Phylodynamic approaches to studying avian influenza virus

ABSTRACT

Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.

KEYWORDS:

• Phylodynamics
• avian influenza virus
• poultry
• wild birds
• epidemiology
• phylogeography

Disclosure Statement

No potential conflict of interest was reported by the authors.

Additional Information

Author contributions: L.C. wrote the manuscript. S.C.H., G.F., and J.R, edited the manuscript and supervised the work.

Additional information

Funding

L.C. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) London Interdisciplinary Biosciences Consortium (LIDo) studentship [grant number BB/T008709/1]. S.C.H. is supported by a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust [220414/Z/20/Z] (https://wellcome.org/). GF and JR were supported by the UKRI GCRF One Health Poultry Hub (BB/S011269/1), one of twelve interdisciplinary research hubs funded under the UK government’s Grand Challenge Research Fund Interdisciplinary Research Hub initiative. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission.