Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence

Kaneko, Hisatoshi; Aoki, Koki; Ishida, Susumu; Ohno, Shigeaki; Ishiko, Hiroaki; Fujimoto, Tsuguto; Ikeda, Yoshifumi; Nakamura, Masako; González, Gabriel; Koyanagi, Kanako O.; Watanabe, Hidemi; Suzutani, Tatsuo

doi:10.1099/vir.0.030361-0

Cited by 37 publications

(38 citation statements)

References 34 publications

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“…Recently, whole-genome analysis of HAdVs has shown that serum neutralization, by relying on a small fraction of the viral genome as a means of virus identification, can be misleading (21,27,28). For example, HAdV-D53 isolates were originally mistyped as HAdV-D8, -D22, or -D37 on the basis of serum neutralization or limited sequencing (7).…”

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confidence: 99%

Overreliance on the Hexon Gene, Leading to Misclassification of Human Adenoviruses

Singh

Robinson

Dehghan

et al. 2012

J Virol

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The genome of human adenovirus (HAdV) D30 was sequenced in depth. Sequence assembly and analysis revealed two distinct viral sequences with identical hexon genes, which were the same as the one previously reported for HAdV-D30. However, one of the two viruses was found to be a recombinant of HAdV-D29. Exclusive reliance on serum neutralization can lead to mischaracterization of adenoviruses and miss coinfections. Whole-genome sequencing remains the gold standard for proper classification of HAdVs.

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confidence: 99%

Overreliance on the Hexon Gene, Leading to Misclassification of Human Adenoviruses

Singh

Robinson

Dehghan

et al. 2012

J Virol

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“…Among these putative parents of HAdV_Chiba_ E086/2012, only HAdV-22 has been previously clinically reported in ocular infections (30) and it has also been suggested to be a putative recombination parent of HAdV-GT53 (31) and its variants (32,33), which were all isolated from epidemic keratoconjunctivitis patients. Although originally isolated from a respiratory infection, an experimental study has suggested that HAdV-GT60 may have a potential corneal tropism (34).…”

Section: Discussionmentioning

confidence: 99%

“…A lot of new genotypes of HAdV-D, which were defined in this report as the HAdV genotypes without serological determinations, that is those from type number 53 onward, have been recently reported and characterized in terms of evolution and neutralization assays, e.g., HAdV genotype 53 (HAdV-GT53) (2) and HAdV-GT64 (3) (abbreviated as HAdV-GT53 and so on for such genotypes in this report). Except for a few types, such as HAdV-GT54, most of the new genotypes have been suggested to be originated from recombination between the types which were designated by serological typing criteria, i.e., HAdV-1 to 51, particularly in the penton base, hexon and fiber genes (2)(3)(4). It has also been speculated that recombinant viruses exhibiting similar phenotypes to their original viruses (e.g., in tropism and pathogenesis) would have been recognized as known types (3)(4)(5)(6).…”

Section: Introductionmentioning

confidence: 99%

A Novel Complex Recombinant Form of Type 48-Related Human Adenovirus Species D Isolated in Japan

et al. 2014

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SUMMARY:Recently, new genotypes of human adenoviruses (HAdVs) have been reported and many of them have been found to be recombinant forms of different known types of HAdV species D (HAdV-D). The objective of this study was to document the evolutionary features of a novel isolate (HAdV_ Chiba_E086/2012) obtained from the eye swab of a patient with conjunctivitis in Japan. Viral DNA was extracted from the isolate to sequence the whole genome by the Sanger method and aligned with available genome sequences of HAdV-Ds. The phylogenetic trees of the nucleotide sequences of the penton base, hexon, and fiber genes and the E3 region showed that HAdV_Chiba_E086/2012 is closest to HAdV genotype 65 (HAdV-GT65), HAdV-48, HAdV-GT60 and HAdV-22 at 98z, 99z, 95z and 98z identity, respectively, suggesting that this isolate is a novel recombinant form to be designated as P65H48F60. Further phylogenetic and recombination analyses of the genome alignment of the new isolate implied that nested recombination events involving HAdV-GT59, GT65, 48, GT60, 22, and some ancestral lineages or their close relatives have shaped its genome. These results showed that HAdV_ Chiba_E086/2012 is the first HAdV-48-related HAdV found in Japan, which has the most complicated evolutionary history among the known HAdVs so far.

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“…The vast majority require nested, multiplex, or multiple singleplex PCRs for the detection of multiple virus types. Furthermore, it is unknown if any of these assays are capable of detecting the newly described HAdV types 53 to 57, responsible for human outbreaks in Japan (13,16,18), China (33), France (27), and the United States (14).…”

Section: Discussionmentioning

confidence: 99%

Real-Time Qualitative PCR for 57 Human Adenovirus Types from Multiple Specimen Sources

et al. 2012

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Human adenoviruses (HAdVs) are ubiquitous double-stranded DNA viruses that cause a wide array of diseases in humans including pharyngitis, pneumonia, gastroenteritis, hemorrhagic cystitis, and keratoconjunctivitis. They also cause life-threatening opportunistic infections in immunocompromised individuals and are responsible for outbreaks in certain populations. Diagnosis is traditionally by cell culture or antigen detection methods. However, some HAdVs can take up to 4 weeks to isolate, and diarrheagenic types 40 and 41 will not grow in routine cell culture. Therefore, the goal of this study was to design a rapid, real-time PCR assay to detect all known 57 HAdV types from multiple different specimen sources. Primers and fluorescence resonance energy transfer hybridization probes were designed to target a 185-bp region of the penton base gene of HAdV. The analytical sensitivity was determined to be 10 copies/l for HAdV types showing exact primer/probe homology in specimen matrix. Using whole-virus strains, the analytical sensitivity for representative HAdV types ranged from 10 ؊1 to 10 3 50% tissue culture infective dose (TCID 50 )/ml. The assay demonstrated 100% sensitivity and 99% specificity. This real-time PCR assay provides a rapid method for the detection of all 57 known HAdV types from respiratory specimens, blood, stool, urine, and ocular swabs. Human adenoviruses (HAdVs) are ubiquitous doublestranded DNA viruses that cause a wide array of diseases in humans, including pharyngitis, pneumonia, gastroenteritis, hemorrhagic cystitis, and keratoconjunctivitis (23). Adenoviruses may also cause life-threatening opportunistic infections in immunocompromised individuals and are responsible for outbreaks in certain populations such as day care attendees and military recruits (23).Adenoviruses are classified in the genus Mastadenovirus, which contains 7 known HAdV species (HAdV-A to HAdV-G). Historically, HAdVs were further classified by hemagglutination and serum neutralization reactions into 51 serotypes (29). New adenovirus types have since been identified by several authors based on genomic data, including several emerging and recombinant viruses, for a total of 57 unique HAdV types (1, 14, 16-18, 27, 29, 32, 33). Most recently, a primate adenovirus from New World monkeys was detected which crossed the species barrier to infect humans (2).Diagnosis is traditionally by cell culture or antigen detection methods. Most HAdVs grow readily in cell culture and can be detected in a variety of specimen types including nasopharyngeal, throat and conjunctival swabs, urine, cerebrospinal fluid (CSF), and stool. However, some types can take up to 4 weeks to isolate, and diarrheagenic types 40 and 41 will not grow in routine cell culture. Direct antigen detection from clinical specimens may be used for diagnosis of acute infections but provides markedly low sensitivity compared to culture (30). Less commonly, serology is used to detect a rise in adenovirus-specific antibodies following infection (23).Real-time PCR offers a ...

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Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence

Cited by 37 publications

References 34 publications

Overreliance on the Hexon Gene, Leading to Misclassification of Human Adenoviruses

Overreliance on the Hexon Gene, Leading to Misclassification of Human Adenoviruses

A Novel Complex Recombinant Form of Type 48-Related Human Adenovirus Species D Isolated in Japan

Real-Time Qualitative PCR for 57 Human Adenovirus Types from Multiple Specimen Sources

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