PT  - JOURNAL ARTICLE
AU  - Sebastian J. Schreiber
AU  - Ruian Ke
AU  - Claude Loverdo
AU  - Miran Park
AU  - Prianna Ahsan
AU  - James O. Lloyd-Smith
TI  - Cross-scale dynamics and the evolutionary emergence of infectious diseases
AID  - 10.1101/066688
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 066688
4099  - http://biorxiv.org/content/early/2020/04/21/066688.short
4100  - http://biorxiv.org/content/early/2020/04/21/066688.full
AB  - When emerging pathogens encounter new host species for which they are poorly adapted, they must evolve to escape extinction. Pathogens experience selection on traits at multiple scales, including replication rates within host individuals and transmissibility between hosts. We analyze a stochastic model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor, the cross-scale reproductive number of a mutant virion, that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale reproductive number combines with viral mutation rates, single-strain reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. We find that wider transmission bottlenecks facilitate emergence of pathogens with short-term infections, but hinder emergence of pathogens exhibiting cross-scale selective conflict and long-term infections. Our results provide a framework to advance the integration of laboratory, clinical and field data in the context of evolutionary theory, laying the foundation for a new generation of evidence-based risk assessment of emergence threats.Competing Interest StatementThe authors have declared no competing interest.