Reference health
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
1 of 55 checkable references need attention · checked 2026-07-22
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
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References needing attention
does not resolve to a known work10.1038/d41586-021-03832-5
The 54 checked references that resolve
resolves10.1101/2021.08.20.21262342
Emergence and phenotypic characterization of C.1.2, a globally detected lineage that rapidly accumulated mutations of concern
resolves10.1101/2021.06.03.21258228
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection
resolves10.1101/2022.01.03.21268111
The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism
resolves10.1101/2021.12.31.474653
The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein
resolves10.1101/2021.12.12.472269
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
resolves10.1101/2021.12.28.474380
Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
resolves10.1101/2021.05.24.445313
Identification of evolutionary trajectories shared across human betacoronaviruses
resolves10.1002/gch2.1018
Data, disease and diplomacy: GISAID's innovative contribution to global health
resolves10.1093/molbev/msi105
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
resolves10.1093/molbev/msz197
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
resolves10.1016/j.cell.2021.09.003
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
resolves10.1016/J.CHOM.2020.11.007
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition
resolves10.1016/j.cell.2020.08.012
Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding
resolves10.1126/science.abh1139
Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
resolves10.1038/s41564-021-00954-4
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution
resolves10.1101/2021.04.06.438731
Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike
resolves10.1016/j.celrep.2021.109292
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
resolves10.1126/sciadv.abe5575
Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM
resolves10.1038/s41587-021-01069-1
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
resolves10.1038/s41586-020-2852-1
SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies
resolves10.1038/s41586-021-04388-0
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2
resolves10.1016/J.CHOM.2021.02.003
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies
resolves10.1101/2021.12.19.473380
SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
resolves10.1101/2021.01.22.427830
Exploring the natural origins of SARS-CoV-2 in the light of recombination
resolves10.1371/journal.pgen.1002764
Detecting Individual Sites Subject to Episodic Diversifying Selection
resolves10.1016/j.cell.2021.07.007
A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation
resolves10.1101/2021.12.23.473975
<i>In vitro</i>
evolution predicts emerging CoV-2 mutations with high affinity for ACE2 and cross-species binding
resolves10.1038/s41594-020-0468-7
SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects
resolves10.1101/2021.12.06.471499
Insights on the mutational landscape of the SARS-CoV-2 Omicron variant
resolves10.1101/2021.12.14.472719
Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2
resolves10.1371/journal.pcbi.0030231
An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
resolves10.1038/s41467-021-27096-9
Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands
resolves10.1101/2021.10.31.466677
Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer
resolves10.1371/journal.ppat.1009849
Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks
resolves10.1016/j.immuni.2017.11.002
HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage
resolves10.1101/2021.12.08.21267417
SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection
resolves10.1101/2021.12.19.473354
Variable loss of antibody potency against SARS-CoV-2 B.1.1.529 (Omicron)
resolves10.2139/ssrn.3996320
Clinical Severity of COVID-19 Patients Admitted to Hospitals in Gauteng, South Africa During the Omicron-Dominant Fourth Wave
resolves10.1101/2022.01.12.22269148
Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa
resolves10.1093/bib/bbx108
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
resolves10.1093/molbev/msu300
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
resolves10.1371/journal.pbio.3001115
Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen
The 3 references without a DOI — listed, not checked
no DOI — not checkedRambaut, A. et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 (2020).
no DOI — not checkedLythgoe, K. A. et al. SARS-CoV-2 within-host diversity and transmission. Science 372, (2021).
no DOI — not checkedArctic Network. SARS-CoV-2 V4.1 update for Omicron variant. https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342.
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