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Yoshitomi H, Sera N, Gonzalez G, Hanaoka N, Fujimoto T. First isolation of a new type of human adenovirus (genotype 79), species Human mastadenovirus B (B2) from sewage water in Japan. J Med Virol 2016; 89:1192-1200. [PMID: 27943297 DOI: 10.1002/jmv.24749] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 11/11/2022]
Abstract
Human mastadenoviruses (HAdVs) are highly infectious viral pathogens that survive for prolonged periods in environmental waters. We monitored the presence of HAdVs in sewage waters between April 2014 and March 2015. A total of 27 adenoviral strains were detected in 75% (18/24 in occasion-base) of 24 wastewater collected samples. We identified the types of the strains as HAdV-C2 (n = 5), HAdV-A31 (5), HAdV-C1 (4), HAdV-B3 (4), HAdV-C5 (4), HAdV-B11 (2), P11H34F11 (2), and HAdV-D56 (1). The complete genome sequence of one P11H34F11 (strain T150125) was determined by next-generation sequencing and compared to other genome sequences of HAdV-B strains. The comparisons revealed evidence of a recombination event with breaking point in the hexon encoding region, which evidenced high similarity to HAdV-B34, while half of the rest of the genome showed similarity to HAdV-B11, including regions encoding fiber and E3 region proteins. The penton base encoding region seemed to be a recombinant product of HAdV-B14, -34; however, it was evidenced to be divergent to both as a novel type despite showing low bootstrap to support a new clade. We propose T150125 (P11H34F11) is a strain of a novel genotype, HAdV-79. These results support the usefulness of environmental surveillance approaches to monitor circulating HAdVs including novel types.
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Affiliation(s)
- Hideaki Yoshitomi
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Nobuyuki Sera
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Nozomu Hanaoka
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuguto Fujimoto
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
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Kaneko H, Aoki K, Ishida S, Ohno S, Kitaichi N, Ishiko H, Fujimoto T, Ikeda Y, Nakamura M, Gonzalez G, Koyanagi KO, Watanabe H, Suzutani T. Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence. J Gen Virol 2011; 92:1251-1259. [PMID: 21402595 DOI: 10.1099/vir.0.030361-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human adenovirus type 53 (HAdV-53) has commonly been detected in samples from epidemic keratoconjunctivitis (EKC) patients in Japan since 1996. HAdV-53 is an intermediate virus, containing hexon-chimeric, penton base and fiber structures similar to HAdV-22 and -37, HAdV-37 and HAdV-8, respectively. HAdV-53-like intermediate strains were first isolated from EKC samples in Japan in the 1980s. Here, the complete genome sequences of three such HAdV-53-like intermediate strains (870006C, 880249C and 890357C) and four HAdV-53 strains were determined, and their relationships were analysed. The seven HAdV strains were classified into three groups, 870006C/880249C, 890357C and the four HAdV-53 strains, on the basis of phylogenetic analyses of the partial and complete genome sequences. HAdV strains within the same group showed the highest nucleotide identities (99.87-100.00 %). Like HAdV-53, the hexon loop 1 and 2 regions of 870006C, 880249C and 890357C showed the highest identity with HAdV-22. However, these strains did not show a hexon-chimeric structure similar to HAdV-22 and -37, or a penton base similar to HAdV-37. The fiber genes of 870006C and 880249C were identical to that of HAdV-37, but not HAdV-8. Thus, the three intermediate HAdVs isolated in the 1980s were similar to each other but not to HAdV-53. The recombination breakpoints were inferred by the Recombination Detection Program (rdp) using whole-genome sequences of these seven HAdV and of 12 HAdV-D strains from GenBank. HAdV-53 may have evolved from intermediate HAdVs circulating in the 1980s, and from HAdV-8, -22 and -37, by recombination of sections cut at the putative breakpoints.
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Affiliation(s)
- Hisatoshi Kaneko
- Department of Microbiology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Koki Aoki
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Susumu Ishida
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Shigeaki Ohno
- Department of Ocular Inflammation and Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan.,Department of Ocular Inflammation and Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hiroaki Ishiko
- Host Defense Laboratory, Mitsubishi Chemical Medience Corporation, Tokyo, Japan
| | | | | | - Masako Nakamura
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan
| | - Gabriel Gonzalez
- Laboratory of Genome Sciences, Research Groups of Bioinformatics, Division of Bioengineering and Bioinformatics, Hokkaido University Graduate School of Information Science and Technology, Sapporo, Japan
| | - Kanako O Koyanagi
- Laboratory of Genome Sciences, Research Groups of Bioinformatics, Division of Bioengineering and Bioinformatics, Hokkaido University Graduate School of Information Science and Technology, Sapporo, Japan
| | - Hidemi Watanabe
- Laboratory of Genome Sciences, Research Groups of Bioinformatics, Division of Bioengineering and Bioinformatics, Hokkaido University Graduate School of Information Science and Technology, Sapporo, Japan
| | - Tatsuo Suzutani
- Department of Microbiology, Fukushima Medical University School of Medicine, Fukushima, Japan
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Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan. J Clin Microbiol 2010; 49:484-90. [PMID: 21147954 DOI: 10.1128/jcm.01044-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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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Spread of epidemic keratoconjunctivitis due to a novel serotype of human adenovirus in Japan. J Clin Microbiol 2009; 47:2678-9. [PMID: 19644130 DOI: 10.1128/jcm.r00313-09] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kaneko H, Iida T, Ishiko H, Ohguchi T, Ariga T, Tagawa Y, Aoki K, Ohno S, Suzutani T. Analysis of the complete genome sequence of epidemic keratoconjunctivitis-related human adenovirus type 8, 19, 37 and a novel serotype. J Gen Virol 2009; 90:1471-1476. [DOI: 10.1099/vir.0.009225-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We determined the complete genome sequence of epidemic keratoconjunctivitis (EKC)-related human adenoviruses (HAdVs). We analysed a total of 12 HAdV strains; three prototype strains and two HAdV-8, three HAdV-19 and three HAdV-37 clinical isolates from EKC patients in Japan, and one novel serotype of HAdV. Genome organization of these serotypes was identical to those of the recently determined HAdV-19 and HAdV-37. The identities of the whole genome were over 99 % among strains from the same serotype, except for HAdV-19p, which is not associated with conjunctivitis, resulting in the formation of a distinct cluster in the phylogenetic analysis. The penton, loop 1 and loop 2 of hexon, early region 3 (E3) and fiber were hypervariable regions between serotypes. Results suggest that the HAdV-19 clinical strain is a recombinant of HAdV-19p-like and HAdV-37-like strains, and that the acquisition of the penton, E3 or fiber may be related to ocular tropism.
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Affiliation(s)
- Hisatoshi Kaneko
- Department of Microbiology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomohiro Iida
- Department of Ophthalmology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroaki Ishiko
- Host Defense Laboratory, Mitsubishi Chemical Medience Corporation, Tokyo, Japan
| | - Takeshi Ohguchi
- Department of Ophthalmology and Visual Sciences, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshihide Ariga
- Department of Ophthalmology and Visual Sciences, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yoshitsugu Tagawa
- Department of Ophthalmology and Visual Sciences, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Koki Aoki
- Department of Ophthalmology and Visual Sciences, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology and Visual Sciences, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Tatsuo Suzutani
- Department of Microbiology, Fukushima Medical University School of Medicine, Fukushima, Japan
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Aoki K, Ishiko H, Konno T, Shimada Y, Hayashi A, Kaneko H, Ohguchi T, Tagawa Y, Ohno S, Yamazaki S. Epidemic keratoconjunctivitis due to the novel hexon-chimeric-intermediate 22,37/H8 human adenovirus. J Clin Microbiol 2008; 46:3259-69. [PMID: 18701656 PMCID: PMC2566102 DOI: 10.1128/jcm.02354-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Revised: 03/05/2008] [Accepted: 07/22/2008] [Indexed: 01/25/2023] Open
Abstract
In a 2-month period in 2003, we encountered an outbreak of epidemic keratoconjunctivitis (EKC) in Japan. We detected 67 human adenoviruses (HAdVs) by PCR from eye swabs of patients with EKC at five eye clinics in different parts of Japan. Forty-one of the 67 HAdV DNAs from the swabs were identified as HAdV-37 by phylogenetic analysis using a partial hexon gene sequence. When the restriction patterns of these viral genomes were compared with that of the HAdV-37 prototype strain, one isolate showed a never-before-seen restriction pattern. Within 1 year, we encountered three more EKC cases caused by a genetically identical virus: two nosocomial infections at two different university hospitals and a sporadic infection at an eye clinic. We determined the nucleotide sequences of the full-length hexon and fiber genes of these isolates and compared them to those of the 51 prototype strains. Surprisingly, the sequence of the hexon (epsilon determinant) loop-1 and -2 regions showed the highest nucleotide identity with HAdV-22, a rare EKC isolate. However, the nucleotide sequence of the fiber gene was identical to that of the HAdV-8 prototype strain. 22 We propose that this virus is a new hexon-chimeric intermediate HAdV-22,37/H8, and may be an etiological agent of EKC.
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Affiliation(s)
- Koki Aoki
- Department of Ophthalmology and Visual Sciences, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
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Abstract
In 2000, we encountered cases of nosocomial infections with epidemic keratoconjunctivitis (EKC) at a university hospital in Kobe, in the western part of Japan. Two human adenovirus (HAdV) strains, Kobe-H and Kobe-S, were isolated from patients with nosocomial EKC infection. They were untypeable by existing neutralizing antisera; however, the isolate was neutralized with homologous antisera. We then encountered several cases of EKC due to nosocomial infections in eye clinics in different parts of Japan. A total of 80 HAdVs were isolated from patients with EKC at eight different hospitals. The partial hexon gene sequences of the isolates were determined and compared to those of the prototype strains of 51 serotypes. All isolates had identical partial hexon nucleotide sequences. Phylogenetic analysis classified these isolates into species of HAdV-D. The isolates showed 93.9 to 96.7% nucleotide identity with HAdV-D prototype strains, while all 32 HAdV-D prototype strains ranged from 93.2 to 99.2% identity. The sequences of the loop 2 and fiber knob regions from the representative strain, Kobe-H, were dissimilar in all prototype strains of 51 serotypes. We believe that this virus is a novel serotype of HAdV that causes EKC.
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Engelmann I, Madisch I, Pommer H, Heim A. An outbreak of epidemic keratoconjunctivitis caused by a new intermediate adenovirus 22/H8 identified by molecular typing. Clin Infect Dis 2006; 43:e64-6. [PMID: 16941356 DOI: 10.1086/507533] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 06/08/2006] [Indexed: 11/03/2022] Open
Abstract
In a 4-week period, 12 patients contracted adenoviral keratoconjunctivitis. Eight of these patients had visited the same ophthalmologist's practice before onset of symptoms. Adenovirus was detected in swab specimens obtained from 9 patients. Sequence-based typing of 2 isolates revealed type 22/H8. This is, to our knowledge, the first report of a keratoconjunctivitis outbreak caused by an intermediate adenovirus type 22/H8.
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Affiliation(s)
- Ilka Engelmann
- Institut für Virologie, Medizinische Hochschule Hannover, Hannover, 30625, Germany
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Noda M, Yoshida T, Sakaguchi T, Ikeda Y, Yamaoka K, Ogino T. Molecular and epidemiological analyses of human adenovirus type 7 strains isolated from the 1995 nationwide outbreak in Japan. J Clin Microbiol 2002; 40:140-5. [PMID: 11773107 PMCID: PMC120110 DOI: 10.1128/jcm.40.1.140-145.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The adenovirus type 7 (Ad7) isolates from the 1995 nationwide outbreak in Japan were genetically and seroepidemiologically analyzed in comparison with Japanese Ad7 strains isolated before 1995 to determine their genome type and to speculate on their origin and causative factors of the outbreak. Twenty-six Ad7 isolates from the outbreak were identified by restriction enzyme analysis as the Ad7d2 genome type, while 22 Ad7 strains sporadically isolated in Japan before 1995 were identified as Ad7d. Partial nucleotide sequencing of the E3 region of Ad7d2 revealed a nucleotide substitution of G to A at position 265, resulting in the absence of the BstEII site and making Ad7d2 distinct from Ad7d. In Hiroshima City, Japan, no Ad7 was isolated from 1982 to 1994, but 43 and 50 Ad7 strains were isolated in 1995 and 1996, respectively. A seroepidemiological study of 251 serum samples collected in 1989 in Hiroshima City showed that only 2.8% of the samples were positive for Ad7. These results indicate that the 1995 outbreak of Ad7 in Japan was caused by the Ad7d2 genome type, which might have been introduced from outside Japan. The results also suggest that the low mass immunity in Japan was critical for the outbreak and that the mutation in the E3 region in Ad7d2 may have influenced transmission.
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Affiliation(s)
- Mamoru Noda
- Department of Bacteriology, Hiroshima University School of Medicine, Hiroshima, Japan.
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Elnifro EM, Cooper RJ, Klapper PE, Bailey AS. PCR and restriction endonuclease analysis for rapid identification of human adenovirus subgenera. J Clin Microbiol 2000; 38:2055-61. [PMID: 10834953 PMCID: PMC86727 DOI: 10.1128/jcm.38.6.2055-2061.2000] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/1999] [Accepted: 03/10/2000] [Indexed: 02/01/2023] Open
Abstract
Subgenus identification of adenoviruses is of clinical importance and is as informative as identification by serotype in most clinical situations. A PCR-based identification of adenovirus subgenera A, B, C, D, E, and F and sometimes serotypes is described. The PCR uses nonnested primer pair ADRJC1-ADRJC2, which targets a highly conserved region of the adenovirus hexon gene, has a sensitivity of 10 to 40 copies of adenovirus type 2 (Ad2) DNA, and generates 140-bp PCR products from adenovirus serotypes representative of all the subgroups. The PCR products of all subgroups can be differentiated on the basis of the restriction fragment patterns produced by a total of five restriction endonucleases. In addition, serotypes Ad40 and Ad41 (subgroup F) and important serotypes of subgroup D (Ad8, Ad10, Ad19, and Ad37) can easily be differentiated, but serotypes within subgroups B and C cannot. The method was assessed by blind subgenus identification of 56 miscellaneous clinical isolates of adenoviruses. The identities of these isolates at the subgenus level by the PCR correlated 91% (51 of 56) with the results of serotyping by the neutralization test, and 9% (5 of 56) of clinical isolates produced discordant results.
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Affiliation(s)
- E M Elnifro
- School of Medicine, The University of Manchester, Manchester M13 9WL, United Kingdom
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