Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus |
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| Authors: | Carney Jennifer Daly Janet M Nisalak Ananda Solomon Tom |
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| Institution: | (1) Brain Infections Group, Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 3GA, UK;(2) Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand;(3) School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK; |
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| Abstract: | The mosquito-borne Japanese encephalitis virus (JEV) causes encephalitis in man but not in pigs. Complete genomes of a human,
mosquito and pig isolate from outbreaks in 1982 and 1985 in Thailand were sequenced with the aim of identifying determinants
of virulence that may explain the differences in outcomes of JEV infection between pigs and man. Phylogenetic analysis revealed
that five of these isolates belonged to genotype I, but the 1982 mosquito isolate belonged to genotype III. There was no evidence
of recombination among the Thai isolates, but there were phylogenetic signals suggestive of recombination in a 1994 Korean
isolate (K94P05). Two sites of the genome under positive selection were identified: codons 996 and 2296 (amino acids 175 of
the non-structural protein NS1 and 24 of NS4B, respectively). A structurally significant substitution was seen at NS4B position
24 of the human isolate compared with the mosquito and pig isolates from the 1985 outbreak in Thailand. The potential importance
of the two sites in the evolution and ecology of JEV merits further investigation. |
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