title: The Molecular Epidemiology and Evolution of Murray Valley Encephalitis Virus: Recent Emergence of Distinct Sub-lineages of the Dominant Genotype 1.
abstract: BACKGROUND
  Recent increased activity of the mosquito-borne Murray Valley encephalitis virus (MVEV) in Australia has renewed concerns regarding its potential to spread and cause disease.
  
  
  RESULTS
  To better understand the genetic relationships between earlier and more recent circulating strains, patterns of virus movement, as well as the molecular basis of MVEV evolution, complete pre-membrane (prM) and Envelope (Env) genes were sequenced from sixty-six MVEV strains from different regions of the Australasian region, isolated over a sixty year period (1951-2011). Phylogenetic analyses indicated that, of the four recognized genotypes, only G1 and G2 are contemporary. G1 viruses were dominant over the sampling period and found across the known geographic range of MVEV. Two distinct sub-lineages of G1 were observed (1A and 1B). Although G1B strains have been isolated from across mainland Australia, Australian G1A strains have not been detected outside northwest Australia. Similarly, G2 is comprised of only Western Australian isolates from mosquitoes, suggesting G1B and G2 viruses have geographic or ecological restrictions. No evidence of recombination was found and a single amino acid substitution in the Env protein (S332G) was found to be under positive selection, while several others were found to be under directional evolution. Evolutionary analyses indicated that extant genotypes of MVEV began to diverge from a common ancestor approximately 200 years ago. G2 was the first genotype to diverge, followed by G3 and G4, and finally G1, from which subtypes G1A and G1B diverged between 1964 and 1994.
  
  
  CONCLUSIONS
  The results of this study provides new insights into the genetic diversity and evolution of MVEV. The demonstration of co-circulation of all contemporary genetic lineages of MVEV in northwestern Australia, supports the contention that this region is the enzootic focus for this virus.
authors.affiliation: CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors.forename: David T
authors.initials: DT
authors.lastname: Williams
authors.affiliation: Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia.
authors.forename: Sinéad M
authors.initials: SM
authors.lastname: Diviney
authors.affiliation: Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia.
authors.forename: Aziz-ur-Rahman
authors.initials: AU
authors.lastname: Niazi
authors.affiliation: CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Durr
authors.affiliation: Office of Research and Development, Curtin University, Perth, Western Australia, Australia.
authors.forename: Beng Hooi
authors.initials: BH
authors.lastname: Chua
authors.affiliation: Infectious Diseases and Immunology, University of Sydney, New South Wales, Australia.
authors.forename: Belinda
authors.initials: B
authors.lastname: Herring
authors.affiliation: Public Health Virology, Queensland Health Forensic and Scientific Services, Coopers Plains, Queensland, Australia.
authors.forename: Alyssa
authors.initials: A
authors.lastname: Pyke
authors.affiliation: Department of Medical Entomology, Westmead Hospital, University of Sydney and Institute for Clinical Pathology and Medical Research, New South Wales, Australia.
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Doggett
authors.affiliation: Arbovirus Surveillance and Research Laboratory, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Johansen
authors.affiliation: Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia.
authors.forename: John S
authors.initials: JS
authors.lastname: Mackenzie
mesh_terms: D000818:Animals; D044362:Australasia / Q000453:epidemiology; D016000:Cluster Analysis; D018068:Encephalitis Virus, Murray Valley / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D004671:Encephalitis, Arbovirus / Q000453:epidemiology* / Q000821:virology*; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D051379:Mice; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D015678:Viral Structural Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D015678:Viral Structural Proteins