Widespread transmission of distinct genetic lineages of Murray Valley encephalitis virus in Australia, 2008-2009

Abstract

Increased activity of the mosquito-borne Murray valley encephalitis virus (MVEV) was observed in Australia in 2008 and 2009, leading to fatal human and equine cases, and renewed concerns regarding its potential to spread and cause disease. Complete prM-Env genes were sequenced from over 50 MVEV strains from different regions of Australia and PNG, and from different times, in order to establish genetic relationships between recent circulating strains with earlier isolates. Phylogenetic analyses showed that genotype 1 (G1) was the dominant circulating genotype sampled over a 60 year period. Two distinct sub-lineages of G1 were observed: G1A included the prototype strain, recent PNG isolates as well as 2008 and 2009 Western Australian strains; G1B comprised early Western Australian viruses (isolated from 1972), including 2009 (but not 2008) strains, and all 2008 isolates from eastern Australia. The finding that 2008 strains from eastern Australia and Western Australia belonged to different sub-lineages suggests these originated from distinct foci of activity in this year, and raises questions regarding the transmission and spread of MVEV within Australia. An additional finding of importance was the identification of G2 strains for the first time since 1995. Unlike earlier strains isolated in the northeast Kimberley region, recent G2 viruses were found in the western and southern parts of Kimberley, indicating this genotype has a broader geographic distribution than first thought. The demonstration of co-circulation of three distinct genetic lineages (G1A, G1B and G2) of MVEV in northwestern Australia provides further evidence that it has an enzootic focus there.