Mutational spectra distinguish SARS-CoV-2 replication niches
Ruis, C.; Peacock, T. P.; Polo, L. M.; Masone, D.; Soledad Alvarez, M.; Hinrichs, A. S.; Turakhia, Y.; Ye, C.; McBroome, J.; Corbett-Detig, R.; Parkhill, J.; Floto, R. A.
Show abstract
Exposure to different mutagens leaves distinct mutational patterns that can allow prediction of pathogen replication niches (Ruis 2022). We therefore hypothesised that analysis of SARS-CoV-2 mutational spectra might show lineage-specific differences, dependant on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOC; Konings 2021). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in Omicron, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both upper and lower respiratory tracts (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalisable 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 the mutational burden in Alpha varied consistent with changes in transmission source as social restrictions were lifted. This supports the use of mutational spectra to infer niches of established and emergent pathogens.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E 94%
- Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic 94%
- Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin 93%
Similar papers in this journal
Similar papers in this journal
- Evolution, geographic spreading, and demographic distribution of Enterovirus D68 94%
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses 93%
- Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes 93%
Similar papers in this journal
- Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions 94%
- SARS-CoV-2 within-host population expansion, diversification and adaptation in zoo tigers, lions and hyenas 93%
- Transmission of SARS-CoV-2 from humans to animals and potential host adaptation 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.