## 1 Introduction  
Murray Valley Encephalitis Virus (MVEV) is a mosquito-borne member of the Flaviviridae family belonging to the Japanese Encephalitis serocomplex. It is an arbovirus of considerable public health importance in Australia due to the significant morbidity and mortality it may cause.  
MVEV is enzootic to Northern Australia, existing in a complex transmission cycle in mosquitoes (_Culex_ spp.) and water birds [1]; with periodic 'dead-end' involvement of other vertebrate hosts, including humans, where infection results in insufficient replication to perpetuate the viral life cycle [2]. Consequently, the incidence of MVEV outside of Northern Australia follows the migration of infected carrier birds, and is influenced by meteorological factors such as heavy rainfall, temperature, and humidity, which facilitate widespread movement of waterbirds and increase mosquito population [3]. This was exemplified by an outbreak in 2011 where seasons of excessive rainfall and flooding widened the migration grounds of waterbirds and allowed for the passage of MVEV into South-Eastern Australia [4; 5].  
Infection with MVEV is generally asymptomatic, or characterized by a mild, non-specific febrile illness, with only 1/150-1/2000 infections resulting in clinically apparent disease [3; 4; 6]. However, when it does occur, disease is frequently severe with a case fatality rate of 15-30% and long-term neurological sequelae persisting in 30-50% of survivors [4; 6]. Several epidemics have been recorded in Australia in the past century, most notably in 1974 where 58 cases and 4 deaths were reported. Since then, a further 127 human cases have been recorded [5], including 17 cases in a 2011 outbreak where only 4 out of 17 patients achieved a full recovery [4].  
As no vaccine or treatment exists for MVEV, outcomes are reliant on early diagnosis and good supportive care in Intensive Care Units [6]. Diagnosis of MVEV often relies heavily on serology, the interpretation of which may be challenging due to cross-reactivity of anti-Flavivirus antibodies [6]. Furthermore, in the absence of IgM, it is important to demonstrate increasing levels of IgG [3]. Radiological imaging may provide useful supporting information which is faster than serology [6] but not specific for MVEV.  
At present, virological detection of MVEV is generally performed by PCR, which is favored due to its speed and sensitivity compared to traditional methods of virus isolation. Within our laboratory, detection of flaviviruses is performed using a nested pan-_Flavivirus_ PCR targeting the whole Flaviviridae family, plus a species-specific real-time PCR, where available. Rapid identification of MVEV is achieved using an MVEV-specific real-time PCR, and verified by sequencing of the pan-_Flavivirus_ PCR product.  
Traditionally, MVEV has proved difficult to isolate from clinical specimens. All recorded isolations have been derived from post mortem brain tissue, and only one successful isolation has been reported since 1974 [3; 7; 8].  
To date, only five MVEV isolates, four of them isolated over 40 years ago, have been sequenced using next generation sequencing technologies [1; 8]. Accordingly, there is limited genomic information relating to active strains currently circulating in Australia. Four genotypes of the virus are currently recognized. In Australia type 1 has been identified as the dominant and most virulent genotype, with type 2 considered less virulent, and types 3 & 4 are extinct/non-circulating [5].  
In this study, we describe detection by PCR, isolation, and full genome sequencing of a contemporary MVEV from a living patient's cerebrospinal fluid (CSF), with identification of the genotype as type 2. This is the first reported isolation of MVEV from CSF and has significant implications for public health surveillance, epidemiology, and understanding of MVEV evolution.