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  - 2016 Jan 01
TA  - bioRxiv
PG  - 066688
4099  - http://biorxiv.org/content/early/2016/07/29/066688.short
4100  - http://biorxiv.org/content/early/2016/07/29/066688.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 individuals. We introduce and analyze a stochastic, multi-scale model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale quantity combines with viral mutation rates, reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. 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. These results provide a framework for a new generation of evidence-based risk assessment of emergence threats.