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. 2012 Jan;157(1):75-83.
doi: 10.1007/s00705-011-1143-4. Epub 2011 Oct 28.

Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

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Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

Jennifer Carney et al. Arch Virol. 2012 Jan.

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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Figures

Fig. 1
Fig. 1
Phylogenetic tree of complete genomes of 28 Japanese encephalitis virus isolates. The six isolates from KPP, Thailand, sequenced for this study are highlighted in bold text, and the host species is indicated after the strain names (H, human; M, mosquito; P, pig). Amino acid combinations present at codons 996 and 2296 are indicated by symbols. Percent bootstrap values (n = 1000) of major nodes are indicated. The genotype IV isolate JKT6468 was used as an outgroup. Bar, 0.02 nucleotide substitutions per site
Fig. 2
Fig. 2
Splits Tree analysis of complete genomes of 28 Japanese encephalitis virus isolates. The names of the six isolates from KPP, Thailand, are in italics, and the putative recombinant strain K94P05 is highlighted in bold text. Bar, 0.01 nucleotide substitutions per site
Fig. 3
Fig. 3
Simplot comparison of complete genome sequences of K94P05, Ishikawa and JaOArS982. The x-axis indicates the nucleotide position, and the y-axis, the percent nucleotide similarity between the sequence of the putative recombinant K94P05 and each parent, plotted at the midpoint of the window. The window size was 400 bp, and the increment was 50 bp
Fig. 4
Fig. 4
Phylogenetic trees showing shifts in phylogenetic position of segments of K94P05 on either side of the putative breakpoints: nucleotides 1–8822 (a), 8823–9246 (b), and 9247–10,982 (c). Percent bootstrap support (n = 1000) for the putative recombinant strain K94P05 (highlighted in a square text box) clustering with different genotypes is indicated. The trees are unrooted, and branch lengths are drawn to scale. The genotype IV isolate JKT6468 was used as an outgroup

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