ArticleEmerging microbes & infections2022
Spike mutations contributing to the altered entry preference of SARS-CoV-2 omicron BA.1 and BA.2.
Article in Emerging microbes & infections, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
54 citing papers in PubMed, 85 citations in OpenAlex.
- Ability of SpikoGen®, an Advax-CpG adjuvanted recombinant spike protein vaccine, to induce cross-neutralising antibodies against SARS-CoV-2 variants.Immunology · 2023Trial
- Article
- Functional characterization of spike RBD mutations in SARS-CoV-2 Omicron-derived subvariants KP.3.1.1, LP.8.1, and NB.1.8.1.Journal of microbiology (Seoul, Korea) · 2026Article
- Prolonged dysregulation and pathological changes in the upper respiratory tract of SARS-CoV-2 infected hamsters.Npj viruses · 2026Article
- Pathogenicity, virological features, and immune evasion of SARS-CoV-2 JN.1-derived variants including JN.1.7, KP.2, KP.3, and KP.3.1.1.Nature communications · 2025Article
- Identification of Cathepsin L as the Molecular Target of Hydroxychloroquine With Chemical Proteomics.Molecular & cellular proteomics : MCP · 2025Article
- Combining antigenic data from public sources gives an early indication of the immune escape of emerging virus variants.Scientific reports · 2025Article
- An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations.International journal of molecular sciences · 2025Article
- Critical amino acid residues in human ACE2 for SARS-CoV-2 spike protein binding and virus entry.Microbiology spectrum · 2025Article
- An orally available MNature communications · 2025Article
- RAB5 is a host dependency factor for the generation of SARS-CoV-2 replication organelles.mBio · 2025Article
- CRISPR-Cas9 genetic screens reveal regulation of TMPRSS2 by the Elongin BC-VHL complex.Scientific reports · 2025Article
- The Compensatory Effect of S375F on S371F Is Vital for Maintaining the Infectivity of SARS-CoV-2 Omicron Variants.Journal of medical virology · 2025Article
- Article
- SARS-CoV-2 Omicron variations reveal mechanisms controlling cell entry dynamics and antibody neutralization.PLoS pathogens · 2024Article
- SARS-CoV-2 Genomic Variants and Their Relationship with the Expressional and Genomic Profile of Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2).Microorganisms · 2024Article
- Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.Nature communications · 2024Article
- Recreating the biological steps of viral infection on a cell-free bioelectronic platform to profile viral variants of concern.Nature communications · 2024Article
- A Targeted LC-MRMMolecular & cellular proteomics : MCP · 2024Article
- Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning.Nature communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 B.1.1.529.1 (Omicron BA.1) emerged in November 2021 and quickly became the predominant circulating SARS-CoV-2 variant globally. Omicron BA.1 contains more than 30 mutations in the spike protein, which contribute to its altered virological features when compared to the ancestral SARS-CoV-2 or previous SARS-CoV-2 variants. Recent studies by us and others demonstrated that Omicron BA.1 is less dependent on transmembrane serine protease 2 (TMPRSS2), less efficient in spike cleavage, less fusogenic, and adopts an altered propensity to utilize the plasma membrane and endosomal pathways for virus entry. Ongoing studies suggest that these virological features of Omicron BA.1 are in part retained by the subsequent Omicron sublineages. However, the exact spike determinants that contribute to these altered features of Omicron remain incompletely understood. In this study, we investigated the spike determinants for the observed virological characteristics of Omicron. By screening for the individual changes on Omicron BA.1 and BA.2 spike, we identify that 69-70 deletion, E484A, and H655Y contribute to the reduced TMPRSS2 usage while 25-27 deletion, S375F, and T376A result in less efficient spike cleavage. Among the shared spike mutations of BA.1 and BA.2, S375F and H655Y reduce spike-mediated fusogenicity. Interestingly, the H655Y change consistently reduces serine protease usage while increases the use of endosomal proteases. In keeping with these findings, the H655Y substitution alone reduces plasma membrane entry and facilitates endosomal entry when compared to SARS-CoV-2 WT. Overall, our study identifies key changes in Omicron spike that contributes to our understanding on the virological determinant and pathogenicity of Omicron.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.