ArticlePathogens (Basel, Switzerland)2022
SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations.
Article in Pathogens (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication.Antimicrobial agents and chemotherapy · 2026Article
- Shared quasispecies architecture in experimental and natural RNA virus populations.Virus evolution · 2026Article
- Methods to Characterize Mutant Spectra of RNA Viruses: The Case of SARS-CoV-2.Methods in molecular biology (Clifton, N.J.) · 2026Article
- SARS-CoV-2 mutant spectrum complexity is an epidemiologically evolvable trait.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues.Journal of virology · 2025Article
- A general and biomedical perspective of viral quasispecies.RNA (New York, N.Y.) · 2025Review
- Quasispecies theory and emerging viruses: challenges and applications.Npj viruses · 2024Review
- Point mutations at specific sites of the nsp12-nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Editorial for the Topical Collection "SARS-CoV-2 Infection and COVID-19 Disease".Pathogens (Basel, Switzerland) · 2024Article
- SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice.Communications biology · 2024Article
- SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?Frontiers in microbiology · 2024Article
- Puzzles, challenges, and information reservoir of SARS-CoV-2 quasispecies.Journal of virology · 2023Review
- Article
- Article
- Diversity of Short Linear Interaction Motifs in SARS-CoV-2 Nucleocapsid Protein.bioRxiv : the preprint server for biology · 2023Article
- The Mutational Landscape of SARS-CoV-2.International journal of molecular sciences · 2023Article
- Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations.Virus research · 2023Article
- Atypical Mutational Spectrum of SARS-CoV-2 Replicating in the Presence of Ribavirin.Antimicrobial agents and chemotherapy · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
32 authors.
Funding
Abstract
Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.
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.