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.2011 Feb;49(2):484-90.
doi: 10.1128/JCM.01044-10. Epub 2010 Dec 8.

Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan

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Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan

Hisatoshi Kaneko et al. J Clin Microbiol.2011 Feb.

Abstract

For 4 months from September 2008, 102 conjunctival swab specimens were collected for surveillance purposes from patients across Japan suspected of having epidemic keratoconjunctivitis (EKC). Human adenovirus (HAdV) DNA was detected in 61 samples by PCR, though the HAdV type for 6 of the PCR-positive samples could not be determined by phylogenetic analysis using a partial hexon gene sequence. Moreover, for 2 months from January 2009, HAdV strains with identical sequences were isolated from five conjunctival swab samples obtained from EKC patients in five different regions of Japan. For the analyses of the 11 samples mentioned above, we determined the nucleotide sequences of the entire penton base, hexon, and fiber genes and early 3 (E3) region, which are variable regions among HAdV types, and compared them to those of other HAdV species D strains. The nucleotide sequences of loops 1 and 2 in the hexons of all 11 samples showed high degrees of identity with those of the HAdV type 15 (HAdV-15) and HAdV-29 prototype strains. However, the fiber gene and E3 region sequences showed high degrees of identity with those of HAdV-9, and the penton base gene sequence showed a high degree of identity with the penton base gene sequences of HAdV-9 and -26. Moreover, the complete genome sequence of the 2307-S strain, which was isolated by viral culture from 1 of the 11 samples, was determined. The 2307-S strain was a recombinant HAdV between HAdV-9, -15, -26, -29, and/or another HAdV type; however, the recombination sites in the genome were not obvious. We propose that this virus is a novel intertypic recombinant, HAdV-15/29/H9, and may be an etiological agent of EKC.

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Figures

Fig. 1.
Fig. 1.
Eleven conjunctival swab samples collected from epidemic keratoconjunctivitis patients in 2008 and 2009 in Japan. Samples are named by sample number/geographic origin/year of collection. Black circles indicate the collection sites in Japan.
Fig. 2.
Fig. 2.
Phylogenetic analysis of the nucleotide sequences of the 350-bp partial hexon gene C4 for HAdV typing (A), loop 1 in the hexon gene (B), loop 2 in the hexon gene (C), the entire hexon gene (D), the penton base gene (E), the fiber gene (F), the E3 region (G), and the complete genome (H).
Fig. 3.
Fig. 3.
(A) Organization of the complete 2307-S strain genome. The gray horizontal bar in the center shows the linear double-strand HAdV genome, with each vertical line representing 5,000 bp. Transcription units are shown by black arrows relative to their position and orientation in the HAdV genome. Gray arrows show the positions of the penton base, hexon and fiber genes. (B to F) Global pairwise sequence comparison of the complete genome between 2307-S and HAdV-9 (B), HAdV-26 (C), HAdV-15 (D), and HAdV-29 (E) and between HAdV-15 and HAdV-29 (F). The vertical axis indicates the nucleotide identities, expressed as decimals. The horizontal axis indicates the nucleotide positions of the complete sequences.
Fig. 4.
Fig. 4.
Similarity plots (A) and boot scanning (B) of the complete genome sequence of strain 2307-S compared to the sequences of the 15 other HAdV-D genomes. The gray horizontal bar at the top shows the linear double-strand HAdV genome, with each vertical line representing 5,000 bp. The vertical axis indicates the nucleotide identities, expressed as decimals. The horizontal axis indicates the nucleotide positions of the complete sequences.
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References

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