U.S. Department of Agriculture: Animal and Plant Health Inspection Service


Date of this Version



Pepin, K.M., M.W. Hopken, S.A. Shriner, E. Spackman, Z. Abdo, C. Parrish, S. Riley, J.O. Lloyd-Smith, and A.J. Piaggio. 2019. Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance. Philosophical Transactions of the Royal Society B 374(1782):20180346. doi: 10.1098/rstb.2018.0346


Reassortment is an evolutionary mechanism by which influenza A viruses (IAV) generate genetic novelty. Reassortment is an important driver of host jumps and is widespread according to retrospective surveillance studies.However, predicting the epidemiological risk of reassortant emergence in novel hosts from surveillance data remains challenging. IAV strains persist and cooccur in the environment, promoting co-infection during environmental transmission. These conditions offer opportunity to understand reassortant emergence in reservoir and spillover hosts. Specifically, environmental RNA could provide rich information for understanding the evolutionary ecology of segmented viruses, and transform our ability to quantify epidemiological risk to spillover hosts. However, significant challenges with recovering and interpreting genomic RNA from the environment have impeded progress towards predicting reassortant emergence from environmental surveillance data.We discuss how the fields of genomics, experimental ecology and epidemiologicalmodelling arewell positioned to address these challenges.Coupling quantitative disease models and natural transmission studies with new molecular technologies, such as deep-mutational scanning and single-virus sequencing of environmental samples, should dramatically improve our understanding of viral co-occurrence and reassortment.We define observable risk metrics for emerging molecular technologies and propose a conceptual research framework for improving accuracy and efficiency of risk prediction.

This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.