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Title: Cellular dynamics shape recombination frequency in coronaviruses
Coronavirus genomes have evolutionary histories shaped extensively by recombination. Yet, how often recombination occurs at a cellular level, or the factors that regulate recombination rates, are poorly understood. Utilizing experimental co-infections with pairs of genetically distinct coronaviruses, we found that recombination is both frequent and rare during coinfection. Recombination occurred in every instance of co-infection yet resulted in relatively few recombinant RNAs. By integrating a discrete-time Susceptible-Infected-Removed (SIR) model, we found that rates of recombination are determined primarily by rates of cellular co-infection, rather than other possible barriers such as RNA compartmentalization. By staggering the order and timing of infection with each virus we also found that rates of co-infection are themselves heavily influenced by genetic and ecological mechanisms, including superinfection exclusion and the relative fitness of competing viruses. Our study highlights recombination as a potent yet regulated force: frequent enough to ensure a steady influx of genetic variation but also infrequent enough to maintain genomic integrity. As recombination is thought to be an important driver of host-switching and disease emergence, our study provides new insights into the factors that regulate coronavirus recombination and evolution more broadly.  more » « less
Award ID(s):
2200221
PAR ID:
10556289
Author(s) / Creator(s):
; ;
Editor(s):
Blanco-Melo, Daniel
Publisher / Repository:
PLOS
Date Published:
Journal Name:
PLOS Pathogens
Volume:
20
Issue:
9
ISSN:
1553-7374
Page Range / eLocation ID:
e1012596
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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