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Park A, Lee C, Lee JY. Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis. J Microbiol 2024; 62:393-407. [PMID: 38451451 DOI: 10.1007/s12275-024-00112-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 03/08/2024]
Abstract
Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.
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Affiliation(s)
- Anyeseu Park
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Chanhee Lee
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Jeong Yoon Lee
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.
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First Record of HAdV-D20 Among Keratoconjunctivitis Patients in Iraq. Rep Biochem Mol Biol 2022; 11:176-181. [PMID: 35765528 PMCID: PMC9208557 DOI: 10.52547/rbmb.11.1.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 01/11/2023]
Abstract
Background Human Adenovirus species D (HAdV-D) was common human viral pathogen especially in eye infection, consists of several types of which HAdV-D8, -D19 and -D37 were common in eye infection. This study includes detection of HAdV-D types implicated in conjunctivitis based on L2 (Penton protein) gene similarity. Methods Conjunctival swabs were collected from Keratoconjunctivitis patients as eye infection related to adenovirus. Viral nucleic acids were extracted and specific primer pairs for HAdV-D L2 gene (encoding for penton base protein) was used to amplify the target gene and only positive samples were sent to sequencing. Results The results revealed that only 6 samples give positive results for L2 gene amplification and then sent for sequencing for L2 (penton protein) gene-based typing. The results show that 4 local isolates (S1, S2, S3, S6) were similar to HAdV-D8 and 2 local isolates (S4, S5) were similar to HAdV-D20. Also the results display that the HAdV-37, prominent HAdV-D type of human eye infection, may be variant of HAdV-D20 due to that six variation were seen in S4and S5 local isolates nucleotide sequence in relation to HAdV-D37: T>C at position 14364, A>C at position 14411, T>C at position 14427, C>A at position 14448, G>A at position 14540 and T>C at position 14617, leading to only 2 amino acid change in resulted penton protein: T (Threonine) instead of K (Lysine) at position 204 and N (Asparagine) instead of D (Aspartic acid) at position 247. Conclusion The current study concludes the possibility of implication of HAdV-D20 in eye infections especially conjunctivitis.
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Nguyen TTH, Le TA, Nguyen VH, Nguyen TU, Nguyen PT, Tran TTA, Nguyen QH, Hoang AT, Hoang MH, Le TS, Nguyen VS. Molecular typing of conjunctivitis-causing adenoviruses in Hanoi, Vietnam from 2017 to 2019 and complete genome analysis of the most prevalent type (HAdV-8). J Med Virol 2020; 92:3100-3110. [PMID: 32266999 DOI: 10.1002/jmv.25844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/12/2020] [Accepted: 04/06/2020] [Indexed: 11/11/2022]
Abstract
Adenoviral conjunctivitis is a common epidemic worldwide. In Vietnam, up to 80,000 patients are infected with adenoviral conjunctivitis annually. However, there are few investigations on the pathogenic adenoviruses that cause conjunctivitis. In total, 120 eye-swab samples were collected from patients with viral conjunctivitis symptoms in Hanoi, Vietnam from 2017 to 2019. Human adenoviruse (HAdV) was detected in 67 samples (55.83%) using polymerase chain reaction amplification of at least one of three HAdV-specific marker genes (hexon, penton, and fiber). Of the 67 HAdV samples, 46 samples could be analyzed by all three marker genes. DNA sequence analysis and phylogenetic tree building based on the three marker genes from the 46 HAdV samples revealed five different HAdV types associated with conjunctivitis in Hanoi, including HAdV-3 (4.3%), HAdV-4 (2.2%), HAdV-8 (89.1%), HAdV-37 (2.2%), and a potential recombinant type between types HAdV-8 and HAdV-3 (2.2%). This showed that HAdV-8 was the most common type identified in Hanoi. Complete genome analysis of HAdV-8 isolated from a Vietnamese patient (VN2017) using Sanger sequencing revealed 34 unique nucleotide changes, indicating that the adenovirus continuously accumulates new mutations. Hence, continuous surveillance of HAdV-8 changes in Vietnam is necessary in the future.
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MESH Headings
- Humans
- Vietnam/epidemiology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/classification
- Adenoviruses, Human/isolation & purification
- Phylogeny
- Adenovirus Infections, Human/virology
- Adenovirus Infections, Human/epidemiology
- Genome, Viral/genetics
- Molecular Typing
- Male
- Conjunctivitis, Viral/virology
- Conjunctivitis, Viral/epidemiology
- Female
- Adult
- Whole Genome Sequencing
- Middle Aged
- Prevalence
- Sequence Analysis, DNA
- DNA, Viral/genetics
- Young Adult
- Genotype
- Adolescent
- Child
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Affiliation(s)
- Thi Thu Huyen Nguyen
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tuan Anh Le
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Viet Ha Nguyen
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Thi Uyen Nguyen
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Phuong Thao Nguyen
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Thi Thuy Anh Tran
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Quang Hung Nguyen
- Faculty of General Diagnostic, National Hospital of Ophthalmology, Hanoi, Vietnam
| | - Anh Tuan Hoang
- Faculty of General Diagnostic, National Hospital of Ophthalmology, Hanoi, Vietnam
| | - My Hanh Hoang
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tho Son Le
- Department of Molecular Genetics and Gene Technology, College of Forestry Biotechnology, Vietnam National Forestry University, Hanoi, Vietnam
| | - Van Sang Nguyen
- Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
- Molecular and Cellular Biology Laboratory, Center for Life Science, Faculty of Biology, VNU University of Science, Vietnam National University, Hanoi, Vietnam
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Baker AT, Mundy RM, Davies JA, Rizkallah PJ, Parker AL. Human adenovirus type 26 uses sialic acid-bearing glycans as a primary cell entry receptor. SCIENCE ADVANCES 2019; 5:eaax3567. [PMID: 31517055 PMCID: PMC6726447 DOI: 10.1126/sciadv.aax3567] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/29/2019] [Indexed: 05/02/2023]
Abstract
Adenoviruses are clinically important agents. They cause respiratory distress, gastroenteritis, and epidemic keratoconjunctivitis. As non-enveloped, double-stranded DNA viruses, they are easily manipulated, making them popular vectors for therapeutic applications, including vaccines. Species D adenovirus type 26 (HAdV-D26) is both a cause of EKC and other diseases and a promising vaccine vector. HAdV-D26-derived vaccines are under investigation as protective platforms against HIV, Zika, and respiratory syncytial virus infections and are in phase 3 clinical trials for Ebola. We recently demonstrated that HAdV-D26 does not use CD46 or Desmoglein-2 as entry receptors, while the putative interaction with coxsackie and adenovirus receptor is low affinity and unlikely to represent the primary cell receptor. Here, we establish sialic acid as a primary entry receptor used by HAdV-D26. We demonstrate that removal of cell surface sialic acid inhibits HAdV-D26 infection, and provide a high-resolution crystal structure of HAdV-D26 fiber-knob in complex with sialic acid.
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Affiliation(s)
- Alexander T. Baker
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Rosie M. Mundy
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - James A. Davies
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Pierre J. Rizkallah
- Division of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alan L. Parker
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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Aoki K, Gonzalez G, Hinokuma R, Yawata N, Tsutsumi M, Ohno S, Kitaichi N. Assessment of clinical signs associated with adenoviral epidemic keratoconjunctivitis cases in southern Japan between 2011 and 2014. Diagn Microbiol Infect Dis 2019; 95:114885. [PMID: 31607514 DOI: 10.1016/j.diagmicrobio.2019.114885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 01/03/2023]
Abstract
Adenoviral epidemic keratoconjunctivitis (EKC) is a major cause of ocular morbidity worldwide and specific antiviral therapies are not available. EKC is primarily caused by Human adenovirus D (HAdV-D) types 8, 37, 53, 54, 56 and 64. Considering the genomic variation in HAdV-D, we hypothesized that clinical signs could be differentiated by virus type. The hypothesis was retrospectively tested with clinical signs recorded from 250 patients with ocular infections visiting an ophthalmological clinic in southern Japan between 2011 and 2014. The results showed that conjunctival opacity, corneal epithelial disorders and pre-auricular lymphadenopathy, were more frequently associated with EKC than other ocular infections. Furthermore, HAdV types 8, 37 and 54, caused corneal complications and longer infections significantly more frequently than infections by types 53 and 56 (P < 0.05). Our descriptive results supported that symptoms severity vary with the infecting type, however, further research is needed to improve diagnosis of EKC.
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Affiliation(s)
- Koki Aoki
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | - Nobuyo Yawata
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Singapore Eye Research Institute, Singapore; Duke-NUS Medical School, Singapore
| | - Masayuki Tsutsumi
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan.
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Paskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA. Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples. BMC Genomics 2019; 20:155. [PMID: 30808306 PMCID: PMC6390631 DOI: 10.1186/s12864-019-5543-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814 USA
- Leidos, Reston, VA 20190 USA
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | | | | | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, Fort Detrick, Frederick, MD 21702 USA
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Gonzalez G, Yawata N, Aoki K, Kitaichi N. Challenges in management of epidemic keratoconjunctivitis with emerging recombinant human adenoviruses. J Clin Virol 2019; 112:1-9. [PMID: 30654207 DOI: 10.1016/j.jcv.2019.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/21/2018] [Accepted: 01/08/2019] [Indexed: 01/14/2023]
Abstract
Adenoviral epidemic keratoconjunctivitis (EKC) presents as severe conjunctival inflammations involving the cornea that can lead to the development of corneal opacities and blurred vision, which can persist for months. EKC is highly contagious and responsible for outbreaks worldwide, therefore accurate diagnosis and rapid containment are imperative. EKC is caused by a number of types within Human adenovirus species D (HAdV-D): 8, 37 and 64 (formerly known as 19a) and these types were considered the major causes of EKC for over fifty years. Nonetheless, recent improved molecular typing methodologies have identified recombinant HAdV-D types 53, 54 and 56, as newly emerging etiologic agents of EKC infections worldwide. EKC cases due to these recombinant types have potentially been underdiagnosed and underestimated as a source of new EKC outbreaks. Recombination events among circulating HAdV-D types represent a source of new infectious disease threats. Also, the growing number of adenoviral types enabled genomic and phenotypic comparisons to determine pathological properties related to EKC. This review covers the clinical features of EKC, current challenges in clinical practice and recent progress in EKC-related HAdV research, which focuses on the development of novel diagnostic and therapeutic approaches.
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Affiliation(s)
- Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Nobuyo Yawata
- Department of Medicine, Ophthalmology, Fukuoka Dental College, Fukuoka, Japan; Singapore Eye Research Institute, Singapore; Department of Ophthalmology, Kyushu University, Japan; Duke-NUS Medical School, Singapore
| | - Koki Aoki
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo, Japan.
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8
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Uzuner H, Karadenizli A, Er D, Osmani A. Investigation of the efficacy of alcohol-based solutions on adenovirus serotypes 8, 19 and 37, common causes of epidemic keratoconjunctivitis, after an adenovirus outbreak in hospital. J Hosp Infect 2018; 100:e30-e36. [DOI: 10.1016/j.jhin.2018.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/16/2018] [Indexed: 10/16/2022]
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9
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Lamson BS DM, Kajon AE, Shudt M, Quinn M, Newman A, Whitehouse J, Greenko J, Adams E, St. George K. Molecular typing and whole genome next generation sequencing of human adenovirus 8 strains recovered from four 2012 outbreaks of keratoconjunctivitis in New York State. J Med Virol 2018; 90:1471-1477. [DOI: 10.1002/jmv.25223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 05/06/2018] [Indexed: 12/26/2022]
Affiliation(s)
| | - Adriana E. Kajon
- Lovelace Respiratory Research Institute; Infectious Disease Program; Albuquerque New Mexico
| | - Matthew Shudt
- Wadsworth Center; New York State Department of Health; Albany New York
| | - Monica Quinn
- Healthcare Epidemiology and Infection Control Program; New York State Department of Health; Albany New York
| | - Alexandra Newman
- Bureau of Communicable Disease Control; New York State Department of Health; Albany New York
| | - Joan Whitehouse
- Healthcare Epidemiology and Infection Control Program; New York State Department of Health; New Rochelle New York
| | - Jane Greenko
- Healthcare Epidemiology and Infection Control Program; New York State Department of Health; Long Island New York
| | - Eleanor Adams
- Healthcare Epidemiology and Infection Control Program; New York State Department of Health; New Rochelle New York
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Zhang W, Fu J, Liu J, Wang H, Schiwon M, Janz S, Schaffarczyk L, von der Goltz L, Ehrke-Schulz E, Dörner J, Solanki M, Boehme P, Bergmann T, Lieber A, Lauber C, Dahl A, Petzold A, Zhang Y, Stewart AF, Ehrhardt A. An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity. Cell Rep 2018; 19:1698-1709. [PMID: 28538186 DOI: 10.1016/j.celrep.2017.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/12/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Adenoviruses (Ads) are large human-pathogenic double-stranded DNA (dsDNA) viruses presenting an enormous natural diversity associated with a broad variety of diseases. However, only a small fraction of adenoviruses has been explored in basic virology and biomedical research, highlighting the need to develop robust and adaptable methodologies and resources. We developed a method for high-throughput direct cloning and engineering of adenoviral genomes from different sources utilizing advanced linear-linear homologous recombination (LLHR) and linear-circular homologous recombination (LCHR). We describe 34 cloned adenoviral genomes originating from clinical samples, which were characterized by next-generation sequencing (NGS). We anticipate that this recombineering strategy and the engineered adenovirus library will provide an approach to study basic and clinical virology. High-throughput screening (HTS) of the reporter-tagged Ad library in a panel of cell lines including osteosarcoma disease-specific cell lines revealed alternative virus types with enhanced transduction and oncolysis efficiencies. This highlights the usefulness of this resource.
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Affiliation(s)
- Wenli Zhang
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jing Liu
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Maren Schiwon
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Sebastian Janz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas Schaffarczyk
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas von der Goltz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Eric Ehrke-Schulz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Johannes Dörner
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Manish Solanki
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Philip Boehme
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Thorsten Bergmann
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Andre Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195-7720, USA
| | - Chris Lauber
- Institute for Medical Informatics and Biometry, Carl Gustav Carus, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Petzold
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China.
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Anja Ehrhardt
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany.
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11
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Hage E, Espelage W, Eckmanns T, Lamson DM, Pantó L, Ganzenmueller T, Heim A. Molecular phylogeny of a novel human adenovirus type 8 strain causing a prolonged, multi-state keratoconjunctivitis epidemic in Germany. Sci Rep 2017; 7:40680. [PMID: 28084428 PMCID: PMC5234003 DOI: 10.1038/srep40680] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022] Open
Abstract
The German infectious disease surveillance system revealed an increase of epidemic keratoconjunctivitis (EKC) from an average of 320 cases/year (2001 to 2010) up to 2146 and 1986 cases in 2012 and 2013, respectively. From November 2011 until December 2013 (epidemic period) 85% of typed isolates were human adenovirus type 8 (HAdV-D8), whereas only low level circulation (19%) of HAdV-D8 was observed outside the epidemic period. In order to investigate whether a novel monophyletic HAdV-D8 strain prevailed during the epidemic period, complete genomic sequences of 23 HAdV-D8 isolates were generated by deep sequencing and analyzed phylogenetically. For comparison, eight HAdV-D8 isolates from outside the epidemic period were sequenced. HAdV-D8 isolates of the epidemic period had a very high sequence identity of at least 99.9% and formed a monophyletic cluster with two subclusters. A single outlier was closely related to HAdV-D8 strains isolated prior to the epidemic period. Circulation of the epidemic strain was detected as early as 2010 but not after the epidemic period in 2014. In conclusion, molecular phylogeny of complete genomic sequences proved a monophyletic HAdV-D8 epidemic. However, co-circulation of other HAdV types as well as better reporting may have contributed to the huge increase of reported cases.
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Affiliation(s)
- Elias Hage
- Institute of Virology, Konsiliarlabor für Adenoviren (KLA, Adenovirus Reference Laboratory); Hannover Medical School, Hannover, Germany
| | - Werner Espelage
- Department for Infectious Disease Epidemiology, Unit for Nosocomial Infections, Surveillance of Antimicrobial Resistance and Consumption, Robert Koch Institut, Berlin, Germany
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Unit for Nosocomial Infections, Surveillance of Antimicrobial Resistance and Consumption, Robert Koch Institut, Berlin, Germany
| | - Daryl M Lamson
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Laura Pantó
- Laboratory of Genome Sciences, Division of Bioengineering and Bioinformatics, Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Tina Ganzenmueller
- Institute of Virology, Konsiliarlabor für Adenoviren (KLA, Adenovirus Reference Laboratory); Hannover Medical School, Hannover, Germany
| | - Albert Heim
- Institute of Virology, Konsiliarlabor für Adenoviren (KLA, Adenovirus Reference Laboratory); Hannover Medical School, Hannover, Germany
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12
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Hoyle E, Erez JC, Kirk-Granger HR, Collins E, Tang JW. An adenovirus 4 outbreak amongst staff in a pediatric ward manifesting as keratoconjunctivitis-a possible failure of contact and aerosol infection control. Am J Infect Control 2016; 44:602-4. [PMID: 26804304 DOI: 10.1016/j.ajic.2015.11.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022]
Abstract
An adenovirus serotype 4 outbreak was identified on a pediatric ward involving 4 members of the health care staff. Two inpatients on the ward at the time (1 immunocompromised) were shedding this virus from their respiratory tracts and could have acted as independent index cases for the staff infections. Significantly, upon investigation, it was found that staff members were unaware that adenoviruses are not completely eliminated by alcohol gel handrubs and that soap and water handwashing is also required.
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Affiliation(s)
- Elizabeth Hoyle
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Joanne C Erez
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Helen R Kirk-Granger
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Elizabeth Collins
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Julian W Tang
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom.
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13
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Lim MCY, Wang YF, Huang SW, Yang JY, Wang JR. High Incidence of Mammalian Orthoreovirus Identified by Environmental Surveillance in Taiwan. PLoS One 2015; 10:e0142745. [PMID: 26555962 PMCID: PMC4640864 DOI: 10.1371/journal.pone.0142745] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/25/2015] [Indexed: 12/21/2022] Open
Abstract
Wild poliovirus (WPV) persists in diverse locales worldwide, spreading outward from endemic areas. In response to the international threat of WPV transmission and changes in the national vaccination policy, we established an environmental surveillance system to monitor the circulation of wild and vaccine-related poliovirus in Taiwan. From July 2012 to December 2013, we collected sewage specimens every month from 10 sewage treatment plants located throughout Taiwan. The specimens were concentrated by the two-phase separation method and then inoculated into L20B, RD, and A549 cells for virus isolation. Viral isolates were identified and serotyped by immunofluorescence assay or molecular analysis. A total of 300 sewage samples were collected, and the results showed 163 samples (54.3%) were positive for virus, and 268 isolates were identified. Among these, 75 samples (25%) were positive for enterovirus (EV), but no poliovirus was found. In addition, 92 isolates were identified as enteroviruses and the most common serotypes were coxsackievirus B4, coxsackievirus B3, and coxsackievirus B2. Interestingly, 102 (34%) and 82 (27.3%) specimens were positive for mammalian orthoreovirus (MRV) and adenovirus, respectively. This study confirmed that sewage surveillance can be a useful additional modality for monitoring the possible presence of wild-type or vaccine-derived poliovirus in wastewater, and can indicate the current types of viruses circulating in the population. Furthermore, since MRV was found in children with acute necrotizing encephalopathy and meningitis, the high incidence of MRV detected by environmental surveillance warrants further investigation.
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Affiliation(s)
- Matthew C. Y. Lim
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Fang Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Sheng-Wen Huang
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Jyh-Yuan Yang
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
- * E-mail:
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14
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Singh G, Zhou X, Lee JY, Yousuf MA, Ramke M, Ismail AM, Lee JS, Robinson CM, Seto D, Dyer DW, Jones MS, Rajaiya J, Chodosh J. Recombination of the epsilon determinant and corneal tropism: Human adenovirus species D types 15, 29, 56, and 69. Virology 2015; 485:452-9. [PMID: 26343864 DOI: 10.1016/j.virol.2015.08.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 07/03/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022]
Abstract
Viruses within human adenovirus species D (HAdV-D) infect epithelia at essentially every mucosal site. Hypervariable loops 1 and 2 of the hexon capsid protein contain epitopes that together form the epsilon determinant for serum neutralization. We report our analyses comparing HAdV-D15, 29, 56, and the recently identified type 69, each with highly similar hexons and the same serum neutralization profile, but otherwise disparate genomes. Of these, only HAdV-D type 56 is associated with epidemic keratoconjunctivitis (EKC), a severe infection of ocular surface epithelium and underlying corneal stroma. In the mouse adenovirus keratitis model, all four viruses induced inflammation. However, HAdV-D56 entry into human corneal epithelial cells and fibroblasts in vitro dramatically exceeded that of the other three viruses. We conclude that the hexon epsilon determinant is not a prime contributor to corneal tropism.
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Affiliation(s)
- Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Mohammad A Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Mirja Ramke
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Ashrafali M Ismail
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Christopher M Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, United States
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Morris S Jones
- Division of Infectious Diseases, Naval Medical Center San Diego, San Diego, CA, United States
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States.
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States.
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15
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Kelishadi M, Kelishadi M, Moradi A, Javid N, Bazouri M, Tabarraei A. human adenoviruses role in ophthalmic pterygium formation. Jundishapur J Microbiol 2015; 8:e16871. [PMID: 26034543 PMCID: PMC4449841 DOI: 10.5812/jjm.16871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 05/31/2014] [Accepted: 06/08/2014] [Indexed: 02/05/2023] Open
Abstract
Background: Ophthalmic pterygium is a common benign lesion of unknown origin and the pathogenesis might be vision-threatening. This problem is often associated with exposure to solar light. Recent evidence suggests that potentially oncogenic viruses such as human papillomavirus and Epstein-Barr virus may be involved in the pathogenesis of pterygia. Expression of specific adenovirus genes such as E1A and E1B, which potentially have many functions, may contribute to their oncogenic activity as well as relevance to cellular immortalization. Objectives: For the first time, we aimed to investigate involvement of adenoviruses in pterygium formation. Patients and Methods: Fifty tissue specimens of pterygium from patients undergoing pterygium surgery (as cases), 50 conjunctival swab samples from the same patients and 10 conjunctival biopsy specimens from individuals without pterygium such as patients undergoing cataract surgery (as controls) were analyzed for evidence of adenovirus infection with polymerase chain reaction using specific primers chosen from the moderately conserved region of the hexon gene. Furthermore, β-globin primers were used to access the quality of extracted DNA. Data was analyzed using SPSS (version 16) software. Results: Of 50 patients, 20 were men and 30 women with mean age of 61.1 ± 16.9 years ranged between 22 and 85 years. All samples of pterygia had positive results for adenoviruses DNA with polymerase chain reaction, but none of the negative control groups displayed adenoviruses. The pterygium group and the control groups were β-globin positive. Direct sequencing of PCR products confirmed Adenovirus infection. Conclusions: Adenoviruses might act as a possible cause of pterygium formation and other factors could play a synergistic role in the development. However, further larger studies are required to confirm this hypothesis.
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Affiliation(s)
- Mishar Kelishadi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | | | - Abdolvahab Moradi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Naeme Javid
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Masoud Bazouri
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Alijan Tabarraei
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
- Corresponding author: Alijan Tabarraei, Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran. Tel: +98-1714422652, Fax: +98-1714440225, E-mail:
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16
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Li Y, Zhou W, Zhao Y, Wang Y, Xie Z, Lou Y, Tan W. Molecular typing and epidemiology profiles of human adenovirus infection among paediatric patients with severe acute respiratory infection in China. PLoS One 2015; 10:e0123234. [PMID: 25856575 PMCID: PMC4391708 DOI: 10.1371/journal.pone.0123234] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/02/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Human adenoviruses (HAdVs) have been recognised as pathogens that cause a broad spectrum of diseases. The studies on HAdV infection among children with severe acute respiratory infection (SARI) are limited. OBJECTIVE To investigate the prevalence, epidemiology, and genotype of HAdV among children with SARI in China. STUDY DESIGN Nasopharyngeal aspirates (NPAs) or induced sputum (IS) was collected from hospitalised children with SARIs in Beijing (representing Northern China; n = 259) and Zhejiang Province (representing Eastern China; n = 293) from 2007 to 2010. The prevalence of HAdV was screened by polymerase chain reaction (PCR), followed by sequence typing of PCR fragments that targeted the second half of the hexon gene. In addition, co-infection with other human respiratory viruses, related epidemiological profiles and clinical presentations were investigated. RESULTS AND CONCLUSIONS In total, 76 (13.8%) of 552 SARI patients were positive for HAdV, and the infection rates of HAdV in Northern and Eastern China were 20.1% (n = 52) and 8.2% (n = 24), respectively. HAdV co-infection with other respiratory viruses was frequent (infection rates: Northern China, 90.4%; Eastern China, 70.8%). The peak seasons for HAdV-B infection was winter and spring. Additionally, members of multiple species (Human mastadenovirus B, C, D and E) were circulating among paediatric patients with SARI, of which HAdV-B (34/52; 65.4%) and HAdV-C (20/24, 83.3%) were the most predominant in Northern and Eastern China, respectively. These findings provide a benchmark for future epidemiology and prevention strategies for HAdV.
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Affiliation(s)
- Yamin Li
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Weimin Zhou
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yanjie Zhao
- Institute of Medical Virology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanqun Wang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhengde Xie
- Beijing Pediatric Research Institute, BCH-CMU, Beijing, China
| | - Yongliang Lou
- Institute of Medical Virology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenjie Tan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
- * E-mail:
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17
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Fujimoto T, Yamane S, Ogawa T, Hanaoka N, Ogura A, Hotta C, Niwa T, Chiba Y, Gonzalez G, Aoki K, Koyanagi KO, Watanabe H. A novel complex recombinant form of type 48-related human adenovirus species D isolated in Japan. Jpn J Infect Dis 2015; 67:282-7. [PMID: 25056074 DOI: 10.7883/yoken.67.282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
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 98%, 99%, 95% and 98% 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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18
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Adhikary AK, Banik U. Human adenovirus type 8: the major agent of epidemic keratoconjunctivitis (EKC). J Clin Virol 2014; 61:477-86. [PMID: 25464969 DOI: 10.1016/j.jcv.2014.10.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 10/20/2014] [Accepted: 10/25/2014] [Indexed: 11/25/2022]
Abstract
Human adenovirus type 8 (HAdV-8) is the most common causative agent of a highly contagious eye disease known as epidemic keratoconjunctivitis (EKC). HAdV-8 strains have been classified into genome types HAdV-8A to 8K and HAdV/D1 to D12 according to restriction endonuclease analysis. This review focuses on the significance of HAdV-8 as an agent of EKC. Molecular analysis of HAdV-8 genome types HAdV-53 and HAdV-54 was performed to reveal potential genetic variation in the hexon and fiber, which might affect the antigenicity and tropism of the virus, respectively. On the basis of the published data, three patterns of HAdV-8 genome type distribution were observed worldwide: (1) genome types restricted to a microenvironment, (2) genome types distributed within a country, and (3) globally dispersed genome types. Simplot and zPicture showed that the HAdV-8 genome types were nearly identical to each other. HAdV-54 is very close to the HAdV-8P, B and E genomes, except in the hexon. In a restriction map, HAdV-8P, B, and E share a very high percentage of restriction sites with each other. Hypervariable regions (HVRs) of the hexon were conserved and were 100% identical among the genome types. The fiber knob of HAdV-8P, A, E, J and HAdV-53 were 100% identical. In phylogeny, HVRs of the hexon and fiber knob of the HAdV-8 genome types segregated into monophyletic clusters. Neutralizing antibodies against one genome type will provide protection against other genome types, and the selection of future vaccine strains would be simple due to the stable HVRs. Molecular analysis of whole genomes, particularly of the capsid proteins of the remaining genome types, would be useful to substantiate our observations.
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Affiliation(s)
- Arun Kumar Adhikary
- Unit of Microbiology, Faculty of Medicine, AIMST University, 08100 Bedong, Semeling, Kedah Darul Aman, Malaysia.
| | - Urmila Banik
- Unit of Pathology, Faculty of Medicine, AIMST University, 08100 Bedong, Semeling, Kedah Darul Aman, Malaysia
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19
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Ghebremedhin B. Human adenovirus: Viral pathogen with increasing importance. Eur J Microbiol Immunol (Bp) 2014; 4:26-33. [PMID: 24678403 DOI: 10.1556/eujmi.4.2014.1.2] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 12/21/2013] [Indexed: 11/19/2022] Open
Abstract
The aim of this review is to describe the biology of human adenovirus (HAdV), the clinical and epidemiological characteristics of adenoviral epidemic keratoconjunctivitis and to present a practical update on its diagnosis, treatment, and prophylaxis. There are two well-defined adenoviral keratoconjunctivitis clinical syndromes: epidemic keratoconjunctivitis (EKC) and pharyngoconjunctival fever (PCF), which are caused by different HAdV serotypes. The exact incidence of adenoviral conjunctivitis is still poorly known. However, cases are more frequent during warmer months. The virus is endemic in the general population, and frequently causes severe disease in immunocompromised patients, especially the pediatric patients. Contagion is possible through direct contact or fomites, and the virus is extremely resistant to different physical and chemical agents. The clinical signs or symptoms of conjunctival infection are similar to any other conjunctivitis, with a higher incidence of pseudomembranes. In the cornea, adenoviral infection may lead to keratitis nummularis. Diagnosis is mainly clinical, but its etiology can be confirmed using cell cultures, antigen detection, polymerase chain reaction or immunochromatography. Multiple treatments have been tried for this disease, but none of them seem to be completely effective. Prevention is the most reliable and recommended strategy to control this contagious infection.
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20
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Pauly M, Hoppe E, Mugisha L, Petrzelkova K, Akoua-Koffi C, Couacy-Hymann E, Anoh AE, Mossoun A, Schubert G, Wiersma L, Pascale S, Muyembe JJ, Karhemere S, Weiss S, Leendertz SA, Calvignac-Spencer S, Leendertz FH, Ehlers B. High prevalence and diversity of species D adenoviruses (HAdV-D) in human populations of four Sub-Saharan countries. Virol J 2014; 11:25. [PMID: 24512686 PMCID: PMC3928611 DOI: 10.1186/1743-422x-11-25] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/07/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human adenoviruses of species D (HAdV-D) can be associated with acute respiratory illness, epidemic keratoconjunctivitis, and gastroenteritis, but subclinical HAdV-D infections with prolonged shedding have also been observed, particularly in immunocompromised hosts. To expand knowledge on HAdV-D in Sub-Saharan Africa, we investigated the prevalence, epidemiology and pathogenic potential of HAdV-D in humans from rural areas of 4 Sub-Saharan countries, Côte d'Ivoire (CI), Democratic Republic of the Congo (DRC), Central African Republic (CAR) and Uganda (UG). METHODS Stool samples were collected from 287 people living in rural regions in CI, DRC, CAR and UG. HAdV-D prevalence and diversity were determined by PCR and sequencing. A gene block, spanning the genes pV to hexon, was used for analysis of genetic distance. Correlation between adenovirus infection and disease symptoms, prevalence differences, and the effect of age and gender on infection status were analyzed with cross tables and logistic regression models. RESULTS The prevalence of HAdV-D in the investigated sites was estimated to be 66% in CI, 48% in DRC, 28% in CAR (adults only) and 65% in UG (adults only). Younger individuals were more frequently infected than adults; there was no difference in HAdV-D occurrence between genders. No correlation could be found between HAdV-D infection and clinical symptoms. Highly diverse HAdV-D sequences were identified, among which a number are likely to stand for novel types. CONCLUSIONS HAdV-D was detected with a high prevalence in study populations of 4 Sub-Saharan countries. The genetic diversity of the virus was high and further investigations are needed to pinpoint pathological potential of each of the viruses. High diversity may also favor the emergence of recombinants with altered tropism and pathogenic properties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bernhard Ehlers
- Division 12 "Measles, Mumps, Rubella and Viruses affecting immunocompromised patients", Robert Koch Institute, Berlin 13353, Germany.
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Ylihärsilä M, Harju E, Arppe R, Hattara L, Hölsä J, Saviranta P, Soukka T, Waris M. Genotyping of clinically relevant human adenoviruses by array-in-well hybridization assay. Clin Microbiol Infect 2013; 19:551-7. [PMID: 22712766 PMCID: PMC7129513 DOI: 10.1111/j.1469-0691.2012.03926.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A robust oligonucleotide array-in-well hybridization assay using novel up-converting phosphor reporter technology was applied for genotyping clinically relevant human adenovirus types. A total of 231 adenovirus-positive respiratory, ocular swab, stool and other specimens from 219 patients collected between April 2010 and April 2011 were included in the study. After a real-time PCR amplification targeting the adenovirus hexon gene, the array-in-well assay identified the presence of B03 (n = 122; 57.5% of patients), E04 (29; 13.7%), C02 (21; 9.9%), D37 (14; 6.6%), C01 (12; 5.7%), C05 (5; 2.4%), D19 (4; 1.9%), C06 (2; 0.9%), D08 (1; 0.5%), A31 (1; 0.5%) and F41 (1; 0.5%) genotypes among the clinical sample panel. The typing result was obtained for all specimens that could be amplified (n = 223; 97%), and specificity of the typing was confirmed by sequencing specimens representing each of the different genotypes. No hybridization signal was obtained in adenovirus-negative specimens or specimens with other viruses (n = 30). The array-in-well hybridization assay has great potential as a rapid and multiplex platform for the typing of clinically relevant human adenovirus genotypes in different specimen types.
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Affiliation(s)
- M Ylihärsilä
- Department of Virology, University of Turku, Turku, Finland.
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22
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Fongaro G, Nascimento MAD, Rigotto C, Ritterbusch G, da Silva ADA, Esteves PA, Barardi CRM. Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays. Virol J 2013; 10:166. [PMID: 23714224 PMCID: PMC3686584 DOI: 10.1186/1743-422x-10-166] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/24/2013] [Indexed: 11/10/2022] Open
Abstract
Background Human adenoviruses (HAdVs) are the second-leading cause of childhood gastroenteritis worldwide. This virus is commonly found in environmental waters and is very resistant to water disinfection and environmental stressors, especially UV light inactivation. Molecular techniques, such as PCR-based methods (Polymerase Chain Reaction), are commonly used to detect and identify viral contamination in water, although PCR alone does not allow the discrimination between infectious and non-infectious viral particles. A combination of cell culture and PCR has allowed detection of infectious viruses that grow slowly or fail to produce cytopathic effects (CPE) in cell culture. This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system. Methods Water samples were collected, concentrated and HAdV quantified by real-time PCR. Viral integrity was evaluated by enzymatic assay (DNase I) and infectivity by plaque assay (PA) and integrated cell culture using transcribed mRNA (ICC-RT-qPCR). Samples containing particles of infectious HAdV were selected for sequencing and molecular characterization. Results The analyzed sites contained 83, 66 and 58% undamaged HAdV particles (defined as those in which the genetic material is protected by the viral capsid) at Peri Lagoon, spring source water and public supply system water, respectively. Of these, 66% of the particles (by PA) and 75% (by ICC-RT-qPCR) HAdV were shown to be infectious, due to being undamaged in Peri Lagoon, 33% (by PA) and 58% (by ICC-RT-qPCR) in spring source water and 8% (by PA) and 25% (by ICC-RT-qPCR) in the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1 × 102 HAdV genome copies per milliliter of infectious viral particles in the environmental water samples. The molecular characterization studies indicated that HAdV-2 was the prevalent serotype. Conclusions These results indicate a lack of proper public health measures. We suggest that HAdV can be efficiently used as a marker of environmental and drinking water contamination and ICC-RT-qPCR demonstrated greater sensitivity and speed of detection of infectious viral particles compared to PA.
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Affiliation(s)
- Gislaine Fongaro
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil
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23
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Robinson CM, Zhou X, Rajaiya J, Yousuf MA, Singh G, DeSerres JJ, Walsh MP, Wong S, Seto D, Dyer DW, Chodosh J, Jones MS. Predicting the next eye pathogen: analysis of a novel adenovirus. mBio 2013; 4:e00595-12. [PMID: 23572555 PMCID: PMC3622935 DOI: 10.1128/mbio.00595-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/12/2013] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED For DNA viruses, genetic recombination, addition, and deletion represent important evolutionary mechanisms. Since these genetic alterations can lead to new, possibly severe pathogens, we applied a systems biology approach to study the pathogenicity of a novel human adenovirus with a naturally occurring deletion of the canonical penton base Arg-Gly-Asp (RGD) loop, thought to be critical to cellular entry by adenoviruses. Bioinformatic analysis revealed a new highly recombinant species D human adenovirus (HAdV-D60). A synthesis of in silico and laboratory approaches revealed a potential ocular tropism for the new virus. In vivo, inflammation induced by the virus was dramatically greater than that by adenovirus type 37, a major eye pathogen, possibly due to a novel alternate ligand, Tyr-Gly-Asp (YGD), on the penton base protein. The combination of bioinformatics and laboratory simulation may have important applications in the prediction of tissue tropism for newly discovered and emerging viruses. IMPORTANCE The ongoing dance between a virus and its host distinctly shapes how the virus evolves. While human adenoviruses typically cause mild infections, recent reports have described newly characterized adenoviruses that cause severe, sometimes fatal human infections. Here, we report a systems biology approach to show how evolution has affected the disease potential of a recently identified novel human adenovirus. A comprehensive understanding of viral evolution and pathogenicity is essential to our capacity to foretell the potential impact on human disease for new and emerging viruses.
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MESH Headings
- Adenoviridae Infections/virology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Animals
- Cell Line
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Disease Models, Animal
- Eye Diseases/virology
- Female
- Humans
- Infant, Newborn
- Male
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Protein Conformation
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Deletion
- Systems Biology
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Tropism
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Michael P. Walsh
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Sallene Wong
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
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Chigor VN, Okoh AI. Quantitative detection and characterization of human adenoviruses in the Buffalo River in the Eastern Cape Province of South Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2012; 4:198-208. [PMID: 23412891 DOI: 10.1007/s12560-012-9090-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 10/06/2012] [Indexed: 05/18/2023]
Abstract
Buffalo River is an important water resource in the Eastern Cape Province of South Africa. Over a 1-year period (August 2010-July 2011), we assessed the prevalence of human adenoviruses (HAdVs) at a total of 6 sites on the river and three dams along its course. HAdVs were detected by real-time quantitative PCR in about 35 % of the samples with concentrations ranging from 1.2 × 10(1) genome copies (GC)/l to 4.71 × 10(3) GC/l. HAdVs were detected at 5 of the 6 sampling sites with the detection rate ranging from 8.3 % at Rooikrantz Dam to 92 % at Parkside. The HAdV concentrations across the sampling sites were as follows: Parkside (3.25 × 10(2)-4.71 × 10(3) GC/); King William's Town (1.02 × 10(2)-4.56 × 10(3) GC/l); and Eluxolzweni (1.17 × 10(2)-3.97 × 10(2) GC/l). Significantly (P < 0.05) higher concentrations were detected at the non-dam sites compared to the dam sites. A very low mean concentration of 1.86 × 10(1) HAdV GC/l was observed at Bridle Drift Dam. While HAdVs were detected only once at Rooikrantz Dam (1.74 × 10(1) GC/l), no HAdV was detected at Maden Dam. Epidemiologically important serotypes, Ad40/41, constituted 83.3 %, while Ad21 made up 16.7 % of the all HAdVs detected and were characterized by qualitative PCR. The Buffalo River presents a public health risk heightened by the presence of Ad 40/41 and Ad21. Our results make imperative the need for assessing water sources for viral contamination in the interest of public health. This work is a significant contribution to the molecular epidemiology of adenoviruses and to the best of our knowledge this is the first report on detection of enteric virus from surface waters in the Eastern Cape.
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Affiliation(s)
- Vincent N Chigor
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice, 5700, South Africa.
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25
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Identification of contamination in the American type culture collection stock of human adenovirus type 8 by whole-genome sequencing. J Virol 2012; 87:1285-6. [PMID: 23152510 DOI: 10.1128/jvi.02875-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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26
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Al Qurashi YMA, Alkhalaf MA, Lim L, Guiver M, Cooper RJ. Sequencing and phylogenetic analysis of the hexon, fiber, and penton regions of adenoviruses isolated from AIDS patients. J Med Virol 2012; 84:1157-65. [PMID: 22711343 DOI: 10.1002/jmv.23331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sequencing and phylogenetic analysis of the hexon, fiber, and penton regions of adenoviruses isolated between 1986 and 1997 from AIDS patients has been performed. Sequencing the L2 part of the hexon gene of 51 adenoviruses isolated between 1986 and 1997 from AIDS patients revealed only one type each from species A and C and two types from species B with all the remaining isolates from species D. Further sequencing and phylogenetic analysis of the fiber knob region of these species D adenoviruses revealed that 28/46 were intermediate strains with conflicting hexon and fiber sequences. When the penton regions of these intermediate strains were sequenced, it became clear that some had originated from a third adenovirus type presumably by intergene recombination events. Evidence from sequencing the L1 hexon and fiber shaft regions showed no evidence of intragene recombination but penton sequences showed that recombination between the hypervariable region (HVR) and RGD regions was common. Six isolates appear to be from three new adenovirus types. Five AIDS patients showed sequential infection with different adenovirus variants and six such variants were isolated from a single patient in 2 years.
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Zhou X, Robinson CM, Rajaiya J, Dehghan S, Seto D, Jones MS, Dyer DW, Chodosh J. Analysis of human adenovirus type 19 associated with epidemic keratoconjunctivitis and its reclassification as adenovirus type 64. Invest Ophthalmol Vis Sci 2012; 53:2804-11. [PMID: 22467570 PMCID: PMC3367469 DOI: 10.1167/iovs.12-9656] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/19/2012] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Human adenovirus species D type 19 (HAdV-D19) has been associated with epidemic keratoconjunctivitis (EKC), a highly inflammatory infection of the ocular surface. Confusion exists regarding the origins of HAdV-D19. The prototype virus (HAdV-D19p) does not cause EKC, while a virus identified later with the identical serologic determinant is a significant ocular pathogen. METHODS High throughput genome sequencing and bioinformatics analysis were performed on HAdV-D19p and three HAdV-D19 EKC strains, and compared to the previously sequenced clinical isolate, HAdV-D19 (C) and HAdV-D37. Corneas of C57BL/6J mice were injected with HAdV-D19p, HAdV-D19 (C), or virus-free buffer, and inflammation assessed by clinical examination, flow cytometry, and cytokine ELISA. Confocal microscopy and real-time PCR of infected corneal cell cultures were used to test viral entry. RESULTS HAdV-D19 (C) and the other clinical EKC isolates showed nearly 100% sequence identity. EKC strains diverged from HAdV-D19p in the penton base, E3, and fiber transcription units. Simplot analysis showed recombination between EKC-associated HAdV-D19 with HAdV-D37, HAdV-D22, and HAdV-D19p, the latter contributing only the hexon gene, the principal serum neutralization determinant. HAdV-D19p induced stromal keratitis in the C57BL/6J mouse, but failed to infect productively human corneal epithelial cells. These data led to retyping of the clinical EKC isolates with a HAdV-D19 hexon gene as HAdV-D64. CONCLUSIONS HAdV-D19 associated with EKC (HAdV-D64) originated from a recombination between HAdV-D19p, HAdV-D37, and HAdV-D22, and was mischaracterized because of a shared hexon gene. HAdV-D19p is not infectious for corneal epithelial cells, thus explaining the lack of any association with keratitis.
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Affiliation(s)
- Xiaohong Zhou
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Christopher M. Robinson
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Jaya Rajaiya
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - David W. Dyer
- and the
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - James Chodosh
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
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28
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Singh G, Robinson CM, Dehghan S, Schmidt T, Seto D, Jones MS, Dyer DW, Chodosh J. Overreliance on the hexon gene, leading to misclassification of human adenoviruses. J Virol 2012; 86:4693-5. [PMID: 22301156 PMCID: PMC3318657 DOI: 10.1128/jvi.06969-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/25/2012] [Indexed: 02/02/2023] Open
Abstract
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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Affiliation(s)
- Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Timothy Schmidt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
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29
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Alharbi S, Van Caeseele P, Consunji-Araneta R, Zoubeidi T, Fanella S, Souid AK, Alsuwaidi AR. Epidemiology of severe pediatric adenovirus lower respiratory tract infections in Manitoba, Canada, 1991-2005. BMC Infect Dis 2012; 12:55. [PMID: 22414179 PMCID: PMC3323892 DOI: 10.1186/1471-2334-12-55] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 03/13/2012] [Indexed: 01/19/2023] Open
Abstract
Background Most pediatric adenovirus respiratory infections are mild and indistinguishable from other viral causes. However, in a few children, the disease can be severe and result in substantial morbidity. We describe the epidemiologic, clinical, radiologic features and outcome of adenovirus lower respiratory tract infections (LRTI) in Aboriginal and Non-Aboriginal children in Manitoba, Canada during the years 1991 and 2005. Methods This was a retrospective study of 193 children who presented to the department of pediatrics at Winnipeg Children's Hospital, Manitoba, Canada with LRTI and had a positive respiratory culture for adenovirus. Patients' demographics, clinical and radiologic features and outcomes were collected. Adenovirus serotype distributions and temporal associations were described. Approximate incidence comparisons (detection rates) of adenovirus LRTI among Aboriginal and Non-Aboriginal children were estimated with 95% confidence intervals. Results Adenovirus infections occurred throughout the year with clusters in the fall and winter. Serotypes 1 to 3 were the predominant isolates (two thirds of the cases). The infection was more frequent among Canadian Aboriginals, as illustrated in 2004, where its incidence in children 0-4 years old was 5.6 fold higher in Aboriginals (13.51 vs. 2.39 per 10,000, p < 0.000). There were no significant differences in length of hospitalization and use of ventilator assistance between the two groups (p > 0.185 and p > 0.624, respectively) nor across serotypes (p > 0.10 and p > 0.05, respectively). The disease primarily affected infants (median age, 9.5 months). Most children presented with bronchiolitis or pneumonia, with multi-lobar consolidations on the chest x-ray. Chronic (residual) changes were documented in 16 patients, with eight patients showing bronchiectasis on the chest computerized tomography scan. Conclusions Adenovirus infection is associated with significant respiratory morbidities, especially in young infants. The infection appears to be more frequent in Aboriginal children. These results justify a careful follow-up for children with adenovirus LRTI.
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30
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Robinson CM, Seto D, Jones MS, Dyer DW, Chodosh J. Molecular evolution of human species D adenoviruses. INFECTION GENETICS AND EVOLUTION 2011; 11:1208-17. [PMID: 21570490 DOI: 10.1016/j.meegid.2011.04.031] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 12/15/2022]
Abstract
Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined among human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens.
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Affiliation(s)
- Christopher M Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA. USA
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31
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Kovács ER, Benko M. Complete sequence of raptor adenovirus 1 confirms the characteristic genome organization of siadenoviruses. INFECTION GENETICS AND EVOLUTION 2011; 11:1058-65. [PMID: 21463713 DOI: 10.1016/j.meegid.2011.03.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/22/2011] [Accepted: 03/27/2011] [Indexed: 11/28/2022]
Abstract
Currently, the family Adenoviridae contains five genera, out of which Siadenovirus is one of the two least densely populated ones. A new member representing a new species in this genus has been detected in various birds of prey. The virus, named raptor adenovirus 1 (RAdV-1), could not be isolated, probably because no appropriate permissive cell-line was available. Partial genomic sequences, obtained by PCR and suggesting that the virus is a new siadenovirus species, have been published earlier. In the present paper, determination and analysis of the complete RAdV-1 genome are reported. This is the first complete genome sequence acquired from a non-isolated adenovirus (AdV). The sole source was a mixture of the internal organs of the diseased and dead birds. Until now, the genomic organization considered characteristic to siadenoviruses had been deduced from the detailed study of only two virus species, one of which originated from birds and the other from a frog. The present analysis of RAdV-1 confirmed the genus-specific genetic content and genomic features of siadenoviruses, and a putative novel gene was found as well. In general, AdVs and most of the AdV genera are thought to be strictly host specific. In the genus Siadenovirus, however, two virus species of rather divergent (avian and amphibian) host origin were present when the genus was found. Although by now the greatest number of known siadenoviruses infect birds, the original hosts of the genus remain unknown.
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Affiliation(s)
- Endre R Kovács
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, PO Box 18, H-1581 Budapest, Hungary.
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32
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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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Robinson CM, Singh G, Henquell C, Walsh MP, Peigue-Lafeuille H, Seto D, Jones MS, Dyer DW, Chodosh J. Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. Virology 2011; 409:141-7. [PMID: 21056888 PMCID: PMC3006489 DOI: 10.1016/j.virol.2010.10.020] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/29/2010] [Accepted: 10/13/2010] [Indexed: 11/30/2022]
Abstract
Adenoviral infections are typically acute, self-limiting, and not associated with death. However, we present the genomic and bioinformatics analysis of a novel recombinant human adenovirus (HAdV-D56) isolated in France that caused a rare neonatal fatality, and keratoconjunctivitis in three health care workers who cared for the neonate. Whole genome alignments revealed the expected diversity in the penton base, hexon, E3, and fiber coding regions, and provided evidence for extensive recombination. Bootscan analysis confirmed recombination between HAdV-D9, HAdV-D26, HAdV-D15, and HAdV-D29 in the penton base and hexon proteins, centered around hypervariable loops within the putative proteins. Protein structure analysis of the fiber coding region revealed similarity with HAdV-D8, HAdV-D9, and HAdV-D53, possibly accounting for the ocular tropism of the virus. Based on these data, this virus appears to be a new HAdV-D type (HAdV-D56), underscoring the importance of recombination events in human adenovirus evolution and the emergence of new adenovirus pathogens.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Cluster Analysis
- Computational Biology
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Evolution, Molecular
- Fatal Outcome
- France
- Genome, Viral
- Humans
- Infant, Newborn
- Keratoconjunctivitis/virology
- Molecular Sequence Data
- Phylogeny
- Recombination, Genetic
- Respiratory Tract Infections/mortality
- Respiratory Tract Infections/transmission
- Respiratory Tract Infections/virology
- Sequence Alignment
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Christopher M. Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 N.E. 10, Oklahoma City, Oklahoma, 73104, USA
| | - Gurdeep Singh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
| | - Cécile Henquell
- CHU Clermont-Ferrand, Laboratoire de Virologie, Hôpital Gabriel Montpied, France, Université d'Auvergne, EA-3843, France
| | - Michael P. Walsh
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA, 20110, USA
| | - Hélène Peigue-Lafeuille
- CHU Clermont-Ferrand, Laboratoire de Virologie, Hôpital Gabriel Montpied, France, Université d'Auvergne, EA-3843, France
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA, 20110, USA
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center, 101 Bodin Circle Travis AFB, California, 94535, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 N.E. 10, Oklahoma City, Oklahoma, 73104, USA
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
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Uchio E, Inoue H, Fuchigami A, Kadonosono K. Anti-adenoviral effect of interferon-β and interferon-γ in serotypes that cause acute keratoconjunctivitis. Clin Exp Ophthalmol 2011; 39:358-63. [DOI: 10.1111/j.1442-9071.2010.02457.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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36
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Uchio E, Inoue H, Kadonosono K. Antiadenoviral effects of N-chlorotaurine in vitro confirmed by quantitative polymerase chain reaction methods. Clin Ophthalmol 2010; 4:1325-9. [PMID: 21139673 PMCID: PMC2993107 DOI: 10.2147/opth.s14282] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Adenoviral keratoconjunctivitis is recognized as one of the major pathogens of ophthalmological nosocomial infection worldwide. N-Chlorotaurine (Cl-HN-CH(2)-CH(2)-SO(3)H, NCT) is the N-chloro derivative of the amino acid taurine, which is an oxidant produced by human granulocytes and monocytes during inflammatory reactions. Using conventional viral plaque assay, it was previously shown that NCT causes inactivation of several human adenovirus (HAdV) serotypes. In this study, we evaluated the antiadenoviral effect of NCT by quantitative polymerase chain reaction (PCR) methods. METHODS A549 cells were used for viral cell culture, and HAdV serotypes 3, 4, 8, 19, and 37 were used. After calculating 50% cytotoxic concentration (CC(50)) of NCT by MTS (3-(4,5- dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) method, HAdV was cultured with NCT for 7 days, and extracted adenoviral DNA was quantitatively measured by real-time PCR. RESULTS A statistically significant (P < 0.05) dose-dependent inhibition was indicated for all serotypes except HAdV type 4 (HAdV4), which was maximally inhibited by only ~50%. Among the serotypes, NCT was particularly effective against HAdV8, HAdV19a, and HAdV37. The 50% effective concentration (EC(50)) obtained by real-time PCR of NCT ranged between 49 and 256 μM. EC(50) of NCT against HAdV3 was slightly higher than that against serotypes of species D. The selective index (CC(50)/EC(50)) ranged between 41 and 60 except for HAdV4 (11.5). CONCLUSIONS These results show that NCT has an antiviral effect against most serotypes of human HAdV inducing keratoconjunctivitis, indicating its possible therapeutic use.
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Affiliation(s)
- Eiichi Uchio
- Department of Ophthalmology, Fukuoka University School of Medicine, Fukuoka, Japan.
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37
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Torres S, Chodosh J, Seto D, Jones MS. The revolution in viral genomics as exemplified by the bioinformatic analysis of human adenoviruses. Viruses 2010; 2:1367-1381. [PMID: 21994684 PMCID: PMC3185712 DOI: 10.3390/v2071367] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 06/24/2010] [Indexed: 12/23/2022] Open
Abstract
Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV), HAdV-C2 and HAdV-C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910) within the hexon gene, of which HAdV-C2 and HAdV-C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.
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Affiliation(s)
- Sarah Torres
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, CA 94535, USA; E-Mail:
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, 02114 MA, USA; E-Mail:
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110, USA; E-Mail:
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, CA 94535, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-415-279-1869; Fax: +1-707-423-7267
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Kaneko H, Ishiko H, Ohguchi T, Tagawa Y, Aoki K, Suzutani T, Ohno S. Nucleotide sequence variation in the hexon gene of human adenovirus type 8 and 37 strains from epidemic keratoconjunctivitis patients in Japan. J Gen Virol 2009; 90:2260-5. [PMID: 19458172 DOI: 10.1099/vir.0.010934-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human adenovirus type 8 (HAdV-8) and 37 (HAdV-37) cause epidemic keratoconjunctivitis (EKC) associated with community-acquired and nosocomial infections. The nucleotide sequences of the entire hexon and fiber genes of eight HAdV-8 and 26 HAdV-37 strains were analysed and the transition mutations in each gene were compared among strains. Compared with prototype strains, the hexon gene of HAdV-8 and -37 strains showed between two and seven and one and twelve variations at nine and 21 different positions, respectively. All of these, except one position in HAdV-37, were located in the conserved region 4 (C4). There were only three polymorphisms in the fiber gene of both HAdV-8 and HAdV-37, fewer than those in C4. The nucleotide sequence of HAdV-8 and -37 C4 might be readily modified during EKC epidemics.
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Affiliation(s)
- Hisatoshi Kaneko
- Department of Microbiology, Fukushima Medical University School of Medicine, Fukushima, Japan.
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