ArticleFrontiers in cellular and infection microbiology2022
Perspectives: SARS-CoV-2 Spike Convergent Evolution as a Guide to Explore Adaptive Advantage.
Article in Frontiers in cellular and infection microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Concepts of RNA virus evolution for the design of better antiviral countermeasures.Nature reviews. Microbiology · 2026Review
- Stringent selection drives convergence toward omicron-like SARS-CoV-2 receptor-binding motifs.Nature communications · 2026Article
- Paying attention to the SARS-CoV-2 dialect : a deep neural network approach to predicting novel protein mutations.Communications biology · 2025Article
- Studying SARS-CoV-2 interactions using phage-displayed receptor binding domain as a model protein.Scientific reports · 2024Article
- Surveillance for variants of SARS-CoV-2 to inform risk assessments.Bulletin of the World Health Organization · 2023Article
- Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics.Journal of virology · 2023Article
- Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms.Journal of chemical information and modeling · 2023Article
- A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India.Journal of infection and public health · 2023Article
- The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37.Viruses · 2023Article
- SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works.International journal of molecular sciences · 2023Article
- A Simple Epidemiologic Model for Predicting Impaired Neutralization of New SARS-CoV-2 Variants.Vaccines · 2023Article
- Design of a mutation-integrated trimeric RBD with broad protection against SARS-CoV-2.Cell discovery · 2022Article
- SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.Cell · 2022Article
- Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants.Computational and structural biotechnology journal · 2022Article
- Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.bioRxiv : the preprint server for biology · 2021Article
- Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups.Computational and structural biotechnology journal · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses rapidly co-evolve with their hosts. The 9 million sequenced SARS-CoV-2 genomes by March 2022 provide a detailed account of viral evolution, showing that all amino acids have been mutated many times. However, only a few became prominent in the viral population. Here, we investigated the emergence of the same mutations in unrelated parallel lineages and the extent of such convergent evolution on the molecular level in the spike (S) protein. We found that during the first phase of the pandemic (until mid 2021, before mass vaccination) 31 mutations evolved independently ≥3-times within separated lineages. These included all the key mutations in SARS-CoV-2 variants of concern (VOC) at that time, indicating their fundamental adaptive advantage. The omicron added many more mutations not frequently seen before, which can be attributed to the synergistic nature of these mutations, which is more difficult to evolve. The great majority (24/31) of S-protein mutations under convergent evolution tightly cluster in three functional domains; N-terminal domain, receptor-binding domain, and Furin cleavage site. Furthermore, among the S-protein receptor-binding motif mutations, ACE2 affinity-improving substitutions are favoured. Next, we determined the mutation space in the S protein that has been covered by SARS-CoV-2. We found that all amino acids that are reachable by single nucleotide changes have been probed multiple times in early 2021. The substitutions requiring two nucleotide changes have recently (late 2021) gained momentum and their numbers are increasing rapidly. These provide a large mutation landscape for SARS-CoV-2 future evolution, on which research should focus now.
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.