The evolution of SARS-CoV-2

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

Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.02.052 · Cited by 20,286

EVOLUTION IN MENDELIAN POPULATIONS

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Virological assessment of hospitalized patients with COVID-2019

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Origin and evolution of pathogenic coronaviruses

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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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Coronaviruses: An Overview of Their Replication and Pathogenesis

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Structural basis of receptor recognition by SARS-CoV-2

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SARS-CoV-2 variants, spike mutations and immune escape

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Nextstrain: real-time tracking of pathogen evolutionPreprint

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Nextstrain: real-time tracking of pathogen evolution

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Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

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Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

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

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Oral Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19

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Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID-19-related mortality, 2020–21

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Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding

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The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

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

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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

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SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis

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Viral Mutation Rates

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Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

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How generation intervals shape the relationship between growth rates and reproductive numbers

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Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection

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Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 bindingPreprint

Starr, T. N., Greaney, A. J., Hilton, S. K., Crawford, K. H. D., Navarro, M., Bowen, J., Tortorici, M. A., Walls, A., Veesler, D., & Bloom, J. D. (2020) · bioRxiv · doi:10.1101/2020.06.17.157982 · Cited by 1,180

The Molecular Biology of Coronaviruses

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Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population

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Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Munnink, B. B. O., Sikkema, R. S., Nieuwenhuijse, D. F., Molenaar, R. J., Münger, E., Molenkamp, R., van der Spek, A. N., Tolsma, P., Rietveld, A., Brouwer, M., et al. (2020) · Science · doi:10.1126/science.abe5901 · Cited by 1,116

Predicting infectious severe acute respiratory syndrome coronavirus 2 from diagnostic samples

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Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

Pulliam, J. R. C., van Schalkwyk, C., Govender, N., Gottberg, A. V., Cohen, C., Groome, M. J., Dushoff, J., Mlisana, K., & Moultrie, H. (2021) · doi:10.1101/2021.11.11.21266068 · Cited by 1,037

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.032 · Cited by 1,025

GISAID’s Role in Pandemic Response

Khare, S., GISAID Global Data Science Initiative (GISAID), M., Gurry, C., Freitas, L. A., Schultz, M. B., Bach, G., Diallo, A. B., Akite, N., Ho, J., Lee, R. T., et al. (2021) · China CDC Weekly · doi:10.46234/ccdcw2021.255 · Cited by 1,023

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

Greaney, A. J., Starr, T. N., Gilchuk, P., Zost, S. J., Binshtein, E., Loes, A. N., Hilton, S. K., Huddleston, J., Eguia, R., Crawford, K. H. D., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.11.007 · Cited by 1,016

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

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The biological and clinical significance of emerging SARS-CoV-2 variants

Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

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Mechanisms of viral mutation

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Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera

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Hosts and Sources of Endemic Human Coronaviruses

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Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognitionPreprint

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SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

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SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo

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SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

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Effect of Bamlanivimab as Monotherapy or in Combination With Etesevimab on Viral Load in Patients With Mild to Moderate COVID-19

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Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies

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Long COVID after breakthrough SARS-CoV-2 infection

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SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo

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HIV Drug Resistance

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The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets

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Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021

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Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion

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

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Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China

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Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

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An Anthropoid-Specific Locus of Orphan C to U RNA-Editing Enzymes on Chromosome 22

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

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Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

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A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures

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SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters

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Attenuated replication and pathogenicity of SARS-CoV-2 B.1.1.529 Omicron

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Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong

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Evolutionary analysis of the dynamics of viral infectious disease

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Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA synthesis.

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T cell responses to SARS-CoV-2 spike cross-recognize Omicron

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Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event

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Heavily mutated Omicron variant puts scientists on alert

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Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

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SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

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Experimental Transmission Studies of SARS-CoV-2 in Fruit Bats, Ferrets, Pigs and Chickens

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Drug resistance in influenza A virus: the epidemiology and management

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Evolution of enhanced innate immune evasion by SARS-CoV-2

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The evolution of virulence

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Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies

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Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies.

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Immunological characteristics govern the transition of COVID-19 to endemicity

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SARS-CoV-2 infection in free-ranging white-tailed deer

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Ancestral SARS-CoV-2-specific T cells cross-recognize the Omicron variant

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