Hantaviruses (family Bunyaviridae, genus Hantavirus) are single-stranded RNA viruses. Unlike other members of the Bunyaviridae, hantaviruses are not transmitted by arthropods but primarily by rodents of the families Cricetidae and Muridae, although insectivore and bat hosts have also been reported [1, 2]. Each hantavirus appears to be adapted and largely restricted to an individual reservoir host species, implying that they have co-evolved, although phylogenetic analyses suggests that this apparent co-evolution may be more attributed to recent preferential host switching and local adaptation .
Transmission to humans is 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 morbidity and mortality . Surveillance in Europe has detected six rodent-borne hantaviruses; Dobrava-Belgrade virus (DOBV), Saaremaa virus (SAAV), Seoul virus (SEOV), Puumala virus (PUUV), Tatenale virus (TATV) and Tula virus (TULV) plus two insectivore-borne hantaviruses; Seewis virus (SWSV) and Nova virus (NVAV) [4–7]. The relative geographic distribution of each hantavirus is defined by their reservoir host . The most common and widespread hantavirus across northern, central and eastern Europe is PUUV, which is associated with the mildest form of HFRS .
Unlike other hantaviruses, SEOV has a global distribution due to the worldwide dispersal of its carrier host (Rattus sp). Confirmed human SEOV infections have been reported in Asia (Japan , South Korea , China [10, 11]) and the Americas (USA , Brazil ). Norwegian/brown rats (Rattus norvegicus) are a cosmopolitan species and represent an emerging and widely distributed host of hantavirus in China, where, a total of 1,557,622 cases of HFRS were reported in humans between 1950–2007 with 46,427 deaths (3%) [11, 14]. Historically, the presence of Seoul virus in Europe was considered anecdotal and speculated to be driven by the sporadic introduction of infected brown rats via ports . Previously, a single HFRS case near the port city of Lyon, France, had only been confirmed serologically by SEOV FRNT  and SEOV antibodies had been reported in brown rats in France (10-78.9%) and Belgium (27.1%) [15, 16]. However, more recently the virus has been isolated from wild brown rats in the UK  and pet rats in the UK and Sweden [18–20]. In addition, SEOV associated HFRS has been reported in four cases in the UK and France, all of which were clinically severe and involved renal impairment [17, 21, 22].
This study aimed to determine the presence of SEOV in wild rats (R. norvegicus) trapped in and around Lyon, France and analyse any resulting molecular epidemiological data. The study also determined the optimal approach to obtaining SEOV genomic sequence data directly from infected lung tissue by comparing different sample preparation techniques and next generation sequencing (NGS) platforms.