ArticleMicrobial genomics2023
A lung-specific mutational signature enables inference of viral and bacterial respiratory niche.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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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.
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Who cites it
16 citing papers in PubMed.
- Mutation-biased adaptation is consequential even in large bacterial populations.Nature communications · 2026Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.Nature methods · 2026Article
- Signatures of omicron-like adaptation in early SARS-CoV-2 variants and chronic infection.Cell reports · 2025Article
- A single mutation may contribute to accelerated evolution of SARS-CoV-2 toward Omicron.Nature communications · 2025Article
- The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure.Nucleic acids research · 2025Article
- A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data.Molecular biology and evolution · 2025Article
- A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum.Molecular biology and evolution · 2025Article
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
- A phylogenetic method identifies candidate drivers of the evolution of the SARS-CoV-2 mutation spectrum.bioRxiv : the preprint server for biology · 2025Article
- The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure.bioRxiv : the preprint server for biology · 2025Article
- Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.bioRxiv : the preprint server for biology · 2024Article
- Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry.Nature microbiology · 2024Article
- SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks".Cellular & molecular immunology · 2024Review
- Mutational spectra are associated with bacterial niche.Nature communications · 2023Article
- Article
- Evolution of the SARS-CoV-2 Mutational Spectrum.Molecular biology and evolution · 2023Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens.
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