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Detection and genetic characterization of Seoul Virus from commensal brown rats in France

Tatiana Dupinay1, Kieran C Pounder2, Florence Ayral1, Maria-Halima Laaberki1, Denise A Marston3, Sandra Lacôte4, Catherine Rey5, Fabienne Barbet5, Katja Voller3, Nicolas Nazaret5, Marc Artois1, Philippe Marianneau4, Joel Lachuer5, Anthony R Fooks36, Michel Pépin1*, Catherine Legras-Lachuer5 and Lorraine M McElhinney36*

Author Affiliations

1 Université de Lyon, VetAgro Sup, USC 1233/Equipe « Pathogènes émergents et rongeurs sauvages (PERS), F-69280 Marcy-L’Etoile, France

2 Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK

3 Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal Health and Veterinary Laboratories Agency (AHVLA), New Haw, Addlestone, Surrey KT15 3NB, UK

4 Anses-Laboratoire de Lyon, Unité Virologie, F-69347 Lyon, France

5 Viroscan 3D / Profilexpert, Faculté de Médecine et de Pharmacie, 3453 CNRS-US7 Inserm, 8 avenue Rockefeller, aile C2, 69373, Lyon Cedex 08, France

6 National Consortium for Zoonosis Research, University of Liverpool, Leahurst, Neston, South Wirral CH64 7TE, UK

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Virology Journal 2014, 11:32  doi:10.1186/1743-422X-11-32

Published: 20 February 2014



Hantaviruses are single-stranded RNA viruses, which are transmitted to humans primarily via inhalation of aerosolised virus in contaminated rodent urine and faeces. Whilst infected reservoir hosts are asymptomatic, human infections can lead to two clinical manifestations, haemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with varying degrees of clinical severity. The incidence of rodent and human cases of Seoul virus (SEOV) in Europe has been considered to be low, and speculated to be driven by the sporadic introduction of infected brown rats (Rattus norvegicus) via ports.


Between October 2010 and March 2012, 128 brown rats were caught at sites across the Lyon region in France.


SEOV RNA was detected in the lungs of 14% (95% CI 8.01 – 20.11) of brown rats tested using a nested pan-hantavirus RT-PCR (polymerase gene). Phylogenetic analysis supports the inclusion of the Lyon SEOV within Lineage 7 with SEOV strains originating from SE Asia and the previously reported French & Belgian SEOV strains. Sequence data obtained from the recent human SEOV case (Replonges) was most similar to that obtained from one brown rat trapped in a public park in Lyon city centre. We obtained significantly improved recovery of virus genome sequence directly from SEOV infected lung material using a simple viral enrichment approach and NGS technology.


The detection of SEOV in two wild caught brown rats in the UK and the multiple detection of SEOV infected brown rats in the Lyon region of France, suggests that SEOV is circulating in European brown rats. Under-reporting and difficulties in identifying the hantaviruses associated with HFRS may mask the public health impact of SEOV in Europe.

Hantavirus; SEOV; France; Brown rat; Rattus norvegicus; Next generation sequencing; Viral enrichment