bogetti, A. T., Calvó‐Tusell, C., Braza, M. K. E., Casalino, L., Gramm, A. J., Braet, S. M., Rosenfeld, M. A., Rajapaksha, H., Barker, B., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2504793123 · Cited by 7

Bat sarbecovirus WIV1-CoV bears an adaptive mutation that alters spike dynamics and enhances ACE2 binding

Tse, A. L., Lasso, G., Berrigan, J. L., McLellan, J. S., Chandran, K., & Miller, E. H. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013123 · Cited by 7

Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach

Boon, S. S., Xia, C., Wang, M. H., Yip, K. L., Luk, H. Y., Li, S., Ng, R. W. Y., Lai, C. K. C., Chan, P. K. S., & Chen, Z. (2021) · mBio · doi:10.1128/mbio.02687-21 · Cited by 7

SARS-CoV-2 spike protein reduces burst activities in neurons measured by micro-electrode arrays

Salvador, M., Tseng, N., Park, C., Williams, G., Vethan, A., Thomas, G., Baker, J., Hemry, J., Hammond, E., Freeburg, P., et al. (2023) · Annals of Medicine and Surgery · doi:10.1097/ms9.0000000000000950 · Cited by 7

Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif

Lorenzo, R., Defelipe, L. A., Aliperti, L., Niebling, S., Custódio, T. F., Löw, C., Schwarz, J., Remans, K., Craig, P. O., Otero, L. H., et al. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101175 · Cited by 7

HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene

Fass, E., Valenci, G. Z., Rubinstein, M., Freidlin, P. J., Rosencwaig, S., Kutikov, I., Werner, R. A., Ben-Tovim, N., Bucris, E. D., Erster, O., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2021.798130 · Cited by 7

Involvement of sialoglycans in SARS‐COV ‐2 infection: Opportunities and challenges for glyco‐based inhibitors

Kuhaudomlarp, S., & Imberty, A. (2022) · IUBMB Life · doi:10.1002/iub.2692 · Cited by 7

SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works

Cassari, L., Pavan, A., Zoia, G., Chinellato, M., Zeni, E., Grinzato, A., Rothenberger, S., Cendron, L., Dettin, M., & Pasquato, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054791 · Cited by 8

Understanding the role of conserved proline and serine residues in the SARS-CoV-2 spike cleavage sites in the virus entry, fusion, and infectivity

Khatri, R., Lohiya, B., Kaur, G., Maithil, V., Goswami, A., Sarmadhikari, D., Asthana, S., & Samal, S. (2023) · 3 Biotech · doi:10.1007/s13205-023-03749-y · Cited by 7

Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2

Cornish, K. A. S., Huo, J., Jones, L. M., Sharma, P., Thrush, J. W., Abdelkarim, S., Kipar, A., Ramadurai, S., Weckener, M., Mikolajek, H., et al. (2024) · Open Biology · doi:10.1098/rsob.230252 · Cited by 7

Profile of SARS-CoV-2

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COVID-19 status quo: Emphasis on gastrointestinal and liver manifestations

Bhurwal, A., Minacapelli, C. D., Orosz, E. L., Gupta, K., Tait, C., Dalal, I., Zhang, C., Zhao, E., & Rustgi, V. K. (2021) · World Journal of Gastroenterology · doi:10.3748/wjg.v27.i46.7969 · Cited by 7

Analysis of SARS-CoV-2 Mutations Over Time Reveals Increasing Prevalence of Variants in the Spike Protein and RNA-Dependent RNA PolymerasePreprint

Showers, W. M., Leach, S. M., Kechris, K., & Strong, M. (2021) · bioRxiv · doi:10.1101/2021.03.05.433666 · Cited by 8

High-throughput Mutational Surveillance of the SARS-CoV-2 Spike GenePreprint

Özkan, E., Strobl, M. M., Novatchkova, M., Yelagandula, R., Albanese, T. G., Tříska, P., Endler, L., Penz, T., Patocka, T., Felsenstein, V., et al. (2021) · medRxiv · doi:10.1101/2021.07.22.21259587 · Cited by 6

Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamsterPreprint

Port, J. R., Morris, D. H., Riopelle, J. C., Yinda, C. K., Avanzato, V. A., Holbrook, M. G., Bushmaker, T., Schulz, J. E., Saturday, T. A., Barbian, K., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.15.504010 · Cited by 7

Biosafety level‐3 cryo‐electron tomography of active severe acute respiratory syndrome coronavirus 2 virions

Fukuhara, H., Dokainish, H. M., Kita, S., Tabata, K., Takasu, A., Huiskonen, J. T., Anraku, Y., Nomai, T., Someya, T., Senda, T., et al. (2026) · Protein Science · doi:10.1101/2023.10.10.561643 · Cited by 8

Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2

Gomez, L. R. E., Weber, A., Kocher, A., & Kühnert, D. (2024) · Scientific Reports · doi:10.1038/s41598-023-50952-1 · Cited by 6

Structure and dynamics of the interaction of Delta and Omicron BA.1 SARS-CoV-2 variants with REGN10987 Fab reveal mechanism of antibody action

Lyukmanova, E. N., Pichkur, E., Nolde, D. E., Kocharovskaya, M. V., Manuvera, V. A., Shirokov, D. A., Kharlampieva, D. D., Grafskaia, E. N., Svetlova, J. I., Лазарев, В. Н., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-07422-9 · Cited by 6

Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner

Wang, X., Hu, M., Liu, B., Xu, H., Jin, Y., Wang, B., Zhao, Y., Wu, J., Yue, J., & Ren, H. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1161445 · Cited by 7

High seroprevalence for SARS-CoV-2 infection in dogs: Age as risk factor for infection in shelter and foster home animals

Nilsson, M. G., Cordeiro, M. D. C. S., Gonçalves, A. C. A., Conzentino, M. S., Huergo, L. F., Vicentini, F., Reis, J. B. L., Biondo, A. W., Kmetiuk, L. B., & da Silva, A. V. (2023) · Preventive Veterinary Medicine · doi:10.1016/j.prevetmed.2023.106094 · Cited by 6

Variation in structural motifs within SARS-related coronavirus spike proteins

Hills, F. R., Eruera, A.-R., Hodgkinson‐Bean, J., Jorge, F., Easingwood, R. A., Brown, S. H. J., Bouwer, J. C., Li, Y., Burga, L. N., & Bostina, M. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012158 · Cited by 6

Study of protease-mediated processes initiating viral infection and cell–cell viral spreading of SARS-CoV-2

Thaingtamtanha, T., & Baeurle, S. A. (2022) · Journal of Molecular Modeling · doi:10.1007/s00894-022-05206-8 · Cited by 6

Cross-Neutralization of SARS-CoV-2-Specific Antibodies in Convalescent and Immunized Human Sera against the Bat and Pangolin Coronaviruses

Srisutthisamphan, K., Saenboonrueng, J., Wanitchang, A., Viriyakitkosol, R., & Jongkaewwattana, A. (2022) · Viruses · doi:10.3390/v14081793 · Cited by 6

Spike mutation T403R allows bat coronavirus RaTG13 to use human ACE2Preprint

Zech, F., Schniertshauer, D., Jung, C., Herrmann, A., Xie, Q., Nchioua, R., Bozzo, C. P., Volčič, M., Koepke, L., Krüger, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.31.446386 · Cited by 6

Commentary: Lethal Pneumonia Cases in Mojiang Miners (2012) and the Mineshaft Could Provide Important Clues to the Origin of SARS-CoV-2

Speciale, A. C. (2021) · Frontiers in Public Health · doi:10.3389/fpubh.2021.702199 · Cited by 6

COVID-19 vaccines uptake: Public knowledge, awareness, perception and acceptance among adult AfricansPreprint

Ahiakpa, J. K., Cosmas, N. T., Anyiam, F. E., Enalume, K. O., Lawan, I., Gabriel, I. B., Oforka, C. L., Dahir, H. G., Fausat, S. T., Nwobodo, M. A., et al. (2022) · medRxiv · doi:10.1101/2022.02.06.22270405 · Cited by 6

Vaccination shapes evolutionary trajectories of SARS-CoV-2Preprint

Meijers, M., Ruchnewitz, D., Łuksza, M., & Lässig, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.19.500637 · Cited by 6

Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamstersPreprint

Port, J. R., Yinda, C. K., Riopelle, J. C., Weishampel, Z. A., Saturday, T. A., Avanzato, V. A., Schulz, J. E., Holbrook, M. G., Barbian, K., Perry-Gottschalk, R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.29.502072 · Cited by 6

Mutagenic Distinction between the Receptor-Binding and Fusion Subunits of the SARS-CoV-2 Spike Glycoprotein and Its Upshot

Penner, R. (2021) · Vaccines · doi:10.3390/vaccines9121509 · Cited by 5

Insight into genomic organization of pathogenic coronaviruses, SARS-CoV-2: Implication for emergence of new variants, laboratory diagnosis and treatment options

Bedada, F. B., Gorfu, G., Teng, S., & Neita, M. E. (2022) · Frontiers in Molecular Medicine · doi:10.3389/fmmed.2022.917201 · Cited by 6

Viral and Host Attributes Underlying the Origins of Zoonotic Coronaviruses in Bats

Stout, A. E., Guo, Q., Millet, J. K., & Whittaker, G. R. (2021) · Comparative Medicine · doi:10.30802/aalas-cm-21-000027 · Cited by 6

Current Update of Phytotherapeutic Agents in the Treatment of COVID-19: In-Silico Based Virtual Screening Approach for the Development of Antiviral Drug

Ramesh, V., Kulkarni, S. A., Velusamy, P., Velmurugan, D., Devaraju, P., Rajnish, K. N., Madhavan, T., Anbu, P., Ramasamy, P., & Sundarraj, R. (2022) · Frontiers in Bioscience-Landmark · doi:10.31083/j.fbl2704123 · Cited by 5

Human Cell Organelles in SARS-CoV-2 Infection: An Up-to-Date Overview

Gorący, A., Rosik, J., Szostak, B., Ustianowski, Ł., Ustianowska, K., & Gorący, J. (2022) · Viruses · doi:10.3390/v14051092 · Cited by 5

Discovery of novel spike/ACE2 inhibitory macrocycles using in silico reinforcement learning

Shapira, L., Lerner, S., Assayag, G., Vardi, A., Haham, D., Bar, G., Fidelsky, V., Robicsek, M. E., Lerner, I., & Michaeli, A. (2022) · Frontiers in Drug Discovery · doi:10.3389/fddsv.2022.1085701 · Cited by 7

Comprehensive deep mutational scanning reveals the pH induced stability and binding differences between SARS-CoV-2 spike RBD and human ACE2

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