1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Shaheen MNF, Ahmed N, Rady Badr K, Elmahdy EM. Detection and quantification of adenovirus, polyomavirus, and papillomavirus in urban sewage. JOURNAL OF WATER AND HEALTH 2024; 22:401-413. [PMID: 38421633 PMCID: wh_2024_322 DOI: 10.2166/wh.2024.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The objective of this study was to assess the occurrence and seasonal frequency of human adenovirus (HAdV), human polyomavirus (HPyV), and human papillomavirus (HPV) in urban sewage. The detection of these viruses was carried out by polymerase chain reaction (PCR), and then the viral concentrations in the positive samples were quantified by quantitative PCR (qPCR). Additionally, HAdV and HPyV genotyping was also performed by PCR. A total of 38/60 (63.3%) positive samples were found. HAdV was the most prevalent virus (26/60; 43.3%), followed by HPyV (21/60; 35%) and HPV (21/60; 35%). The viral concentrations ranged from 3.56 × 102 to 7.55 × 107 genome copies/L. The most common dual viral agents was found between HAdV and HPyV, in eight samples (8/38, 21%). HAdV types 40 and 41 as well as HPyV types JC and BK were identified, with HAdV-40 and HPyV JC being the most prevalent types. Furthermore, the detection rates of HAdV, HPyV, and HPV were higher during the winter season than the other seasons. The high prevalence of HAdV and HPyV supports their suitability as viral indicators of sewage contamination. Furthermore, this study demonstrates the advantages of environmental surveillance as a tool to elucidate the community-circulating viruses.
Collapse
Affiliation(s)
- Mohamed N F Shaheen
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, 12622 Dokki, Cairo, Egypt E-mail: ;
| | - Nehal Ahmed
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, 12622 Dokki, Cairo, Egypt
| | - Kareem Rady Badr
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, 12622 Dokki, Cairo, Egypt
| | - Elmahdy Mohamed Elmahdy
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, 12622 Dokki, Cairo, Egypt
| |
Collapse
|
3
|
Kajon AE, Lamson DM, George KS. Characterization of Human Adenoviruses of Medical Importance: Isolation of Infectious Virus from Clinical Specimens and Molecular Typing. Curr Protoc 2023; 3:e916. [PMID: 37971417 PMCID: PMC10659126 DOI: 10.1002/cpz1.916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Human adenoviruses (HAdVs) constitute a group of ubiquitous viruses that currently comprises 51 well-defined serotypes and more than 113 genotypes classified into seven species, HAdV-A through HAdV-G. The members of these species differ considerably in their genomic characteristics and also in their tropism and pathogenicity. Virus isolation in cell culture remains critical for the preservation and comprehensive characterization of viruses of biomedical interest but has been almost completely abandoned by diagnostic laboratories. Currently, the most frequently used approach for the detection of HAdV in clinical specimens is real-time qPCR targeting a region of the hexon gene, conserved among all genotypes described to the present. In the absence of typing, the detection of an HAdV in association with disease provides limited information. Molecular typing is therefore highly desirable and required in the epidemiological investigation of HAdV-associated disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Virus isolation from plasma and whole blood Alternate Protocol 1: Virus isolation from stool Alternate Protocol 2: Virus isolation from respiratory specimens and urine Alternate Protocol 3: Virus isolation from tissue specimens Support Protocol: Inoculation of shell vials Basic Protocol 2: Extraction of highly pure viral genomic DNA from infected cells Basic Protocol 3: Molecular detection of human adenovirus by real-time PCR Basic Protocol 4: Molecular typing for basic identification of species and hexon type Basic Protocol 5: Typing human adenoviruses by next-generation whole-genome sequencing and analysis.
Collapse
Affiliation(s)
- Adriana E. Kajon
- Lovelace Biomedical Research Institute, 2425 Ridgecrest Drive SE, Albuquerque, New Mexico, USA +1(505) 348-9159
| | - Daryl M. Lamson
- Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120 New Scotland Ave, Albany, New York, USA +1 (518) 402-4707
| | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, David Axelrod Institute, 120 New Scotland Ave, Albany, New York, USA +1 (518) 402-4707
| |
Collapse
|
4
|
Kosoltanapiwat N, van der Hoek L, Kinsella CM, Tongshoob J, Prasittichai L, Klein M, Jebbink MF, Deijs M, Reamtong O, Boonnak K, Khongsiri W, Phadungsombat J, Tongthainan D, Tulayakul P, Yindee M. A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023; 15:1371. [PMID: 37376670 PMCID: PMC10303043 DOI: 10.3390/v15061371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.
Collapse
Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Jarinee Tongshoob
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Luxsana Prasittichai
- Wildlife Conservation Division, Protected Areas Regional Office 3 (Ban Pong), Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Ratchaburi 70110, Thailand;
| | - Michelle Klein
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Maarten F. Jebbink
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Kobporn Boonnak
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Wathusiri Khongsiri
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Juthamas Phadungsombat
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Daraka Tongthainan
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi 20110, Thailand;
| | - Phitsanu Tulayakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Marnoch Yindee
- Akkhraratchakumari Veterinary College, Walailak University, Nakhonsithammarat 80161, Thailand;
| |
Collapse
|
5
|
Wu X, Zhang J, Lan W, Quan L, Ou J, Zhao W, Wu J, Woo PCY, Seto D, Zhang Q. Molecular Typing and Rapid Identification of Human Adenoviruses Associated With Respiratory Diseases Using Universal PCR and Sequencing Primers for the Three Major Capsid Genes: Penton Base, Hexon, and Fiber. Front Microbiol 2022; 13:911694. [PMID: 35633710 PMCID: PMC9133664 DOI: 10.3389/fmicb.2022.911694] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Human adenoviruses (HAdVs) within species B, C, and E are responsible for highly contagious and potentially severe respiratory disease infections. The traditional method to type these pathogens was based on virus neutralization and hemagglutination assays, which are both time-consuming and difficult, particularly due to the nonavailability of reagents. Subsequent molecular typing based on the partial characterization of the hexon gene and/or the restriction enzyme analysis (REA) of the genomes is inadequate, particularly in identifying recombinants. Here, a rapid, simple, and cost-effective method for molecular typing HAdV respiratory pathogens is presented. This incorporates three pairs of universal PCR primers that target the variable regions of the three major capsid genes, i.e., hexon, penton base, and fiber genes, that span the genome. The protocol enables typing and characterization of genotypes within species B, C, and E, as well as of some genotypes within species D and F. To validate this method, we surveyed 100 children with HAdV-associated acute respiratory infections identified by direct immunofluorescence (Hong Kong; July through October, 2014). Throat swab specimens were collected and analyzed by PCR amplification and sequencing; these sequences were characterized by BLAST. HAdVs were detected in 98 out of 100 (98%) samples, distributing as follows: 74 HAdV-B3 (74%); 10 HAdV-E4 (10%); 7 HAdV-C2 (7%); 2 HAdV-C6 (2%); 1 HAdV-B7 (1%); 1 HAdV-C1 (1%); 2 co-infection (2%); and 1 novel recombinant (1%). This study is the first detailed molecular epidemiological survey of HAdVs in Hong Kong. The developed method allows for the rapid identification of HAdV respiratory pathogens, including recombinants, and bypasses the need for whole genome sequencing for real-time surveillance of circulating adenovirus strains in outbreaks and populations by clinical virologists, public health officials, and epidemiologists.
Collapse
Affiliation(s)
- Xiaowei Wu
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jing Zhang
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wendong Lan
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lulu Quan
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Junxian Ou
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei Zhao
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, China
| | - Patrick C. Y. Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, United States
- Donald Seto,
| | - Qiwei Zhang
- BSL-3 Laboratory, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, China
- *Correspondence: Qiwei Zhang,
| |
Collapse
|
6
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
7
|
Yu J, Zhao S, Rao H. Molecular Characterization of Human Respiratory Adenoviruses Infection in Xining City, China In 2018. Virol Sin 2020; 36:545-549. [PMID: 32926331 PMCID: PMC8257811 DOI: 10.1007/s12250-020-00282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/05/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- Juan Yu
- Department of Basic Medical Sciences, Changzhi Medical College, Changzhi, 046000, China.,Center of Hygiene Inspection, Qinghai Center for Disease Control and Prevention, Xining, 810007, China
| | - Shengcang Zhao
- Center of Hygiene Inspection, Qinghai Center for Disease Control and Prevention, Xining, 810007, China
| | - Huaxiang Rao
- Department of Public Health and Preventive Medicine, Changzhi Medical College, Changzhi, 046000, China. .,Institute for Communicable Disease Control and Prevention, Qinghai Center for Disease Control and Prevention, Xining, 810007, China.
| |
Collapse
|
8
|
Ismail AM, Zhou X, Dyer DW, Seto D, Rajaiya J, Chodosh J. Genomic foundations of evolution and ocular pathogenesis in human adenovirus species D. FEBS Lett 2019; 593:3583-3608. [PMID: 31769017 PMCID: PMC7185199 DOI: 10.1002/1873-3468.13693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/16/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Human adenovirus commonly causes infections of respiratory, gastrointestinal, genitourinary, and ocular surface mucosae. Although most adenovirus eye infections are mild and self-limited, specific viruses within human adenovirus species D are associated with epidemic keratoconjunctivitis (EKC), a severe and highly contagious ocular surface infection, which can lead to chronic and/or recurrent, visually disabling keratitis. In this review, we discuss the links between adenovirus ontogeny, genomics, immune responses, and corneal pathogenesis, for those viruses that cause EKC.
Collapse
Affiliation(s)
- Ashrafali M. Ismail
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Jaya Rajaiya
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - James Chodosh
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
9
|
|
10
|
Xie L, Zhang B, Xiao N, Zhang F, Zhao X, Liu Q, Xie Z, Gao H, Duan Z, Zhong L. Epidemiology of human adenovirus infection in children hospitalized with lower respiratory tract infections in Hunan, China. J Med Virol 2018; 91:392-400. [PMID: 30286268 PMCID: PMC7159165 DOI: 10.1002/jmv.25333] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/02/2018] [Indexed: 12/18/2022]
Abstract
To investigate the current genotypes of circulating human adenovirus (HAdV) strains, we molecularly genotyped HAdV in the nasopharyngeal aspirates (NPAs) of patients with acute lower respiratory tract infections (ALRTIs) and attempted to determine their associations with clinical symptoms. A total of 4751 NPA samples were collected from 4751 patients admitted to Hunan Provincial People's Hospital from September 2007 to March 2014, of which 447 (9.4%) samples were HAdV positive. Fourteen different HAdV types were identified; HAdV types 1 to 7 (HAdV 1‐7) were identified in 95.7% of the 447 NPA samples with HAdV‐7 and HAdV‐3 being the most prevalent. In addition, 93.3% (417 of 447) of patients were younger than 5 years. The incidence of HAdV infection peaked in summer. Different HAdV types showed a predilection for different age groups and different seasonal distribution patterns. Coinfection of HAdVs and other respiratory viruses was detected in 63.3% (283 of 447) of the HAdV‐positive samples. The most common clinical diagnosis was pneumonia and the most common symptoms were fever and cough. In comparison with children infected with HAdV‐3 alone, those infected with HAdV‐7 alone had an increased frequency of severe pneumonia involvement (11.6% vs 32.4%; P = 0.031), higher intensive care unit admission rates (7.0% vs 26.5%; P = 0.019), and a longer length of hospital stay (P = 0.03). Mixed infections in younger children were associated with a longer hospital stay (P = 0.023). Our results demonstrate the recent changes in the trends of circulating HAdV genotypes associated with ALRTIs in Hunan China.
Collapse
Affiliation(s)
- Leyun Xie
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Bing Zhang
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Niguang Xiao
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Fei Zhang
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Xin Zhao
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Qin Liu
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| | - Zhiping Xie
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Hanchun Gao
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhaojun Duan
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Lili Zhong
- Hunan Provincial People's Hospital, Children's Medical Center, Changsha, China
| |
Collapse
|
11
|
Ismail AM, Lee JS, Lee JY, Singh G, Dyer DW, Seto D, Chodosh J, Rajaiya J. Adenoviromics: Mining the Human Adenovirus Species D Genome. Front Microbiol 2018; 9:2178. [PMID: 30254627 PMCID: PMC6141750 DOI: 10.3389/fmicb.2018.02178] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/24/2018] [Indexed: 12/19/2022] Open
Abstract
Human adenovirus (HAdV) infections cause disease world-wide. Whole genome sequencing has now distinguished 90 distinct genotypes in 7 species (A-G). Over half of these 90 HAdVs fall within species D, with essentially all of the HAdV-D whole genome sequences generated in the last decade. Herein, we describe recent new findings made possible by mining of this expanded genome database, and propose future directions to elucidate new functional elements and new functions for previously known viral components.
Collapse
Affiliation(s)
- Ashrafali M Ismail
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Molecular Virology Laboratory, Korea Zoonosis Research Institute, Jeonbuk National University, Jeonju, South Korea
| | - Gurdeep Singh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VI, United States
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jaya Rajaiya
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
12
|
Cheng Z, Yan Y, Jing S, Li WG, Chen WW, Zhang J, Li M, Zhao S, Cao N, Ou J, Zhao S, Wu X, Cao B, Zhang Q. Comparative Genomic Analysis of Re-emergent Human Adenovirus Type 55 Pathogens Associated With Adult Severe Community-Acquired Pneumonia Reveals Conserved Genomes and Capsid Proteins. Front Microbiol 2018; 9:1180. [PMID: 29922263 PMCID: PMC5996824 DOI: 10.3389/fmicb.2018.01180] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/15/2018] [Indexed: 12/14/2022] Open
Abstract
Human adenovirus type 55 (HAdV-B55) is a recently identified acute respiratory disease (ARD) pathogen in HAdV species B with a recombinant genome between renal HAdV-B11 and respiratory HAdV-B14. Since HAdV-B55 first appeared in China school in 2006, no more ARD cases associated with it had been reported until 2011, when there was an outbreak of adult severe community-acquired pneumonia (CAP) in Beijing, China. Reported here is the bioinformatics analysis of the re-emergent HAdV-B55 responsible for this outbreak. Recombination and protein sequence analysis re-confirmed that this isolate (BJ01) was a recombinant virus with the capsid hexon gene from HAdV-B11. The selection pressures for the three capsid proteins, i.e., hexon, penton base, and fiber genes, were all negative, along with very low non-synonymous (dN) and synonymous (dS) substitutions/site (<0.0007). Phylogenetic analyses of the whole genome and the three major capsid genes of HAdV-B55 revealed the close phylogenetic relationship among all HAdV-B55 strains. Comparative genomic analysis of this re-emergent HAdV-B55 strain (BJ01; 2011) with the first HAdV-B55 strain (QS-DLL; 2006) showed the high genome identity (99.87%), including 10 single-nucleotide non-synonymous substitutions, 11 synonymous substitutions, 3 insertions, and one deletion in non-coding regions. The major non-synonymous substitutions (6 of 10) occurred in the protein pVI in its L3 region, which protein has different functions at various stages of an adenovirus infection, and may be associated with the population distribution of HAdV-B55 infection. No non-synonymous substitutions were found in the three major capsid proteins, which proteins are responsible for type-specific neutralizing antibodies. Comparative genomic analysis of the re-emergent HAdV-B55 strains associated with adult severe CAP revealed conserved genome and capsid proteins, providing the foundation for the development of effective vaccines against this pathogen. This study also facilitates the further investigation of HAdV-B55 epidemiology, molecular evolution, patterns of pathogen emergence and re-emergence, and the predication of genome recombination between adenoviruses.
Collapse
Affiliation(s)
- Zetao Cheng
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuqian Yan
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shuping Jing
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wen-Gang Li
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing, China
| | - Wei-Wei Chen
- Treatment and Research Center for Infectious Diseases, 302 Military Hospital of China, Beijing, China
| | - Jing Zhang
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Min Li
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shan Zhao
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Na Cao
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Junxian Ou
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Suhui Zhao
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xianbo Wu
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Qiwei Zhang
- Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
13
|
Li J, Lu X, Jiang B, Du Y, Yang Y, Qian H, Liu B, Lin C, Jia L, Chen L, Wang Q. Adenovirus-associated acute conjunctivitis in Beijing, China, 2011-2013. BMC Infect Dis 2018; 18:135. [PMID: 29558885 PMCID: PMC5859447 DOI: 10.1186/s12879-018-3014-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human adenovirus (HAdV)-associated acute conjunctivitis is a common infectious disease and causes significant morbidity among residents in Beijing, China. However, little is known about the epidemiology and type distribution of acute adenoviral conjunctivitis in Beijing. METHODS Acute conjunctivitis surveillance was conducted in 18 hospitals in Beijing from July through October during 2011-2013. HAdVs were detected by PCR from eye swab and types were determined by partial hexon and fiber gene sequencing. Risk factors associated with adenoviral conjunctivitis were analyzed. RESULTS Of 876 conjunctivitis cases, 349 (39.8%) were HAdV positive. HAdV detection was most common in conjunctivitis patients aged 18-40 years; patients with contact history with a conjunctivitis case; patients with specimen collected on days 4-6 post symptom onset and patients who worked in food service as catering attendants. Fifteen types were identified among adenoviral conjunctivitis cases. Five HAdV types (HAdV-4, - 37, - 53, - 64 and - 8) accounted for 81.1% of all adenoviral conjunctivitis cases. HAdV-37, - 4 and - 53 were the most common types associated with adenoviral conjunctivitis in 2011, 2012 and 2013, respectively. CONCLUSION Multiple HAdV types were associated with acute conjunctivitis in Beijing. Predominant types associated with adenoviral conjunctivitis circulating in Beijing varied from year to year.
Collapse
Affiliation(s)
- Jie Li
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Xiaoyan Lu
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA, 30329, USA
| | - Baoming Jiang
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA, 30329, USA
| | - Yiwei Du
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Yang Yang
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Haikun Qian
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Baiwei Liu
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Changying Lin
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Lei Jia
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China
| | - Lijuan Chen
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China. .,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China. .,Research Centre for Preventive Medicine of Beijing, No.16, Hepingli Middle Road, Beijing, 100013, People's Republic of China.
| |
Collapse
|
14
|
Comparative genomic analysis of two emergent human adenovirus type 14 respiratory pathogen isolates in China reveals similar yet divergent genomes. Emerg Microbes Infect 2017; 6:e92. [PMID: 29089589 PMCID: PMC5717082 DOI: 10.1038/emi.2017.78] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/08/2017] [Accepted: 08/21/2017] [Indexed: 02/04/2023]
Abstract
Human adenovirus type 14 (HAdV-B14p) was originally identified as an acute respiratory disease (ARD) pathogen in The Netherlands in 1955. For approximately fifty years, few sporadic infections were observed. In 2005, HAdV-B14p1, a genomic variant, re-emerged and was associated with several large ARD outbreaks across the U.S. and, subsequently, in Canada, the U.K., Ireland, and China. This strain was associated with an unusually higher fatality rate than previously reported for both this prototype and other HAdV types in general. In China, HAdV-B14 was first observed in 2010, when two unrelated HAdV-B14-associated ARD cases were reported in Southern China (GZ01) and Northern China (BJ430), followed by three subsequent outbreaks. While comparative genomic analysis, including indel analysis, shows that the three China isolates, with whole genome data available, are similar to the de Wit prototype, all are divergent from the U.S. strain (303600; 2007). Although the genomes of strains GZ01 and BJ430 are nearly identical, as per their genome type characterization and percent identities, they are subtly divergent in their genome mutation patterns. These genomes indicate possibly two lineages of HAdV-B14 and independent introductions into China from abroad, or subsequent divergence from one; CHN2012 likely represents a separate sub-lineage. Observations of these simultaneously reported emergent strains in China add to the understanding of the circulation, epidemiology, and evolution of these HAdV pathogens, as well as provide a foundation for developing effective vaccines and public health strategies, including nationwide surveillance in anticipation of larger outbreaks with potentially higher fatality rates associated with HAdV-B14p1.
Collapse
|
15
|
Zhang QL, Wang HB, Wang YL, Zhou JS, Cai J, He RR. [Genotypes of adenoviruses in infants and young children with diarrhea]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016. [PMID: 27530788 PMCID: PMC7399515 DOI: 10.7499/j.issn.1008-8830.2016.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
OBJECTIVE To investigate the prevalence of adenoviruses (AdV) and their genotypes in infants and young children with diarrhea. METHODS A total of 380 children with diarrhea aged less than 3 years were enrolled. The genomic DNA was extracted from stool and PCR was used to detect AdV. Clone sequencing and genotyping were performed for DNA in AdV-positive specimens. RESULTS AdV was detected in 24 out of 380 specimens, and the detection rate was 6.3% (24/380). A majority of children with positive AdV were aged 2-3 years. The viral sequence analysis of positive specimens showed that the detection rates of enteric AdV41 and non-enteric AdV were 4.2% (16/380) and 2.1% (8/380), respectively, and among the children with non-enteric AdV, there were 2 with AdV1, 2 with AdV2, 1 with AdV7, 2 with AdV12, and 1 with AdV31. CONCLUSIONS Diarrhea caused by AdV is commonly seen in children aged 2-3 years, and AdV41 is the major predominant strain.
Collapse
Affiliation(s)
- Qiu-Li Zhang
- Department of Pediatrics, First Hospital of Shizuishan Affiliated to Ningxia Medical University, Shizuishan, Ningxia 753200, China.
| | | | | | | | | | | |
Collapse
|
16
|
Zhang QL, Wang HB, Wang YL, Zhou JS, Cai J, He RR. [Genotypes of adenoviruses in infants and young children with diarrhea]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:718-20. [PMID: 27530788 PMCID: PMC7399515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/03/2016] [Indexed: 11/12/2023]
Abstract
OBJECTIVE To investigate the prevalence of adenoviruses (AdV) and their genotypes in infants and young children with diarrhea. METHODS A total of 380 children with diarrhea aged less than 3 years were enrolled. The genomic DNA was extracted from stool and PCR was used to detect AdV. Clone sequencing and genotyping were performed for DNA in AdV-positive specimens. RESULTS AdV was detected in 24 out of 380 specimens, and the detection rate was 6.3% (24/380). A majority of children with positive AdV were aged 2-3 years. The viral sequence analysis of positive specimens showed that the detection rates of enteric AdV41 and non-enteric AdV were 4.2% (16/380) and 2.1% (8/380), respectively, and among the children with non-enteric AdV, there were 2 with AdV1, 2 with AdV2, 1 with AdV7, 2 with AdV12, and 1 with AdV31. CONCLUSIONS Diarrhea caused by AdV is commonly seen in children aged 2-3 years, and AdV41 is the major predominant strain.
Collapse
Affiliation(s)
- Qiu-Li Zhang
- Department of Pediatrics, First Hospital of Shizuishan Affiliated to Ningxia Medical University, Shizuishan, Ningxia 753200, China.
| | | | | | | | | | | |
Collapse
|
17
|
Thounaojam AD, Balakrishnan A, Mun AB. Detection and Molecular Typing of Human Adenoviruses Associated with Respiratory Illnesses in Kerala. Jpn J Infect Dis 2016; 69:500-504. [PMID: 27000448 DOI: 10.7883/yoken.jjid.2015.414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Adenoviruses are responsible for approximately 5-10% of acute respiratory infections globally. However, there are a limited number of reports on the types of circulating respiratory human adenoviruses (HAdV) in India. We detected HAdV in the post-mortem specimens of a young child who died as a result of an acute febrile illness. To retrospectively investigate the circulating adenovirus types in the Alappuzha region, samples (n = 235) collected from patients with influenza-like illnesses who participated in the influenza surveillance program were screened for HAdV. Fourteen samples were identified as positive for adenovirus by PCR analysis. Adenovirus was isolated from 3 of the 14 PCR-positive samples cultured using HEK-293 cell lines. The viral strains isolated in the study were from children between 6 and 10 years of age. The isolates were identified as adenovirus species C and E. Sequencing analysis of the fiber gene and a BLAST search revealed that 2 of the isolates were type HAdV-C2, and the third isolate was a HAdV-E4. A fiber gene sequence-based phylogenetic tree showed that the HAdV-E4 isolate was similar to the Japanese HAdV-E4 strain, whereas the HAdV-C2 isolates formed a distinct cluster. Respiratory infections due to HAdV-E4 are generally observed in adults; this study is the first to demonstrate the involvement of the HAdV-E4 strain in respiratory illnesses in children.
Collapse
Affiliation(s)
- Asia Devi Thounaojam
- National Institute of Virology (Kerala Unit), Government Thirumala Dewaswom Medical College (TDMC) Hospital
| | | | | |
Collapse
|
18
|
Mehta V, Chou PC, Picken MM. Adenovirus disease in six small bowel, kidney and heart transplant recipients; pathology and clinical outcome. Virchows Arch 2015; 467:603-8. [PMID: 26377431 DOI: 10.1007/s00428-015-1846-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 08/15/2015] [Accepted: 09/04/2015] [Indexed: 12/15/2022]
Abstract
Adenoviruses are emerging as important viral pathogens in hematopoietic stem cell and solid organ transplant recipients, impacting morbidity, graft survival, and even mortality. The risk seems to be highest in allogeneic hematopoietic stem cell transplant recipients as well as heart, lung, and small bowel transplant recipients. Most of the adenovirus diseases develop in the first 6 months after transplantation, particularly in pediatric patients. Among abdominal organ recipients, small bowel grafts are most frequently affected, presumably due to the presence of a virus reservoir in the mucosa-associated lymphoid tissue. Management of these infections may be difficult and includes the reduction of immunosuppression, whenever possible, combined with antiviral therapy, if necessary. Therefore, an awareness of the pathology associated with such infections is important in order to allow early detection and specific treatment. We reviewed six transplant recipients (small bowel, kidney, and heart) with adenovirus graft involvement from two institutions. We sought to compare the diagnostic morphology and the clinical and laboratory findings. The histopathologic features of an adenovirus infection of the renal graft and one native kidney in a heart transplant recipient included a vaguely granulomatous mixed inflammatory infiltrate associated with rare cells showing a cytopathic effect (smudgy nuclei). A lymphocytic infiltrate, simulating T cell rejection, with admixture of eosinophils was also seen. In the small bowel grafts, there was a focal mixed inflammatory infiltrate with associated necrosis in addition to cytopathic effects. In the heart, allograft adenovirus infection was silent with no evidence of inflammatory changes. Immunohistochemical stain for adenovirus was positive in all grafts and in one native kidney. All patients were subsequently cleared of adenovirus infection, as evidenced by follow-up biopsies, with no loss of the grafts. Adenovirus infection can involve allografts as well as native organs in solid organ transplant recipients. Infection is associated with variable necrosis and acute inflammation, in addition to a rejection-like infiltrate. Hematuria in non-renal solid organ transplant recipients may be associated with adenovirus nephritis and clinically silent graft involvement. Prompt diagnosis (aided by immunohistochemistry (IHC) and serology), with specific treatment, can prevent graft loss.
Collapse
Affiliation(s)
- Vikas Mehta
- Pathology, Loyola University Medical Center, Chicago, IL, USA
| | - Pauline C Chou
- Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Maria M Picken
- Pathology, Loyola University Medical Center, Chicago, IL, USA.
- Department of Pathology, Renal and Transplant Pathology, Loyola University Medical Center, Bldg#l10, Room#2242, 2160 S. First Avenue, Maywood, IL, 60153, USA.
| |
Collapse
|
19
|
Wang H, Zheng Y, Deng J, Chen X, Liu P, Li X. Molecular epidemiology of respiratory adenovirus detection in hospitalized children in Shenzhen, China. Int J Clin Exp Med 2015; 8:15011-15017. [PMID: 26628985 PMCID: PMC4658874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/06/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE This study aimed to understand the molecular type of respiratory adenovirus in hospitalized children in Shenzhen and the relation to clinical diagnoses. METHODS Nasopharyngeal swab specimens were obtained from 6,479 hospitalized children younger than 14 years with respiratory tract diseases in Shenzhen Children's Hospital from December 2012 to November 2013. Nasopharyngeal swabs were routine examined by direct immunofluorescence assay to detect respiratory agents including seven respiratory viruses. Multiplex PCR of adenovirus types 3, 7, 11 and 21 in a single tube based on the sequence of the encoding gene for hexon was used to type for adenovirus positive specimens. For those strains that could not be typed by multiplex PCR, the gene fragment was amplified by a universal primer pair for all adenovirus types and the PCR products were sequenced directly. RESULTS A total of 1,066 of 6,479 (16.45%) specimens were positive for at least one of the seven viruses and 228 of 6,479 (3.52%) specimens were positive for adenovirus. 86.4% of children with adenovirus infection occurred less than 5 years of age and just over half of the children (54.4%) less than two years old. There was no significant difference in infection rates between males and females. AdV3 (46.3%) and AdV7 (36.3%) were the genotypes most commonly found followed by AdV1 (6.0%), AdV4 (5.0%), AdV2 (3.0%), AdV6 (1.5%), AdV5 (1.5%) and AdV3/7 (0.5%). No type 11, type 21, and other types of adenovirus were detected. Seven children had type 3 or type 7 and one had type 3/7 mixed infection in 15 severe pneumonia cases. CONCLUSIONS Our study demonstrated that respiratory adenovirus infection is an important cause of hospitalizations in children in Shenzhen, China. Types 3 and 7 were the most common followed by types 1 and 4. AdV3 and AdV7 were similarly contributed to the severe cases.
Collapse
Affiliation(s)
- Heping Wang
- Shenzhen Children's Hospital Shenzhen 518026, China
| | - Yuejie Zheng
- Shenzhen Children's Hospital Shenzhen 518026, China
| | - Jikui Deng
- Shenzhen Children's Hospital Shenzhen 518026, China
| | - Xiaowen Chen
- Shenzhen Children's Hospital Shenzhen 518026, China
| | - Ping Liu
- Shenzhen Children's Hospital Shenzhen 518026, China
| | - Xiliang Li
- Shenzhen Children's Hospital Shenzhen 518026, China
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Matsushima Y, Nakajima E, Ishikawa M, Kano A, Komane A, Fujimoto T, Hanaoka N, Okabe N, Shimizu H. Construction of new primer sets for corresponding to genetic evolution of human adenoviruses in major capsid genes through frequent recombination. Jpn J Infect Dis 2015; 67:495-502. [PMID: 25410569 DOI: 10.7883/yoken.67.495] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A number of novel recombinant human adenoviruses (HAdVs) have recently been identified through sequencing of the complete genomes. The recombinant HAdV sequences share similarity with other types in the major capsid genes, namely the hexon, penton base, and fiber genes, implying recombination events, which may result in escape from the immune response and the acquisition of different organotropisms. Therefore, a surveillance system of HAdVs that considers the effect of frequent recombination on genetic evolution in these genes must be constructed. In this study, we designed new primer sets that can amplify the partial penton base and fiber genes from species HAdV-A to HAdV-F and proteotype HAdVs on the basis of sequence analyses, including previously reported primers that amplify loop 1 of the hexon. Phylogenetic analysis through sequencing with these primers correctly classified clinical HAdV isolates in loop 1 of the hexon gene, the Arg-Gly-Asp (RGD) loop of the penton base gene, and the knob of the fiber gene, which contain neutralizing, hemagglutination, and receptor binding epitopes associated with immunogenicity and tissue tropisms of HAdVs. This study contributes to the accumulation of correct information regarding genetic diversity and evolution in the worldwide HAdV surveillance.
Collapse
Affiliation(s)
- Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Ogorzaly L, Walczak C, Galloux M, Etienne S, Gassilloud B, Cauchie HM. Human Adenovirus Diversity in Water Samples Using a Next-Generation Amplicon Sequencing Approach. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:112-121. [PMID: 25917314 DOI: 10.1007/s12560-015-9194-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/30/2015] [Indexed: 05/18/2023]
Abstract
This study aims to establish a straightforward and original workflow for high-throughput typing of human adenoviruses (HAdVs) in environmental samples. Occurrence of HAdVs in water is well documented worldwide, but data on diversity of HAdV types circulating in water are scarcely available. Here, the characterisation of viral particles was performed by determination of amplicon sequences using a next-generation sequencing (NGS) approach. Adenoviral DNA was either directly isolated from wastewater or river water concentrates or after a cell culture passage. Genome amplification targeted a hyper variable region of the hexon gene, allowing the discrimination of the 54 human adenoviral types described until now. After read generation on the benchtop MiSeq platform (Illumina), data were analysed using the Mothur software for identification of all HAdV species and types simultaneously present in a unique sample. NGS results showed a relatively wide HAdV diversity of up to six types in one sample, whereas Sanger sequencing always only retrieved the dominant one. Detected types included HAdV-1, HAdV-2, HAdV-3, HAdV-6, HAdV-12, HAdV-31, HAdV-40 and HAdV-41, HAdV-41 being the most abundant in tested samples. In addition, the influence of the cell line (A549 vs 293A cells) on the infectious HAdV typing results was clearly determined. The 293A appeared to be the most suitable cell line allowing the detection of a larger diversity of infectious HAdVs and reflecting a more realistic initial species distribution than using the A549 cells. These findings demonstrated the feasibility of amplicon sequencing NGS approach to identify viruses in complex environmental water samples.
Collapse
Affiliation(s)
- Leslie Ogorzaly
- Department of Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41, rue du Brill, 4422, Belvaux, Luxembourg,
| | | | | | | | | | | |
Collapse
|
23
|
Kim SJ, Kim K, Park SB, Hong DJ, Jhun BW. Outcomes of early administration of cidofovir in non-immunocompromised patients with severe adenovirus pneumonia. PLoS One 2015; 10:e0122642. [PMID: 25875735 PMCID: PMC4398328 DOI: 10.1371/journal.pone.0122642] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 11/29/2022] Open
Abstract
The benefits of treatment with antiviral therapy for severe adenovirus (AdV) pneumonia are not well established. We described the clinical characteristics and treatment outcomes of early cidofovir treatment of severe AdV pneumonia in non-immunocompromised patients. We retrospectively reviewed the medical records of all patients diagnosed with severe AdV pneumonia between 2012 and 2014. A total of seven non-immunocompromised patients with severe AdV pneumonia were identified, and all isolates typed (n = 6) were human AdV-B55. All patients had progressive respiratory failure with lobar consolidation with or without patchy ground glass opacity. Three patients required vasopressors and mechanical ventilation. All patients had abnormal laboratory findings including: leukopenia, thrombocytopenia, or elevated liver enzymes. After admission, all patients received antiviral therapy with cidofovir, and the median time from admission to cidofovir administration was 48 h and median the time from onset of symptoms to cidofovir administration was 7.1 days. After cidofovir administration, complete symptomatic improvement occurred after a median of 12 days and radiographic resolution occurred after a median of 21 days. Consequently, all patients completely improved without complications. Our data suggest that early administration of cidofovir in the course of treatment for respiratory failure as a result of AdV pneumonia in non-immunocompromised patients could be a treatment strategy worth considering, especially in cases of HAdV-55 infection.
Collapse
Affiliation(s)
- Se Jin Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Kang Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Sung Bum Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Duck Jin Hong
- Department of Laboratory Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Armed Forces Capital Hospital, Seong-nam, Gyeonggi province, South Korea
- * E-mail:
| |
Collapse
|
24
|
Abstract
Human adenoviruses (HAdVs) are an important cause of infections in both immunocompetent and immunocompromised individuals, and they continue to provide clinical challenges pertaining to diagnostics and treatment. The growing number of HAdV types identified by genomic analysis, as well as the improved understanding of the sites of viral persistence and reactivation, requires continuous adaptions of diagnostic approaches to facilitate timely detection and monitoring of HAdV infections. In view of the clinical relevance of life-threatening HAdV diseases in the immunocompromised setting, there is an urgent need for highly effective treatment modalities lacking major side effects. The present review summarizes the recent progress in the understanding and management of HAdV infections.
Collapse
|
25
|
Kajon AE, Lamson D, Shudt M, Oikonomopoulou Z, Fisher B, Klieger S, St George K, Hodinka RL. Identification of a novel intertypic recombinant species D human adenovirus in a pediatric stem cell transplant recipient. J Clin Virol 2014; 61:496-502. [PMID: 25449172 DOI: 10.1016/j.jcv.2014.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/08/2014] [Accepted: 09/19/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Human adenoviruses (HAdV) are known opportunistic pathogens in hematopoietic stem cell transplant (SCT) recipients. The detection of HAdV infection in children after SCT has been implicated as a determinant of poor outcome but specific associations between HAdV species or individual HAdV types and disease are poorly understood. OBJECTIVES Characterization of a HAdV-D strain isolated from multiple clinical specimens of an 11-year-old female recipient of a matched unrelated donor peripheral SCT for T-cell lymphoma and case report. STUDY DESIGN Archived HAdV PCR-positive plasma, urine, and stool specimens were processed for virus isolation and detailed molecular typing. Complete genomic sequencing was carried out on 2 isolates. RESULTS The patient tested positive for HAdV DNA by real-time PCR of a stool specimen at 44 days after initiation of a SCT conditioning regimen. In the subsequent 3 months, HAdV was detected in plasma, urine and stool specimens in association with symptoms of gastroenteritis and hemorrhagic cystitis. A novel HAdV-D with a HAdV20-like hexon gene was isolated from both urine and stool specimens. All isolates yielded identical restriction profiles with endonucleases BamHI, BglII, BstEII, HindIII, PstI and SmaI. Analysis of 2 complete genomic sequences further identified the virus as a novel intertypic recombinant HAdV-D (P20/H20/F42) closely related to HAdV42. CONCLUSIONS This case highlights the identification of a previously unknown HAdV-D from an immunocompromised host. In this patient, the course of adenovirus infection is compatible with reactivation of a latent virus or a primary opportunistic infection. Adenoviremia in this patient resolved without definitive adenovirus-directed antiviral therapy.
Collapse
Affiliation(s)
- Adriana E Kajon
- Infectious Disease Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
| | - Daryl Lamson
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Matthew Shudt
- Applied Genomics Technologies Core, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Zacharoula Oikonomopoulou
- Division of Infectious Diseases, and The Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brian Fisher
- Division of Infectious Diseases, and The Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Klieger
- Division of Infectious Diseases, and The Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kirsten St George
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Richard L Hodinka
- Department of Pathology and Laboratory Medicine and Clinical Virology Laboratory, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
26
|
Tracking novel adenovirus in environmental and human clinical samples: no evidence of endemic human adenovirus type 58 circulation in Córdoba city, Argentina. Epidemiol Infect 2014; 143:1427-31. [PMID: 25165987 DOI: 10.1017/s0950268814002192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In recent years, several types of human adenovirus (HAdV) have arisen from the recombination between two or more previously known HAdV types, but their epidemiology is poorly understood. In this study, we investigated the circulation of HAdV-58, a recently described HAdV isolated from an HIV-positive patient in Córdoba city, Argentina. For this purpose, a 30-month survey was conducted to study the presence of this type of adenovirus in sewage samples collected at the inlet from a wastewater treatment plant in Córdoba city, Argentina. Complementarily, the virus was sought in stools of HIV-positive patients. Although HAdVs were detected in human stool samples and in a high percentage of sewage samples, no evidence of HAdV-58 circulation was detected. We suggest that there is no endemic circulation of HAdV-58 in the geographical local area. The trend is that the number of identified HAdVs increases over time. In this context, understanding the current circulating HAdVs may be biologically relevant.
Collapse
|
27
|
Prediction of B-Cell Epitopes in Listeriolysin O, a Cholesterol Dependent Cytolysin Secreted by Listeria monocytogenes. Adv Bioinformatics 2014; 2014:871676. [PMID: 24523732 PMCID: PMC3909977 DOI: 10.1155/2014/871676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 10/09/2013] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes is a gram-positive, foodborne bacterium responsible for disease in humans and animals. Listeriolysin O (LLO) is a required virulence factor for the pathogenic effects of L. monocytogenes. Bioinformatics revealed conserved putative epitopes of LLO that could be used to develop monoclonal antibodies against LLO. Continuous and discontinuous epitopes were located by using four different B-cell prediction algorithms. Three-dimensional molecular models were generated to more precisely characterize the predicted antigenicity of LLO. Domain 4 was predicted to contain five of eleven continuous epitopes. A large portion of domain 4 was also predicted to comprise discontinuous immunogenic epitopes. Domain 4 of LLO may serve as an immunogen for eliciting monoclonal antibodies that can be used to study the pathogenesis of L. monocytogenes as well as develop an inexpensive assay.
Collapse
|
28
|
Dehghan S, Seto J, Jones MS, Dyer DW, Chodosh J, Seto D. Simian adenovirus type 35 has a recombinant genome comprising human and simian adenovirus sequences, which predicts its potential emergence as a human respiratory pathogen. Virology 2013; 447:265-73. [PMID: 24210123 DOI: 10.1016/j.virol.2013.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/05/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022]
Abstract
Emergent human and simian adenoviruses (HAdVs) may arise from genome recombination. Computational analysis of SAdV type 35 reveals a genome comprising a chassis with elements mostly from two simian adenoviruses, SAdV-B21 and -B27, and regions of high sequence similarity shared with HAdV-B21 and HAdV-B16. Although recombination direction cannot be determined, the presence of these regions suggests prior infections of humans by an ancestor of SAdV-B35, and/or vice versa. Absence of this virus in humans may reflect non-optimal conditions for zoonosis or incomplete typing, e.g., limited epitope-based. The presence of both a critical viral replication element found in HAdV genomes and genes that are highly similar to ones in HAdVs suggest the potential to establish in a human host. This allows a prediction that this virus may be a nascent human respiratory pathogen. The recombination potential of human and simian adenovirus genomes should be considered in the use of SAdVs as vectors for gene delivery in humans.
Collapse
Affiliation(s)
- Shoaleh Dehghan
- Chemistry Department, American University, Washington, D.C. 20016, USA; Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | | | | | | | | | | |
Collapse
|
29
|
Abstract
Genes within the E3 transcription unit of human adenoviruses modulate host immune responses to infection. A comprehensive genomics and bioinformatics analysis of the E3 transcription unit for 38 viruses within human adenovirus species D (HAdV-D) revealed distinct and surprising patterns of homologous recombination. Homologous recombination was identified in open reading frames for E3 CR1α, CR1β, and CR1γ, similar to that previously observed with genes encoding the three major structural capsid proteins, the penton base, hexon, and fiber.
Collapse
|
30
|
Jin Y, Zhang RF, Xie ZP, Yan KL, Gao HC, Song JR, Yuan XH, Hou YD, Duan ZJ. Prevalence of adenovirus in children with acute respiratory tract infection in Lanzhou, China. Virol J 2013; 10:271. [PMID: 23984826 PMCID: PMC4015357 DOI: 10.1186/1743-422x-10-271] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background Human adenovirus (HAdV) is an important agent causing respiratory tract infection in children. Information on the epidemiological and clinical features of HAdV is limited in children with acute respiratory tract infections (ARTIs) in China, especially those of a novel genotype, Ad55. Methods In total, 1169 nasopharyngeal aspirates were collected from children younger than 14 years with ARTIs between November 2006 and November 2009. The polymerase chain reaction (PCR) was used to screen HAdVs. All PCR-positive products were sequenced. Results 74 of 1169 (6.33%) specimens were positive for HAdVs. Among positive cases, AdV3 (58/74) was detected most frequently, followed by AdV11 (10/74), AdV2 (2/74), AdV7 (2/69), AdV6 (1/74), and AdV1 (1/74). AdV55 was found in one case. The incidence of HAdV infection peaked in children aged 3–7 years. The most common clinical diagnosis was upper respiratory infection, and the most common syndrome was fever and cough.The comparison of HAdV and RSV group revealed that Children infected with group AdV were significant older than children infected with group RSV, had more fever but less frequently wheezing, and cough, crackles, and cyanosis, The duration of hospitalization between the AdV group and RSV group was not significant, but a greater frequency of LRTIs was observed in RSV group. Conclusions HAdV is an important viral agent in children with ARTIs in Lanzhou City, China. Multiple HAdV serotypes co-circulated with Ad3, which was predominant in this 3-year study. The novel AdV55 genotype was found in one case. No fixed seasonal rhythm could be identified.
Collapse
Affiliation(s)
- Yu Jin
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Gislaine Fongaro
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil
| | | | | | | | | | | | | |
Collapse
|
32
|
Tang L, An J, Xie Z, Dehghan S, Seto D, Xu W, Ji Y. Genome and bioinformatic analysis of a HAdV-B14p1 virus isolated from a baby with pneumonia in Beijing, China. PLoS One 2013; 8:e60345. [PMID: 23555956 PMCID: PMC3612040 DOI: 10.1371/journal.pone.0060345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/25/2013] [Indexed: 02/01/2023] Open
Abstract
The genome of HAdV-B14p1 strain BJ430, isolated from a six-month-old baby diagnosed with bronchial pneumonia at the Beijing Children’s Hospital in December 2010, was sequenced, analyzed, and compared with reference adenovirus genome sequences archived in GenBank. This genome is 34,762 bp in length, remarkably presenting 99.9% identity with the genome from HAdV14p1 strain 303600, which was isolated in the USA (2006). Even more remarkable, it is 99.7% identical with the HAdV-B14p (prototype “de Wit” strain) genome, isolated from The Netherlands in 1955. The patient and its parents presumably had no or limited contact with persons from the USA and Ireland, both of which reported outbreaks of the re-emergent virus HAdV-14p1 recently. These genome data, its analysis, and this report provide a reference for any additional HAdV-B14 outbreak in China and provide the basis for the development of adenovirus vaccines and molecular pathogen surveillance protocols in high-risk areas.
Collapse
Affiliation(s)
- Liuying Tang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | | | | | | | | | | | | |
Collapse
|
33
|
Abstract
Human adenoviruses function as genetic models and vectors for gene therapy. Upper respiratory, gastrointestinal or ocular infections usually have mild course without any major complication in immunocompetent individuals. However, reactivation from latency in immunocompromised patients may lead to death. Depending on the underlying diseases, different adenovirus serotypes damage different organs. In children with severe combined immunodeficiency syndrome, serotypes of species A and C induce lung, liver or bladder inflammation. Paediatric hematopoietic stem cell transplantation is frequently followed by serotype 31-induced pneumonia, enteritis, cystitis. B serotypes can destroy transplanted organs. In AIDS patients, D and novel F serotypes cause enteritis. Recombinants of B serotypes induce urinary tract infections. Progression of lymphomas, tumours, and systemic lupus erythematosus might be facilitated by immunosuppressive effects of adenoviruses. As far as the diagnostic work-up of adenoviruses, detection of viral DNA and virus copy number is predictive, while serology testing is quite unreliable. For treatment, cidofovir derivates, ribavirin, ganciclovir, vidarabine and microRNA have been used.
Collapse
Affiliation(s)
- Balázs Stercz
- Semmelweis Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Budapest
| | | | | |
Collapse
|
34
|
Matsushima Y, Shimizu H, Kano A, Nakajima E, Ishimaru Y, Dey SK, Watanabe Y, Adachi F, Suzuki K, Mitani K, Fujimoto T, Phan TG, Ushijima H. Novel human adenovirus strain, Bangladesh. Emerg Infect Dis 2013; 18:846-8. [PMID: 22515955 PMCID: PMC3358076 DOI: 10.3201/eid1805.111584] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We report a novel human adenovirus D (HAdV-65) isolated from feces of 4 children in Bangladesh who had acute gastroenteritis. Corresponding genes of HAdV-65 were related to a hexon gene of HAdV-10, penton base genes of HAdV-37 and HAdV-58, and a fiber gene of HAdV-9. This novel virus may be a serious threat to public health.
Collapse
|
35
|
Genome sequence of a novel virus of the species human adenovirus d associated with acute gastroenteritis. GENOME ANNOUNCEMENTS 2013; 1:genomeA00068-12. [PMID: 23405334 PMCID: PMC3569329 DOI: 10.1128/genomea.00068-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 11/26/2022]
Abstract
A novel virus of the species human adenovirus D, HAdV-67 (P-New/H9/F25), was first isolated from diarrheal feces of six children in Dhaka City, Bangladesh. The genome of this novel virus may be composed of multiple recombinations among HAdV-9, HAdV-25, HAdV-26, HAdV-33, HAdV-46, and an unknown human adenovirus D which was an origin of HAdV-67.
Collapse
|
36
|
Genome sequence of human adenovirus type 55, a re-emergent acute respiratory disease pathogen in China. J Virol 2013; 86:12441-2. [PMID: 23087107 DOI: 10.1128/jvi.02225-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human adenovirus type 55 (HAdV-B55) is an acute respiratory disease (ARD) pathogen first completely characterized in China (2006). This is a unique Trojan horse microbe with the virus neutralization attribute of a renal pathogen and the cell tropism and clinical attributes of a respiratory pathogen, bypassing herd immunity. It appeared to be an uncommon pathogen, with earlier putative, sporadic occurrences in Spain (1969) and Turkey (2004); these isolates were incompletely characterized using only two epitopes. Reported here is the genome of a second recent isolate (China, 2011), indicating that it may occur more frequently. The availability of this HAdV-B55 genome provides a foundation for studying adenovirus molecular evolution, the dynamics of epidemics, and patterns of pathogen emergence and re-emergence. These data facilitate studies to predict genome recombination between adenoviruses, as well as sequence divergence rates and hotspots, all of which are important for vaccine development and because HAdVs are used for epitope and/or gene delivery vectors.
Collapse
|
37
|
Tohma K, Bayasgalan N, Suzuki A, Darma B, Oshitani H, Nymadawa P. Detection and serotyping of human adenoviruses from patients with influenza-like illness in mongolia. Jpn J Infect Dis 2012; 65:289-94. [PMID: 22814149 DOI: 10.7883/yoken.65.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human adenoviruses (HAdVs) are responsible for approximately 5%-10% of acute respiratory infections. The serotypes of commonly detected respiratory HAdV in Asian countries are diverse. However, there are no well-documented reports of circulating HAdV serotypes in Mongolia. Between January 2010 and May 2011, 1,950 influenza-negative samples from patients with influenza-like illness, including eye swabs from patients with eye symptoms, were screened for HAdV, and 40 samples (2.1%) were positive for HAdVs. Among these 40 samples, 31 samples were positive for the hexon gene used in phylogenetic analysis, as determined by PCR. We identified 7 different serotypes. We constructed the phylogenetic trees of HAdV-B7 and HAdV-B3, the 2 most commonly detected serotypes in this study. All detected HAdV-B7 and -B3 Mongolian strains had identical sequences. HAdV-D8, known to be associated with epidemic keratoconjunctivitis (EKC), was detected from nasopharyngeal and eye swabs. There was no difference between the amino acid sequences of the hexon and fiber genes that may affect tissue tropism in Mongolian strains and those in EKC-causing strains.
Collapse
Affiliation(s)
- Kentaro Tohma
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
| | | | | | | | | | | |
Collapse
|
38
|
Lee JI, Lee GC, Chung JY, Han TH, Lee YK, Kim MS, Lee CH. Detection and molecular characterization of adenoviruses in Korean children hospitalized with acute gastroenteritis. Microbiol Immunol 2012; 56:523-8. [PMID: 22530970 DOI: 10.1111/j.1348-0421.2012.00469.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human adenoviruses (HAdVs) are an important cause of acute gastroenteritis in children. However, few studies on the epidemiology or types of HAdVs associated with acute gastroenteritis have been conducted in Korea. Therefore, in the present study, the incidence of HAdV in 2064 stool samples from Korean children hospitalized with acute gastroenteritis (2004-2006) was assessed and the types of viruses present determined. Polymerase chain reaction, sequencing, and phylogenic analyses revealed that 113 samples (5.5%) were HAdV-positive. While HAdVs were mainly detected during July to October, no seasonal difference between the enteric and non-enteric viruses in the incidence of HAdV was observed. HAdV-41 and HAdV-40 were found in 54 (47.8%) and 3 (2.6%) HAdV-positive samples, respectively. HAdV-3, HAdV-7, HAdV-2, HAdV-31, HAdV-4, and HAdV-37 were detected in 11 (9.7%), 5 (4.4%), 2 (1.7%), 2 (1.7%), 1 (0.8%), and 1 (0.8%) of sample(s), respectively. Thus, not only enteric, but also non-enteric, HAdVs may play an important role in acute gastroenteritis in Korean children.
Collapse
Affiliation(s)
- Jae In Lee
- Seoul Metropolitan Research Institute of Public Health and Environment, Gwacheon, Gyeonggi, Korea
| | | | | | | | | | | | | |
Collapse
|
39
|
Hiroi S, Furubayashi K, Kawahata T, Morikawa S, Kase T. A case of urethritis caused by human adenovirus type 56. Jpn J Infect Dis 2012; 65:273-4. [PMID: 22627315 DOI: 10.7883/yoken.65.273] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Satoshi Hiroi
- Division of Virology, Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan. hiroi@iph.pref.osaka.jp
| | | | | | | | | |
Collapse
|
40
|
Abstract
Emergent pathogens may be examined rapidly at high resolution on a molecular level using genomics, allowing an understanding of their evolution. China is a unique environment for studying pathogens, having a large, dense, and generally closed population. Human adenovirus type 14 (HAdV-14) was originally identified as an acute respiratory disease (ARD) pathogen in The Netherlands (1955), with a second isolation in England (1957). Since then, few reports of this virus appeared until an ARD pathogen with a similar genome caused multiple outbreaks in the United States (2006 to 2009). This report presents the first genome of HAdV-B14 isolated in China (2010). As China experienced two recent outbreaks of an emergent ARD pathogen, HAdV-B55, containing much of the HAdV-B14 genome, the availability of this HAdV-B14 sequence will facilitate studies of the epidemiology of these pathogens, as well as provide a foundation for studying adenovirus evolution and the genesis of emergent pathogens. These observations may be invaluable in predicting possible recombination between wild-type viruses and adenoviral gene delivery vectors, including adenovirus vaccines.
Collapse
|
41
|
A molecular epidemiology survey of respiratory adenoviruses circulating in children residing in Southern Palestine. PLoS One 2012; 7:e42732. [PMID: 22880092 PMCID: PMC3411832 DOI: 10.1371/journal.pone.0042732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/10/2012] [Indexed: 01/28/2023] Open
Abstract
A molecular epidemiology survey was performed in order to establish and document the respiratory adenovirus pathogen profiles among children in Southern Palestine. Three hundred and thirty-eight hospitalized pediatric cases with adenovirus-associated respiratory tract infections were analyzed. Forty four cases out of the 338 were evaluated in more detail for the adenoviruses types present. All of the children resided in Southern Palestine, that is, in city, village and refugee camp environments within the districts of Hebron and Bethlehem. Human adenoviruses circulated throughout 2005–2010, with major outbreaks occurring in the spring months. A larger percent of the children diagnosed with adenoviral infections were male infants. DNA sequence analysis of the hexon genes from 44 samples revealed that several distinct adenovirus types circulated in the region; these were HAdV-C1, HAdV-C2, HAdV-B3 and HAdV-C5. However, not all of these types were detected within each year. This is the first study ever conducted in Palestine of the genetic epidemiology of respiratory adenovirus infections.
Collapse
|
42
|
Vaccination with adenovirus serotypes 35, 26, and 48 elicits higher levels of innate cytokine responses than adenovirus serotype 5 in rhesus monkeys. J Virol 2012; 86:9590-8. [PMID: 22787208 DOI: 10.1128/jvi.00740-12] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Adenovirus (Ad) vaccine vectors have proven highly immunogenic in multiple experimental models, but the innate immune responses induced by these vectors remain poorly characterized. Here we report innate cytokine responses to 5 different Ad vectors in 26 rhesus monkeys. Vaccination with adenovirus serotype 35 (Ad35), Ad26, and Ad48 induced substantially higher levels of antiviral (gamma interferon [IFN-γ], 10-kDa gamma interferon-induced protein [IP-10]) and proinflammatory (interleukin 1 receptor antagonist [IL-1RA], IL-6) cytokines than vaccination with Ad5 on day 1 following immunization. In vitro studies with capsid chimeric vectors and receptor-blocking monoclonal antibodies suggested that fiber-receptor interactions, as well as other capsid components, were critical for triggering these innate responses. Moreover, multiple cell populations, including dendritic cells, monocytes/macrophages, and T lymphocytes, contributed to these innate cytokine profiles. These data demonstrate that Ad35, Ad26, and Ad48, which utilize CD46 as their primary cellular receptor, induce significantly greater innate cytokine responses than Ad5, which uses the coxsackievirus and adenovirus receptor (CAR). These differences in innate triggering result in markedly different immunologic milieus for the subsequent generation of adaptive immune responses by these vaccine vectors.
Collapse
|
43
|
Hiroi S, Izumi M, Takahashi K, Morikawa S, Kase T. Isolation and characterization of a novel recombinant human adenovirus species D. J Med Microbiol 2012; 61:1097-1102. [PMID: 22538999 DOI: 10.1099/jmm.0.042176-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel recombinant human adenovirus (HAdV) species D was isolated from the stool of a pharyngitis patient in Japan and genetic characterization was performed by sequencing variable regions between HAdV types. The nucleotide sequences of the penton base gene and loops 1 and 2 in the hexon gene showed 100% identity with that of the recently identified HAdV-56. Although we observed greatest identity for the entire hexon gene sequence with that of HAdV-56, we noted even greater similarity between the partial nucleotide sequence of the conserved region 4 and that of HAdV-37. Furthermore, the fibre gene and early region 3 sequences were completely identical to that of HAdV-37. These results suggest that the strain is a novel adenovirus related to HAdV-37 and HAdV-56.
Collapse
Affiliation(s)
- Satoshi Hiroi
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Moriatsu Izumi
- Department of Pediatrics, Matsushita Memorial Hospital, Osaka, Japan
| | - Kazuo Takahashi
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Saeko Morikawa
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Tetsuo Kase
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan
| |
Collapse
|
44
|
Liu EB, Wadford DA, Seto J, Vu M, Hudson NR, Thrasher L, Torres S, Dyer DW, Chodosh J, Seto D, Jones MS. Computational and serologic analysis of novel and known viruses in species human adenovirus D in which serology and genomics do not correlate. PLoS One 2012; 7:e33212. [PMID: 22427992 PMCID: PMC3302849 DOI: 10.1371/journal.pone.0033212] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 02/12/2012] [Indexed: 11/19/2022] Open
Abstract
In November of 2007 a human adenovirus (HAdV) was isolated from a bronchoalveolar lavage (BAL) sample recovered from a biopsy of an AIDS patient who presented with fever, cough, tachycardia, and expiratory wheezes. To better understand the isolated virus, the genome was sequenced and analyzed using bioinformatic and phylogenomic analysis. The results suggest that this novel virus, which is provisionally named HAdV-D59, may have been created from multiple recombination events. Specifically, the penton, hexon, and fiber genes have high nucleotide identity to HAdV-D19C, HAdV-D25, and HAdV-D56, respectively. Serological results demonstrated that HAdV-D59 has a neutralization profile that is similar yet not identical to that of HAdV-D25. Furthermore, we observed a two-fold difference between the ability of HAdV-D15 and HAdV-D25 to be neutralized by reciprocal antiserum indicating that the two hexon proteins may be more similar in epitopic conformation than previously assumed. In contrast, hexon loops 1 and 2 of HAdV-D15 and HAdV-D25 share 79.13 and 92.56 percent nucleotide identity, respectively. These data suggest that serology and genomics do not always correlate.
Collapse
Affiliation(s)
- Elizabeth B. Liu
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Jason Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Maria Vu
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Nolan Ryan Hudson
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - Lisa Thrasher
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - Sarah Torres
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, Fairfield, California, United States of America
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
| |
Collapse
|
45
|
Abstract
As one of the first five human adenoviruses (HAdVs) to be sequenced, type 17 was important as a reference tool for comparative genomics of recently isolated HAdV pathogens in species D. HAdV-D17 was the first species D adenovirus to be sequenced and was deposited in GenBank in 1999. These genome data were not of high quality, and a redetermination of the same stock virus provides corrected data; among the differences are a length of 35,139 bp versus 35,100 bp in the original, and 160 mismatches to the original genome were found. Annotation of the coding sequences reveals 39 as opposed to 8, a finding which is important for phylogenomic studies.
Collapse
|