Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks

Hughes, J. et al. (2012) Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathogens, 8(12), e1003081. (doi:10.1371/journal.ppat.1003081)

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Publisher's URL: http://dx.doi.org/10.1371/journal.ppat.1003081

Abstract

The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales – from the individual to the population – are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV) to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Hughes, Dr Joseph and Hampson, Dr Katie and Murcia, Dr Pablo
Authors: Hughes, J., Allen, R. C., Baguelin, M., Hampson, K., Baillie, G. J., Elton, D., Newton, J. R., Kellam, P., Wood, J. L. N., Holmes, E. C., and Murcia, P. R.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:PLoS Pathogens
Publisher:Public Library of Science
ISSN:1553-7366
ISSN (Online):1553-7374
Published Online:20 December 2012
Copyright Holders:Copyright © 2012 The Authors
First Published:First published in PLoS Pathogens 8(12):e1003081
Publisher Policy:Reproduced under a Creative Commons License
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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
508041Understanding how a complex intervention works: designing large-scale vaccination programsDaniel HaydonMedical Research Council (MRC)G0901135/91914RI BIODIVERSITY ANIMAL HEALTH & COMPMED
501441Centre for Integrated VirologyMassimo PalmariniMedical Research Council (MRC)G0801822MVLS III - CENTRE FOR VIRUS RESEARCH