A lung-specific mutational signature enables inference of viral and bacterial respiratory niche

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.

Medienart:

E-Artikel

Erscheinungsjahr:

2023

Erschienen:

2023

Enthalten in:

Zur Gesamtaufnahme - volume:9

Enthalten in:

Microbial genomics - 9(2023), 5 vom: 27. Mai

Sprache:

Englisch

Beteiligte Personen:

Ruis, Christopher [VerfasserIn]
Peacock, Thomas P [VerfasserIn]
Polo, Luis M [VerfasserIn]
Masone, Diego [VerfasserIn]
Alvarez, Maria Soledad [VerfasserIn]
Hinrichs, Angie S [VerfasserIn]
Turakhia, Yatish [VerfasserIn]
Cheng, Ye [VerfasserIn]
McBroome, Jakob [VerfasserIn]
Corbett-Detig, Russell [VerfasserIn]
Parkhill, Julian [VerfasserIn]
Floto, R Andres [VerfasserIn]

Links:

Volltext

Themen:

Genomics
Journal Article
Mutational spectrum
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.
SARS-CoV-2
Transmission

Anmerkungen:

Date Completed 17.05.2023

Date Revised 19.06.2023

published: Print

Citation Status MEDLINE

doi:

10.1099/mgen.0.001018

funding:

Förderinstitution / Projekttitel:

PPN (Katalog-ID):

NLM356877426