Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic

Fusaro, A. et al. (2016) Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic. Journal of Virology, 90(14), pp. 6401-6411. (doi: 10.1128/jvi.00538-16) (PMID:27147741) (PMCID:PMC4936132)

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Abstract

Next-generation sequencing technology is now being increasingly applied to study the within- and between-host population dynamics of viruses. However, information on avian influenza virus evolution and transmission during a naturally occurring epidemic is still limited. Here, we use deep-sequencing data obtained from clinical samples collected from five industrial holdings and a backyard farm infected during the 2013 highly pathogenic avian influenza (HPAI) H7N7 epidemic in Italy to unravel (i) the epidemic virus population diversity, (ii) the evolution of virus pathogenicity, and (iii) the pathways of viral transmission between different holdings and sheds. We show a high level of genetic diversity of the HPAI H7N7 viruses within a single farm as a consequence of separate bottlenecks and founder effects. In particular, we identified the cocirculation in the index case of two viral strains showing a different insertion at the hemagglutinin cleavage site, as well as nine nucleotide differences at the consensus level and 92 minority variants. To assess interfarm transmission, we combined epidemiological and genetic data and identified the index case as the major source of the virus, suggesting the spread of different viral haplotypes from the index farm to the other industrial holdings, probably at different time points. Our results revealed interfarm transmission dynamics that the epidemiological data alone could not unravel and demonstrated that delay in the disease detection and stamping out was the major cause of the emergence and the spread of the HPAI strain.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Hughes, Dr Joseph and Murcia, Professor Pablo
Authors: Fusaro, A., Tassoni, L., Milani, A., Hughes, J., Salviato, A., Murcia, P. R., Massi, P., Zamperin, G., Bonfanti, L., Marangon, S., Cattoli, G., Monne, I., and Schultz-Cherry, S.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Journal of Virology
Publisher:American Society for Microbiology
ISSN:0022-538X
ISSN (Online):1098-5514
Published Online:04 May 2016
Copyright Holders:Copyright © 2016 American Society for Microbiology
First Published:First published in Journal of Virology 90(14):6401-6411
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
501443Centre for Integrated VirologyMassimo PalmariniMedical Research Council (MRC)G0801822MVLS III - CENTRE FOR VIRUS RESEARCH