Molecular characterization and phylogenetic analysis of Murray Valley encephalitis virus and West Nile virus (Kunjin subtype) from an arbovirus disease outbreak in horses in Victoria, Australia, in 2011

Virus was detected in the central nervous system (CNS) tissue of 11 horses from Victoria that died displaying neurological symptoms during an outbreak of disease in Australia in 2011. Five horses were identified as being infected with Murray Valley encephalitis virus (MVEV) and 6 as being infected with West Nile virus subtype Kunjin (WNVKUN). Analysis of partial sequence information from the NS5 and E genes indicated that the MVEVs within the samples were highly homogenous and all belonged to lineage I, which is enzootic to the tropical regions of northern Australia. Likewise, analysis of partial NS5 and E gene and full genome sequences indicated that the WNVKUN within the samples were also highly homogenous and clustered with WNV lineage 1, clade b, which is consistent with other WNVKUN isolates. Full genomes of 1 MVEV isolate and 2 WNVKUN isolates were sequenced and characterized. The genome sequences of Victorian WNVKUN are almost identical (3 amino acid differences) to that of the recently sequenced WNV isolate WNVNSW2011. Metagenome sequencing directly from CNS tissue identified the presence of WNVKUN and MVEV within infected CNS tissue.