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Pinski AN, Gan T, Lin SC, Droit L, Diamond M, Barouch DH, Wang D. Isolation of a recombinant simian adenovirus encoding the human adenovirus G52 hexon suggests a simian origin for human adenovirus G52. J Virol 2024; 98:e0004324. [PMID: 38497664 PMCID: PMC11019922 DOI: 10.1128/jvi.00043-24] [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: 01/07/2024] [Accepted: 02/25/2024] [Indexed: 03/19/2024] Open
Abstract
Human adenoviruses (HAdVs) are causative agents of morbidity and mortality throughout the world. These double-stranded DNA viruses are phylogenetically classified into seven different species (A-G). HAdV-G52, originally isolated in 2008 from a patient presenting with gastroenteritis, is the sole human-derived member of species G. Phylogenetic analysis previously suggested that HAdV-G52 may have a simian origin, indicating a potential zoonotic spillover into humans. However, evidence of HAdV-G52 in either human or simian populations has not been reported since. Here, we describe the isolation and in vitro characterization of rhesus (rh)AdV-69, a novel simian AdV with clear evidence of recombination with HAdV-G52, from the stool of a rhesus macaque. Specifically, the rhAdV-69 hexon capsid protein is 100% identical to that of HAdV-G52, whereas the remainder of the genome is most similar to rhAdV-55, sharing 95.36% nucleic acid identity. A second recombination event with an unknown adenovirus (AdV) is evident at the short fiber gene. From the same sample, we also isolated a second, highly related recombinant AdV (rhAdV-68) that harbors a distinct hexon gene but nearly identical backbone compared to rhAdV-69. In vitro, rhAdV-68 and rhAdV-69 demonstrate comparable growth kinetics and tropisms in human cell lines, nonhuman cell lines, and human enteroids. Furthermore, we show that coinfection of highly related AdVs is not unique to this sample since we also isolated coinfecting rhAdVs from two additional rhesus macaque stool samples. Our data collectively contribute to elucidating the origins of HAdV-G52 and provide insights into the frequency of coinfections and subsequent recombination in AdV evolution.IMPORTANCEUnderstanding the host origins of adenoviruses (AdVs) is critical for public health as transmission of viruses from animals to humans can lead to emergent viruses. Recombination between animal and human AdVs can also produce emergent viruses. HAdV-G52 is the only human-derived member of the HAdV G species. It has been suggested that HAdV-G52 has a simian origin. Here, we isolated from a rhesus macaque, a novel rhAdV, rhAdV-69, that encodes a hexon protein that is 100% identical to that of HAdV-G52. This observation suggests that HAdV-G52 may indeed have a simian origin. We also isolated a highly related rhAdV, differing only in the hexon gene, from the same rhesus macaque stool sample as rhAdV-69, illustrating the potential for co-infection of closely related AdVs and recombination at the hexon gene. Furthermore, our study highlights the critical role of whole-genome sequencing in understanding AdV evolution and monitoring the emergence of pathogenic AdVs.
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Affiliation(s)
- Amanda N. Pinski
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Tianyu Gan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shih-Ching Lin
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Diamond
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - David Wang
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Veith T, Bleicker T, Eschbach-Bludau M, Brünink S, Mühlemann B, Schneider J, Beheim-Schwarzbach J, Rakotondranary SJ, Ratovonamana YR, Tsagnangara C, Ernest R, Randriantafika F, Sommer S, Stetter N, Jones TC, Drosten C, Ganzhorn JU, Corman VM. Non-structural genes of novel lemur adenoviruses reveal codivergence of virus and host. Virus Evol 2023; 9:vead024. [PMID: 37091898 PMCID: PMC10121206 DOI: 10.1093/ve/vead024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023] Open
Abstract
Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus-host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.
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Affiliation(s)
- Talitha Veith
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University Hospital, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Julia Schneider
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - S Jacques Rakotondranary
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Yedidya R Ratovonamana
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Département Biologie Animale, Faculté des Sciences, Université d’ Antananarivo, P.O. Box 906, Antananarivo 101, Madagascar
| | - Cedric Tsagnangara
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | - Refaly Ernest
- Tropical Biodiversity and Social Enterprise SARL, Immeuble CNAPS, premier étage, Fort Dauphin 614, Madagascar
| | | | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, Ulm 89069, Germany
| | - Nadine Stetter
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, Hamburg 20359, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
| | - Jörg U Ganzhorn
- Institute of Cell and Systems Biology of Animals, Universität Hamburg, Martin-Luther-King Platz 3, Hamburg 20146, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
- German Centre for Infection Research (DZIF), Partner Site Berlin, Charitéplatz 1, Berlin 10117, Germany
- Labor Berlin, Charité—Vivantes GmbH, Sylter Straße 2, Berlin 13353, Germany
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3
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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.
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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
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Schachner A, Gonzalez G, Endler L, Ito K, Hess M. Fowl Adenovirus (FAdV) Recombination with Intertypic Crossovers in Genomes of FAdV-D and FAdV-E, Displaying Hybrid Serological Phenotypes. Viruses 2019; 11:v11121094. [PMID: 31779121 PMCID: PMC6950264 DOI: 10.3390/v11121094] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/24/2019] [Indexed: 12/15/2022] Open
Abstract
After analyzing 27 new genomes from fowl adenovirus (FAdV) field isolates and so-far unsequenced prototypes, we report the first evidence for recombination in FAdVs. Recombination was confined to species FAdV-D and FAdV-E, accommodating the largest number of, and the intraspecies-wise most differentiated, types. The majority of detected events occurred in FAdV-E, involving segments with parental origin of all constitutive types. Together with the diversity of breakpoints, this suggests widespread recombination in this species. With possible constraints through species-specific genes and diversification patterns, the recombinogenic potential of FAdVs attains particular interest for inclusion body hepatitis (IBH), an important disease in chickens, caused by types from the recombination-prone species. Autonomously evolving, recombinant segments were associated with major sites under positive selection, among them the capsid protein hexon and fiber genes, the right-terminal ORFs 19, 25, and the ORF20/20A family. The observed mosaicism in genes indicated as targets of adaptive pressures points toward an immune evasion strategy. Intertypic hexon/fiber-recombinants demonstrated hybrid neutralization profiles, retrospectively explaining reported controversies on reference strains B3-A, T8-A, and X11-A. Furthermore, cross-neutralization supported sequence-based evidence for interdomain recombination in fiber and contributed to a tentatively new type. Overall, our findings challenge the purported uniformity of types responsible for IBH, urging more complete identification strategies for FAdVs. Finally, important consequences arise for in vivo studies investigating cross-protection against IBH.
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Affiliation(s)
- Anna Schachner
- Christian Doppler Laboratory for Innovative Poultry Vaccines, University of Veterinary Medicine, 1210 Vienna, Austria;
- Correspondence: ; Tel.: +43-1-25077-4727
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (G.G.); (K.I.)
| | - Lukas Endler
- Bioinformatics and Biostatistics Platform, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (G.G.); (K.I.)
| | - Michael Hess
- Christian Doppler Laboratory for Innovative Poultry Vaccines, University of Veterinary Medicine, 1210 Vienna, Austria;
- University Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
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5
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Divergent Evolution of E1A CR3 in Human Adenovirus Species D. Viruses 2019; 11:v11020143. [PMID: 30744049 PMCID: PMC6409611 DOI: 10.3390/v11020143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/02/2019] [Accepted: 02/03/2019] [Indexed: 12/31/2022] Open
Abstract
Adenovirus E1A is the first viral protein expressed during infection. E1A controls critical aspects of downstream viral gene expression and cell cycle deregulation, and its function is thought to be highly conserved among adenoviruses. Various bioinformatics analyses of E1A from 38 human adenoviruses of species D (HAdV-D), including likelihood clade model partitioning, provided highly significant evidence of divergence of HAdV-Ds into two distinct groups for the conserved region 3 (CR3), present only in the E1A 13S isoform. This variance within E1A 13S of HAdV-Ds was not found in any other human adenovirus (HAdV) species. By protein sequence and structural analysis, the zinc finger motif of E1A CR3, previously shown as critical for transcriptional activation, showed the greatest differences. Subsequent codon usage bias analysis revealed substantial divergence in E1A 13S between the two groups of HAdV-Ds, suggesting that these two sub-groups of HAdV-D evolved under different cellular conditions. Hence, HAdV-D E1A embodies a previously unappreciated evolutionary divergence among HAdVs.
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6
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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.
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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
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Han JW, La TM, Kim JH, Choi IS, Song CS, Park SY, Lee JB, Lee SW. The possible origin of human adenovirus type 3: Evidence of natural genetic recombination between human and simian adenovirus. INFECTION GENETICS AND EVOLUTION 2018; 65:380-384. [PMID: 30144567 DOI: 10.1016/j.meegid.2018.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/26/2022]
Abstract
We determined a complete genome sequence of the Korean field strain, KUMC-62, of human adenovirus type 3 (HAdV-3) and performed comparative genome analyses. Interestingly HAdV-3 has a distinct genomic sequence for the fiber CDS region on average 62.46% of nucleotide sequence identity to other types of HAdV-B1, while remaining genomic region of HAdV-3 is very similar (on average 95.71% of nucleotide sequence identity) to other types of HAdV-B1. The blast results showed that the fiber CDS region of HAdV-3 exhibited the highest nucleotide sequence identity with that of simian adenovirus type 32 (SAdV-32), except other strains of HAdV-3. In the Simplot analysis, a potential recombination event was detected between HAdV-7 and SAdV-32, which might have created HAdV-3 in the past. These findings suggest that HAdV-3 highly likely was created by a natural inter-species recombination event between human and non-human primate AdVs.
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Affiliation(s)
- Ji-Wung Han
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Tae-Min La
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Ji-Hoon Kim
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea; BioCore Co., Ltd, 33 Digitalro 9-ghil, Geumcheon-gu, Seoul, Republic of Korea
| | - In-Soo Choi
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Seung-Yong Park
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Joong-Bok Lee
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Sang-Won Lee
- College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea.
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8
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Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection. mSphere 2018; 3:3/3/e00105-18. [PMID: 29925671 PMCID: PMC6010623 DOI: 10.1128/msphere.00105-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 06/03/2018] [Indexed: 12/30/2022] Open
Abstract
Adenoviruses are common human mucosal pathogens of the gastrointestinal, respiratory, and genitourinary tracts and ocular surface. Here, we report finding Chi-like sequences in adenovirus recombination hot spots. Adenovirus coinfection in the presence of bacterial RecA protein facilitated homologous recombination between viruses. Genetic recombination led to evolution of an important external feature on the adenoviral capsid, namely, the penton base protein hypervariable loop 2, which contains the arginine-glycine-aspartic acid motif critical to viral internalization. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. Adenovirus infections in humans are common and sometimes lethal. Adenovirus-derived vectors are also commonly chosen for gene therapy in human clinical trials. We have shown in previous work that homologous recombination between adenoviral genomes of human adenovirus species D (HAdV-D), the largest and fastest growing HAdV species, is responsible for the rapid evolution of this species. Because adenovirus infection initiates in mucosal epithelia, particularly at the gastrointestinal, respiratory, genitourinary, and ocular surfaces, we sought to determine a possible role for mucosal microbiota in adenovirus genome diversity. By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. These motifs, referred to here as ChiAD, were identified immediately 5′ to the sequence encoding penton base hypervariable loop 2, which expresses the arginine-glycine-aspartate moiety critical to adenoviral cellular entry. Coinfection with two HAdV-Ds in the presence of an Escherichia coli lysate increased recombination; this was blocked in a RecA mutant strain, E. coli DH5α, or upon RecA depletion. Recombination increased in the presence of E. coli lysate despite a general reduction in viral replication. RecA colocalized with viral DNA in HAdV-D-infected cell nuclei and was shown to bind specifically to ChiAD sequences. These results indicate that adenoviruses may repurpose bacterial recombination machinery, a sharing of evolutionary mechanisms across a diverse microbiota, and unique example of viral commensalism. IMPORTANCE Adenoviruses are common human mucosal pathogens of the gastrointestinal, respiratory, and genitourinary tracts and ocular surface. Here, we report finding Chi-like sequences in adenovirus recombination hot spots. Adenovirus coinfection in the presence of bacterial RecA protein facilitated homologous recombination between viruses. Genetic recombination led to evolution of an important external feature on the adenoviral capsid, namely, the penton base protein hypervariable loop 2, which contains the arginine-glycine-aspartic acid motif critical to viral internalization. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota.
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9
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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.
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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
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10
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Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens. Emerg Microbes Infect 2018; 7:10. [PMID: 29410402 PMCID: PMC5837155 DOI: 10.1038/s41426-017-0004-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 12/23/2022]
Abstract
Human adenoviruses (HAdVs) are uniquely important “model organisms” as they have been used to elucidate fundamental biological processes, are recognized as complex pathogens, and are used as remedies for human health. As pathogens, HAdVs may effect asymptomatic or mild and severe symptomatic disease upon their infection of respiratory, ocular, gastrointestinal, and genitourinary systems. High-resolution genomic data have enhanced the understanding of HAdV epidemiology, with recombination recognized as an important and major pathway in the molecular evolution and genesis of emergent HAdV pathogens. To support this view and to actualize an algorithm for identifying, characterizing, and typing novel HAdVs, we determined the DNA sequence of 95 isolates from archives containing historically important pathogens and collections housing currently circulating strains to be sequenced. Of the 85 samples that were completely sequenced, 18 novel recombinants within species HAdV-B and D were identified. Two HAdV-D genomes were found to contain novel penton base and fiber genes with significant divergence from known molecular types. In this data set, we found additional isolates of HAdV-D53 and HAdV-D58, two novel genotypes recognized recently using genomics. This supports the thesis that novel HAdV genotypes are not limited to “one-time” appearances of the prototype but are of importance in HAdV epidemiology. These data underscore the significance of lateral genomic transfer in HAdV evolution and reinforce the potential public health impact of novel genotypes of HAdVs emerging in the population.
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11
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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.
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12
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Selection Pressure in the Human Adenovirus Fiber Knob Drives Cell Specificity in Epidemic Keratoconjunctivitis. J Virol 2016; 90:9598-9607. [PMID: 27512073 PMCID: PMC5068513 DOI: 10.1128/jvi.01010-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/05/2016] [Indexed: 11/20/2022] Open
Abstract
Human adenoviruses (HAdVs) contain seven species (HAdV-A to -G), each associated with specific disease conditions. Among these, HAdV-D includes those viruses associated with epidemic keratoconjunctivitis (EKC), a severe ocular surface infection. The reasons for corneal tropism for some but not all HAdV-Ds are not known. The fiber protein is a major capsid protein; its C-terminal "knob" mediates binding with host cell receptors to facilitate subsequent viral entry. In a comprehensive phylogenetic analysis of HAdV-D capsid genes, fiber knob gene sequences of HAdV-D types associated with EKC formed a unique clade. By proteotyping analysis, EKC virus-associated fiber knobs were uniquely shared. Comparative structural modeling showed no distinct variations in fiber knobs of EKC types but did show variation among HAdV-Ds in a region overlapping with the known CD46 binding site in HAdV-B. We also found signature amino acid positions that distinguish EKC from non-EKC types, and by in vitro studies we showed that corneal epithelial cell tropism can be predicted by the presence of a lysine or alanine at residue 240. This same amino acid residue in EKC viruses shows evidence for positive selection, suggesting that evolutionary pressure enhances fitness in corneal infection, and may be a molecular determinant in EKC pathogenesis. IMPORTANCE Viruses adapt various survival strategies to gain entry into target host cells. Human adenovirus (HAdV) types are associated with distinct disease conditions, yet evidence for connections between genotype and cellular tropism is generally lacking. Here, we provide a structural and evolutionary basis for the association between specific genotypes within HAdV species D and epidemic keratoconjunctivitis, a severe ocular surface infection. We find that HAdV-D fiber genes of major EKC pathogens, specifically the fiber knob gene region, share a distinct phylogenetic clade. Deeper analysis of the fiber gene revealed that evolutionary pressure at crucial amino acid sites has a significant impact on its structural conformation, which is likely important in host cell binding and entry. Specific amino acids in hot spot residues provide a link to ocular cell tropism and possibly to corneal pathogenesis.
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13
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Buijs PRA, Verhagen JHE, van Eijck CHJ, van den Hoogen BG. Oncolytic viruses: From bench to bedside with a focus on safety. Hum Vaccin Immunother 2016; 11:1573-84. [PMID: 25996182 DOI: 10.1080/21645515.2015.1037058] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Oncolytic viruses are a relatively new class of anti-cancer immunotherapy agents. Several viruses have undergone evaluation in clinical trials in the last decades, and the first agent is about to be approved to be used as a novel cancer therapy modality. In the current review, an overview is presented on recent (pre)clinical developments in the field of oncolytic viruses that have previously been or currently are being evaluated in clinical trials. Special attention is given to possible safety issues like toxicity, environmental shedding, mutation and reversion to wildtype virus.
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Key Words
- CAR, Coxsackie Adenovirus receptor
- CD, cytosine deaminase
- CEA, carcinoembryonic antigen
- CVA, Coxsackievirus type A
- DAF, decay accelerating factor
- DNA, DNA
- EEV, extracellular enveloped virus
- EGF, epidermal growth factor
- EGF-R, EGF receptor
- EMA, European Medicines Agency
- FDA, Food and Drug Administration
- GBM, glioblastoma multiforme
- GM-CSF, granulocyte-macrophage colony-stimulating factor
- HA, hemagglutinin
- HAdV, Human (mast)adenovirus
- HER2, human epidermal growth factor receptor 2
- HSV, herpes simplex virus
- ICAM-1, intercellular adhesion molecule 1
- IFN, interferon
- IRES, internal ribosome entry site
- KRAS, Kirsten rat sarcoma viral oncogene homolog
- Kb, kilobase pairs
- MeV, Measles virus
- MuLV, Murine leukemia virus
- NDV, Newcastle disease virus
- NIS, sodium/iodide symporter
- NSCLC, non-small cell lung carcinoma
- OV, oncolytic virus
- PEG, polyethylene glycol
- PKR, protein kinase R
- PV, Polio virus
- RCR, replication competent retrovirus
- RCT, randomized controlled trial
- RGD, arginylglycylaspartic acid (Arg-Gly-Asp)
- RNA, ribonucleic acid
- Rb, retinoblastoma
- SVV, Seneca Valley virus
- TGFα, transforming growth factor α
- VGF, Vaccinia growth factor
- VSV, Vesicular stomatitis virus
- VV, Vaccinia virus
- cancer
- crHAdV, conditionally replicating HAdV
- dsDNA, double stranded DNA
- dsRNA, double stranded RNA
- environment
- hIFNβ, human IFN β
- immunotherapy
- mORV, Mammalian orthoreovirus
- mORV-T3D, mORV type 3 Dearing
- oHSV, oncolytic HSV
- oncolytic virotherapy
- oncolytic virus
- rdHAdV, replication-deficient HAdV
- review
- safety
- shedding
- ssRNA, single stranded RNA
- tk, thymidine kinase
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Affiliation(s)
- Pascal R A Buijs
- a Department of Surgery; Erasmus MC; University Medical Center ; Rotterdam , The Netherlands
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14
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Martynova EU, Schal C, Mukha DV. Effects of recombination on densovirus phylogeny. Arch Virol 2015; 161:63-75. [PMID: 26475154 DOI: 10.1007/s00705-015-2642-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 10/07/2015] [Indexed: 01/06/2023]
Abstract
Densoviruses are a group of arthropod-infecting viruses with a small single-stranded linear DNA genome. These viruses constitute the subfamily Densovirinae of the family Parvoviridae. While recombination in between vertebrate-infecting parvoviruses has been investigated, to date, no systematic analysis of recombination has been carried out for densoviruses. The aim of the present work was to study possible recombination events in the evolutionary history of densoviruses and to assess possible effects of recombination on phylogenies inferred using amino acid sequences of nonstructural (NS) and capsid (viral protein, VP) proteins. For this purpose, the complete or nearly complete genome nucleotide sequences of 40 densoviruses from the GenBank database were used to construct a phylogenetic cladogram. The viruses under study clustered into five distinct groups corresponding to the five currently accepted genera. Recombination within each group was studied independently. The RDP4 software revealed three statistically highly credible recombination events, two of which involved viruses of the genus Ambidensovirus, and the other, viruses from the genus Iteradensovirus. These recombination events led to mismatches between phylogenetic trees constructed using comparison of amino acid sequences of proteins encoded by genome regions of recombinant and non-recombinant origin (regulatory NS1 and NS3 proteins and capsid VP protein).
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Affiliation(s)
- Elena U Martynova
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
| | - Coby Schal
- North Carolina State University, Raleigh, North Carolina, 27695-7613, USA
| | - Dmitry V Mukha
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia.
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15
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Hoppe E, Pauly M, Robbins M, Gray M, Kujirakwinja D, Nishuli R, Boji Mungu-Akonkwa DD, Leendertz FH, Ehlers B. Phylogenomic evidence for recombination of adenoviruses in wild gorillas. J Gen Virol 2015. [DOI: 10.1099/jgv.0.000250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Eileen Hoppe
- Division 12 ‘Measles, Mumps, Rubella and Viruses affecting immunocompromised patients’, Robert Koch Institute, 13353 Berlin, Germany
| | - Maude Pauly
- Division 12 ‘Measles, Mumps, Rubella and Viruses affecting immunocompromised patients’, Robert Koch Institute, 13353 Berlin, Germany
- P3 ‘Epidemiology of highly pathogenic microorganisms’, Robert Koch Institute, 13353 Berlin, Germany
| | - Martha Robbins
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maryke Gray
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Deo Kujirakwinja
- Wildlife Conservation Society, Grauer's Gorilla Project, Democratic Republic of the Congo
| | - Radar Nishuli
- Institut Congolais pour la Conservation de la Nature, Democratic Republic of the Congo
| | | | - Fabian H. Leendertz
- P3 ‘Epidemiology of highly pathogenic microorganisms’, Robert Koch Institute, 13353 Berlin, Germany
| | - Bernhard Ehlers
- Division 12 ‘Measles, Mumps, Rubella and Viruses affecting immunocompromised patients’, Robert Koch Institute, 13353 Berlin, Germany
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16
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Singh G, Zhou X, Lee JY, Yousuf MA, Ramke M, Ismail AM, Lee JS, Robinson CM, Seto D, Dyer DW, Jones MS, Rajaiya J, Chodosh J. Recombination of the epsilon determinant and corneal tropism: Human adenovirus species D types 15, 29, 56, and 69. Virology 2015; 485:452-9. [PMID: 26343864 DOI: 10.1016/j.virol.2015.08.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 07/03/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022]
Abstract
Viruses within human adenovirus species D (HAdV-D) infect epithelia at essentially every mucosal site. Hypervariable loops 1 and 2 of the hexon capsid protein contain epitopes that together form the epsilon determinant for serum neutralization. We report our analyses comparing HAdV-D15, 29, 56, and the recently identified type 69, each with highly similar hexons and the same serum neutralization profile, but otherwise disparate genomes. Of these, only HAdV-D type 56 is associated with epidemic keratoconjunctivitis (EKC), a severe infection of ocular surface epithelium and underlying corneal stroma. In the mouse adenovirus keratitis model, all four viruses induced inflammation. However, HAdV-D56 entry into human corneal epithelial cells and fibroblasts in vitro dramatically exceeded that of the other three viruses. We conclude that the hexon epsilon determinant is not a prime contributor to corneal tropism.
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Affiliation(s)
- Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Mohammad A Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Mirja Ramke
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Ashrafali M Ismail
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Christopher M Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, United States
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Morris S Jones
- Division of Infectious Diseases, Naval Medical Center San Diego, San Diego, CA, United States
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States.
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, United States.
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17
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Hage E, Gerd Liebert U, Bergs S, Ganzenmueller T, Heim A. Human mastadenovirus type 70: a novel, multiple recombinant species D mastadenovirus isolated from diarrhoeal faeces of a haematopoietic stem cell transplantation recipient. J Gen Virol 2015; 96:2734-2742. [DOI: 10.1099/vir.0.000196] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Elias Hage
- Institut für Virologie, Adenovirus Konsiliarlabor, Medizinische Hochschule Hannover, Hannover, Germany
- Deutsches Zentrum Infektionsforschung, Hannover and Braunschweig, Germany
| | | | - Sandra Bergs
- Institut für Virologie, Universität Leipzig, Leipzig, Germany
| | - Tina Ganzenmueller
- Institut für Virologie, Adenovirus Konsiliarlabor, Medizinische Hochschule Hannover, Hannover, Germany
- Deutsches Zentrum Infektionsforschung, Hannover and Braunschweig, Germany
| | - Albert Heim
- Deutsches Zentrum Infektionsforschung, Hannover and Braunschweig, Germany
- Institut für Virologie, Adenovirus Konsiliarlabor, Medizinische Hochschule Hannover, Hannover, Germany
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18
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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.
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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:
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19
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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.
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20
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Hage E, Huzly D, Ganzenmueller T, Beck R, Schulz TF, Heim A. A human adenovirus species B subtype 21a associated with severe pneumonia. J Infect 2014; 69:490-9. [PMID: 24975176 DOI: 10.1016/j.jinf.2014.06.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/16/2014] [Accepted: 06/20/2014] [Indexed: 12/19/2022]
Abstract
Between 2005 and 2013 six severe pneumonia cases (all requiring mechanical ventilation, two fatal outcomes) caused by human adenovirus type 21 (HAdV-B21) were observed in Germany. So far, HAdV-B21 was mainly associated with non-severe upper and lower respiratory tract infections. However, a few highly virulent HAdV types, e.g. HAdV-B14p1, were previously associated with severe, fatal pneumonia. Complete genomic sequences of the German HAdV-B21 pneumonia isolates formed a single phylogenetic cluster with very high sequence identity (≥ 99.897%). Compared to the HAdV-B21 prototype (only 99.319% identity), all isolates had a unique 15 amino acid deletion and a 2 amino acid insertion in the RGD loop of the penton base which may affect binding to the secondary receptor on the host cells. Moreover, a recombinant E4 gene region derived of HAdV-B3 was identified by bootscan analysis. Thus, the highly virulent, pneumotropic HAdV-B21 was denominated as subtype 21a. Surprisingly, there was 99.963% identity with agent Y/SIBU97 (only 13.4 kb available in GenBank of the 35.4 kb genome) which was associated with 10 fatalities due to cardiopulmonary failure in Sarawak, Malaysia, in 1997. In conclusion, a HAdV-B21 subtype (21a) associated with severe pneumonia in Germany was phylogenetically linked to an adenovirus isolated in Malaysia.
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Affiliation(s)
- Elias Hage
- Institut für Virologie, Medizinische Hochschule, Hannover, Germany
| | - Daniela Huzly
- Institut für Virologie, Albert-Ludwigs-Universität, Freiburg, Germany
| | | | - Robert Beck
- Institut für Medizinische Virologie, Universitätsklinikum Tübingen, Germany
| | - Thomas F Schulz
- Institut für Virologie, Medizinische Hochschule, Hannover, Germany; Deutsches Zentrum Infektionsforschung, Hannover und Braunschweig, Germany
| | - Albert Heim
- Institut für Virologie, Medizinische Hochschule, Hannover, Germany; Netzwerk Atemwegsinfektionen des Robert-Koch-Institutes, Adenovirus Konsiliarlabor, Germany.
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21
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Alkhalaf MA, Guiver M, Cooper RJ. Genome stability of adenovirus types 3 and 7 during a simultaneous outbreak in Greater Manchester, UK. J Med Virol 2014; 87:117-24. [PMID: 24801279 DOI: 10.1002/jmv.23969] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2014] [Indexed: 11/07/2022]
Abstract
A total of 96 isolates of species B adenovirus collected in Greater Manchester, UK and typed previously by serum neutralization were analyzed in five genome regions. Of these, 62 isolates were HAdV-B3 and HAdV-B7 collected during a simultaneous 15 months outbreak. The rest of the isolates were HAdV-B types 3 and 7 and other species B adenovirus types collected in different years following the outbreak. The phylogenetic analysis results of all the isolates in the structural regions hexon L2, penton, and fiber knob were found to be consistent and no mismatches were observed. Most of the isolates in the DNA polymerase and E1A regions had the same clustering patterns as the structural regions. However, one HAdV-B7 and one HAdV-B11 isolate changed their clustering patterns in the DNA polymerase region. In addition, HAdV-B16 isolates changed their clustering patterns in both DNA polymerase and E1A regions. The changes of the clustering patterns of some isolates is more likely related to natural variations rather than recombination which indicate that species B adenovirus genome is stable even when different types are circulating in a limited geographical area simultaneously.
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Affiliation(s)
- Moustafa Alissa Alkhalaf
- Virology Unit, Institute of Inflammation and Repair, The University of Manchester, Manchester, United Kingdom
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22
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Gonzalez G, Koyanagi KO, Aoki K, Kitaichi N, Ohno S, Kaneko H, Ishida S, Watanabe H. Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D. Gene 2014; 547:10-7. [PMID: 24726548 DOI: 10.1016/j.gene.2014.04.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 11/20/2022]
Abstract
Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (dS). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics.
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Affiliation(s)
- Gabriel Gonzalez
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Kanako O Koyanagi
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Koki Aoki
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo 002-8072, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hisatoshi Kaneko
- Department of Ophthalmology, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan; Hobara Eye clinic, Date 960-0612, Japan
| | - Susumu Ishida
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hidemi Watanabe
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan.
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23
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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.
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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
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24
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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.
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25
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Robinson CM, Zhou X, Rajaiya J, Yousuf MA, Singh G, DeSerres JJ, Walsh MP, Wong S, Seto D, Dyer DW, Chodosh J, Jones MS. Predicting the next eye pathogen: analysis of a novel adenovirus. mBio 2013; 4:e00595-12. [PMID: 23572555 PMCID: PMC3622935 DOI: 10.1128/mbio.00595-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/12/2013] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED For DNA viruses, genetic recombination, addition, and deletion represent important evolutionary mechanisms. Since these genetic alterations can lead to new, possibly severe pathogens, we applied a systems biology approach to study the pathogenicity of a novel human adenovirus with a naturally occurring deletion of the canonical penton base Arg-Gly-Asp (RGD) loop, thought to be critical to cellular entry by adenoviruses. Bioinformatic analysis revealed a new highly recombinant species D human adenovirus (HAdV-D60). A synthesis of in silico and laboratory approaches revealed a potential ocular tropism for the new virus. In vivo, inflammation induced by the virus was dramatically greater than that by adenovirus type 37, a major eye pathogen, possibly due to a novel alternate ligand, Tyr-Gly-Asp (YGD), on the penton base protein. The combination of bioinformatics and laboratory simulation may have important applications in the prediction of tissue tropism for newly discovered and emerging viruses. IMPORTANCE The ongoing dance between a virus and its host distinctly shapes how the virus evolves. While human adenoviruses typically cause mild infections, recent reports have described newly characterized adenoviruses that cause severe, sometimes fatal human infections. Here, we report a systems biology approach to show how evolution has affected the disease potential of a recently identified novel human adenovirus. A comprehensive understanding of viral evolution and pathogenicity is essential to our capacity to foretell the potential impact on human disease for new and emerging viruses.
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MESH Headings
- Adenoviridae Infections/virology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Animals
- Cell Line
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Disease Models, Animal
- Eye Diseases/virology
- Female
- Humans
- Infant, Newborn
- Male
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Protein Conformation
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Deletion
- Systems Biology
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Tropism
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaohong Zhou
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Michael P. Walsh
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Sallene Wong
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
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26
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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.
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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.
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27
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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.
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Robinson CM, Singh G, Lee JY, Dehghan S, Rajaiya J, Liu EB, Yousuf MA, Betensky RA, Jones MS, Dyer DW, Seto D, Chodosh J. Molecular evolution of human adenoviruses. Sci Rep 2013; 3:1812. [PMID: 23657240 PMCID: PMC3648800 DOI: 10.1038/srep01812] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/22/2013] [Indexed: 11/15/2022] Open
Abstract
The recent emergence of highly virulent human adenoviruses (HAdVs) with new tissue tropisms underscores the need to determine their ontogeny. Here we report complete high quality genome sequences and analyses for all the previously unsequenced HAdV serotypes (n = 20) within HAdV species D. Analysis of nucleotide sequence variability for these in conjunction with another 40 HAdV prototypes, comprising all seven HAdV species, confirmed the uniquely hypervariable regions within species. The mutation rate among HAdV-Ds was low when compared to other HAdV species. Homologous recombination was identified in at least two of five examined hypervariable regions for every virus, suggesting the evolution of HAdV-Ds has been highly dependent on homologous recombination. Patterns of alternating GC and AT rich motifs correlated well with hypervariable region recombination sites across the HAdV-D genomes, suggesting foci of DNA instability lead to formulaic patterns of homologous recombination and confer agility to adenovirus evolution.
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Jeong Yoon Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
- Chemistry Department, American University, Washington, DC 20016 USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Elizabeth B. Liu
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Rebecca A. Betensky
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115 USA
| | - Morris S. Jones
- Division of Infectious Diseases, Naval Medical Center San Diego, San Diego, CA, 92136, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
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29
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Al Qurashi YMA, Alkhalaf MA, Lim L, Guiver M, Cooper RJ. Sequencing and phylogenetic analysis of the hexon, fiber, and penton regions of adenoviruses isolated from AIDS patients. J Med Virol 2012; 84:1157-65. [PMID: 22711343 DOI: 10.1002/jmv.23331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sequencing and phylogenetic analysis of the hexon, fiber, and penton regions of adenoviruses isolated between 1986 and 1997 from AIDS patients has been performed. Sequencing the L2 part of the hexon gene of 51 adenoviruses isolated between 1986 and 1997 from AIDS patients revealed only one type each from species A and C and two types from species B with all the remaining isolates from species D. Further sequencing and phylogenetic analysis of the fiber knob region of these species D adenoviruses revealed that 28/46 were intermediate strains with conflicting hexon and fiber sequences. When the penton regions of these intermediate strains were sequenced, it became clear that some had originated from a third adenovirus type presumably by intergene recombination events. Evidence from sequencing the L1 hexon and fiber shaft regions showed no evidence of intragene recombination but penton sequences showed that recombination between the hypervariable region (HVR) and RGD regions was common. Six isolates appear to be from three new adenovirus types. Five AIDS patients showed sequential infection with different adenovirus variants and six such variants were isolated from a single patient in 2 years.
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30
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Houlihan C, Valappil M, Waugh S, Cantlay K, Price DA, Dhillon RHP. Severe Adenovirus Infection: An Under-Recognised Disease with Limited Treatment Options. J Intensive Care Soc 2012. [DOI: 10.1177/175114371201300414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Catherine Houlihan
- Department of Infectious Disease and Tropical Medicine, Royal Victoria Hospital, Newcastle upon Tyne
| | - Manoj Valappil
- Health Protection Agency North East, Newcastle General Hospital, Newcastle upon Tyne
| | - Sheila Waugh
- Department of Microbiology, Newcastle upon Tyne Hospitals NHS Trust
| | - Kaye Cantlay
- Department of Anaesthetics and Critical Care, Royal Victoria Hospital, Newcastle upon Tyne
| | - D Ashley Price
- Department of Infectious Disease and Tropical Medicine, Royal Victoria Infirmary, University of Newcastle upon Tyne
| | - Rishi H-P Dhillon
- Specialist Registrar in Microbiology, Department of Infection and Immunity, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London
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31
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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.
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32
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Zhou X, Robinson CM, Rajaiya J, Dehghan S, Seto D, Jones MS, Dyer DW, Chodosh J. Analysis of human adenovirus type 19 associated with epidemic keratoconjunctivitis and its reclassification as adenovirus type 64. Invest Ophthalmol Vis Sci 2012; 53:2804-11. [PMID: 22467570 PMCID: PMC3367469 DOI: 10.1167/iovs.12-9656] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/19/2012] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Human adenovirus species D type 19 (HAdV-D19) has been associated with epidemic keratoconjunctivitis (EKC), a highly inflammatory infection of the ocular surface. Confusion exists regarding the origins of HAdV-D19. The prototype virus (HAdV-D19p) does not cause EKC, while a virus identified later with the identical serologic determinant is a significant ocular pathogen. METHODS High throughput genome sequencing and bioinformatics analysis were performed on HAdV-D19p and three HAdV-D19 EKC strains, and compared to the previously sequenced clinical isolate, HAdV-D19 (C) and HAdV-D37. Corneas of C57BL/6J mice were injected with HAdV-D19p, HAdV-D19 (C), or virus-free buffer, and inflammation assessed by clinical examination, flow cytometry, and cytokine ELISA. Confocal microscopy and real-time PCR of infected corneal cell cultures were used to test viral entry. RESULTS HAdV-D19 (C) and the other clinical EKC isolates showed nearly 100% sequence identity. EKC strains diverged from HAdV-D19p in the penton base, E3, and fiber transcription units. Simplot analysis showed recombination between EKC-associated HAdV-D19 with HAdV-D37, HAdV-D22, and HAdV-D19p, the latter contributing only the hexon gene, the principal serum neutralization determinant. HAdV-D19p induced stromal keratitis in the C57BL/6J mouse, but failed to infect productively human corneal epithelial cells. These data led to retyping of the clinical EKC isolates with a HAdV-D19 hexon gene as HAdV-D64. CONCLUSIONS HAdV-D19 associated with EKC (HAdV-D64) originated from a recombination between HAdV-D19p, HAdV-D37, and HAdV-D22, and was mischaracterized because of a shared hexon gene. HAdV-D19p is not infectious for corneal epithelial cells, thus explaining the lack of any association with keratitis.
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Affiliation(s)
- Xiaohong Zhou
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Christopher M. Robinson
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Jaya Rajaiya
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia
| | - David W. Dyer
- and the
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - James Chodosh
- From the
Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
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33
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Singh G, Robinson CM, Dehghan S, Schmidt T, Seto D, Jones MS, Dyer DW, Chodosh J. Overreliance on the hexon gene, leading to misclassification of human adenoviruses. J Virol 2012; 86:4693-5. [PMID: 22301156 PMCID: PMC3318657 DOI: 10.1128/jvi.06969-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/25/2012] [Indexed: 02/02/2023] Open
Abstract
The genome of human adenovirus (HAdV) D30 was sequenced in depth. Sequence assembly and analysis revealed two distinct viral sequences with identical hexon genes, which were the same as the one previously reported for HAdV-D30. However, one of the two viruses was found to be a recombinant of HAdV-D29. Exclusive reliance on serum neutralization can lead to mischaracterization of adenoviruses and miss coinfections. Whole-genome sequencing remains the gold standard for proper classification of HAdVs.
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Affiliation(s)
- Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Timothy Schmidt
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Morris S. Jones
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
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34
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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.
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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:
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35
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Dehghan S, Liu EB, Seto J, Torres SF, Hudson NR, Kajon AE, Metzgar D, Dyer DW, Chodosh J, Jones MS, Seto D. Five genome sequences of subspecies B1 human adenoviruses associated with acute respiratory disease. J Virol 2012; 86:635-6. [PMID: 22158846 PMCID: PMC3255920 DOI: 10.1128/jvi.06593-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 10/21/2011] [Indexed: 11/20/2022] Open
Abstract
Five genomes of human subspecies B1 adenoviruses isolated from cases of acute respiratory disease have been sequenced and archived for reference. These include representatives of two prevalent genomic variants of HAdV-7, i.e., HAdV-7h and HAdV-7d2. The other three are HAdV-3/16, HAdV-16 strain E26, and HAdV-3+7 strain Takeuchi. All are recombinant genomes. Genomics and bioinformatics provide detailed views into the genetic makeup of these pathogens and insight into their molecular evolution. Retrospective characterization of particularly problematic older pathogens such as HAdV-7h (1987) and intriguing isolates such as HAdV-3+7 strain Takeuchi (1958) may provide clues to their phenotypes and serology and may suggest protocols for prevention and treatment.
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Affiliation(s)
- Shoaleh Dehghan
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
| | - Elizabeth B. Liu
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
| | - Jason Seto
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
| | - Sarah F. Torres
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis Air Force Base, California 94535, USA
| | - Nolan R. Hudson
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis Air Force Base, California 94535, USA
| | - Adriana E. Kajon
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico 87108, USA
| | - David Metzgar
- Department of Respiratory Diseases Research, Naval Health Research Center, San Diego, California 92106, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Morris S. Jones
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Donald Seto
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, USA
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36
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Robinson CM, Rajaiya J, Zhou X, Singh G, Dyer DW, Chodosh J. The E3 CR1-gamma gene in human adenoviruses associated with epidemic keratoconjunctivitis. Virus Res 2011; 160:120-7. [PMID: 21683743 DOI: 10.1016/j.virusres.2011.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 05/31/2011] [Accepted: 05/31/2011] [Indexed: 01/06/2023]
Abstract
Human adenovirus species D type 37 (HAdV-D37) is an important etiologic agent of epidemic keratoconjunctivitis. Annotation of the whole genome revealed an open reading frame (ORF) in the E3 transcription unit predicted to encode a 31.6kDa protein. This ORF, also known as CR1-γ, is predicted to be an integral membrane protein containing N-terminal signal sequence, luminal, transmembrane, and cytoplasmic domains. HAdV-D19 (C), another viral pathogen causing epidemic keratoconjunctivitis, contains an ORF 100% identical to its HAdV-D37 homologue but only 66% identical to other HAdV-D homologues. Kinetics of RNA expression and confirmation of splicing to the adenovirus tripartite leader sequence suggest a role for the protein product of CR1-γ in the late stages of the viral replication cycle. Confocal microscopy is consistent with expression in the cytoplasm. Sequence analysis reveals a hypervariable luminal domain and a conserved cytoplasmic domain. The luminal domain is predicted to contain multiple N-glycosylation sites. The cytoplasmic domain contains a putative protein kinase C phosphorylation site and potential YXXϕ and dileucine (LL) motifs suggesting a potential role in modification of host proteins.
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Affiliation(s)
- Christopher M Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA
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Robinson CM, Seto D, Jones MS, Dyer DW, Chodosh J. Molecular evolution of human species D adenoviruses. INFECTION GENETICS AND EVOLUTION 2011; 11:1208-17. [PMID: 21570490 DOI: 10.1016/j.meegid.2011.04.031] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 12/15/2022]
Abstract
Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined among human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens.
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Affiliation(s)
- Christopher M Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA. USA
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Robinson CM, Singh G, Henquell C, Walsh MP, Peigue-Lafeuille H, Seto D, Jones MS, Dyer DW, Chodosh J. Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. Virology 2011; 409:141-7. [PMID: 21056888 PMCID: PMC3006489 DOI: 10.1016/j.virol.2010.10.020] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/29/2010] [Accepted: 10/13/2010] [Indexed: 11/30/2022]
Abstract
Adenoviral infections are typically acute, self-limiting, and not associated with death. However, we present the genomic and bioinformatics analysis of a novel recombinant human adenovirus (HAdV-D56) isolated in France that caused a rare neonatal fatality, and keratoconjunctivitis in three health care workers who cared for the neonate. Whole genome alignments revealed the expected diversity in the penton base, hexon, E3, and fiber coding regions, and provided evidence for extensive recombination. Bootscan analysis confirmed recombination between HAdV-D9, HAdV-D26, HAdV-D15, and HAdV-D29 in the penton base and hexon proteins, centered around hypervariable loops within the putative proteins. Protein structure analysis of the fiber coding region revealed similarity with HAdV-D8, HAdV-D9, and HAdV-D53, possibly accounting for the ocular tropism of the virus. Based on these data, this virus appears to be a new HAdV-D type (HAdV-D56), underscoring the importance of recombination events in human adenovirus evolution and the emergence of new adenovirus pathogens.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/isolation & purification
- Adenoviruses, Human/pathogenicity
- Amino Acid Sequence
- Cluster Analysis
- Computational Biology
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Evolution, Molecular
- Fatal Outcome
- France
- Genome, Viral
- Humans
- Infant, Newborn
- Keratoconjunctivitis/virology
- Molecular Sequence Data
- Phylogeny
- Recombination, Genetic
- Respiratory Tract Infections/mortality
- Respiratory Tract Infections/transmission
- Respiratory Tract Infections/virology
- Sequence Alignment
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Christopher M. Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 N.E. 10, Oklahoma City, Oklahoma, 73104, USA
| | - Gurdeep Singh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
| | - Cécile Henquell
- CHU Clermont-Ferrand, Laboratoire de Virologie, Hôpital Gabriel Montpied, France, Université d'Auvergne, EA-3843, France
| | - Michael P. Walsh
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA, 20110, USA
| | - Hélène Peigue-Lafeuille
- CHU Clermont-Ferrand, Laboratoire de Virologie, Hôpital Gabriel Montpied, France, Université d'Auvergne, EA-3843, France
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA, 20110, USA
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center, 101 Bodin Circle Travis AFB, California, 94535, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 975 N.E. 10, Oklahoma City, Oklahoma, 73104, USA
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles Street, Boston, Massachusetts, 02114, USA
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Wevers D, Leendertz FH, Scuda N, Boesch C, Robbins MM, Head J, Ludwig C, Kühn J, Ehlers B. A novel adenovirus of Western lowland gorillas (Gorilla gorilla gorilla). Virol J 2010; 7:303. [PMID: 21054831 PMCID: PMC2989969 DOI: 10.1186/1743-422x-7-303] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/05/2010] [Indexed: 01/11/2023] Open
Abstract
Adenoviruses (AdV) broadly infect vertebrate hosts including a variety of primates. We identified a novel AdV in the feces of captive gorillas by isolation in cell culture, electron microscopy and PCR. From the supernatants of infected cultures we amplified DNA polymerase (DPOL), preterminal protein (pTP) and hexon gene sequences with generic pan primate AdV PCR assays. The sequences in-between were amplified by long-distance PCRs of 2-10 kb length, resulting in a final sequence of 15.6 kb. Phylogenetic analysis placed the novel gorilla AdV into a cluster of primate AdVs belonging to the species Human adenovirus B (HAdV-B). Depending on the analyzed gene, its position within the cluster was variable. To further elucidate its origin, feces samples of wild gorillas were analyzed. AdV hexon sequences were detected which are indicative for three distinct and novel gorilla HAdV-B viruses, among them a virus nearly identical to the novel AdV isolated from captive gorillas. This shows that the discovered virus is a member of a group of HAdV-B viruses that naturally infect gorillas. The mixed phylogenetic clusters of gorilla, chimpanzee, bonobo and human AdVs within the HAdV-B species indicate that host switches may have been a component of the evolution of human and non-human primate HAdV-B viruses.
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Affiliation(s)
- Diana Wevers
- FG12 Division of Viral Infections, Robert Koch Institute, Berlin, Germany
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Walsh MP, Seto J, Tirado D, Chodosh J, Schnurr D, Seto D, Jones MS. Computational analysis of human adenovirus serotype 18. Virology 2010; 404:284-92. [PMID: 20542532 PMCID: PMC2902685 DOI: 10.1016/j.virol.2010.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/01/2010] [Accepted: 05/13/2010] [Indexed: 11/26/2022]
Abstract
The genome of the sole remaining unsequenced member of species A, human adenovirus type 18 (HAdV-A18), has been sequenced and analyzed. Members of species A are implicated as gastrointestinal pathogens and were shown to be tumorigenic in rodents. These whole genome and in silico proteome data are important as references for reexamining and integrating earlier work and observations based on lower resolution techniques, such as restriction enzyme digestion patterns, particularly for hypotheses based on pre-genomics data. Additionally, the genome of HAdV-A18 will also serve as reference for current studies examining the molecular evolution and origins of human and simian adenoviruses, particularly genome recombination studies. Applications of this virus as a potential vector for gene delivery protocols may be practical as data accumulate on this and other adenovirus genomes.
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Affiliation(s)
- Michael P. Walsh
- Department of Bioinformatics and Computational Biology, George Mason University. 10900 University Blvd., MSN 5B3, Manassas, VA 20110, USA
| | - Jason Seto
- Department of Bioinformatics and Computational Biology, George Mason University. 10900 University Blvd., MSN 5B3, Manassas, VA 20110, USA
| | - Damaris Tirado
- Clinical Investigation Facility, David Grant USAF Medical Center. Travis, CA 94535, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School. Boston, MA 02114. USA
| | - David Schnurr
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University. 10900 University Blvd., MSN 5B3, Manassas, VA 20110, USA
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center. Travis, CA 94535, USA
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Seto J, Walsh MP, Metzgar D, Seto D. Computational analysis of adenovirus serotype 5 (HAdV-C5) from an HAdV coinfection shows genome stability after 45 years of circulation. Virology 2010; 404:180-6. [PMID: 20627349 DOI: 10.1016/j.virol.2010.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/01/2010] [Accepted: 05/13/2010] [Indexed: 11/19/2022]
Abstract
Adenovirus coinfections present opportunities for genome recombination. Computational analysis of an HAdV-C5 field strain genome, recovered from a patient with acute respiratory disease and coinfected with HAdV-B21, shows that there was no exchange of genomic material into HAdV-C5. Comparison of this genome to the sparsely amplified prototype demonstrates a high level of sequence conservation and stability of this genome across 45 years. Further, comparison to a version of the prototype that had been passaged in laboratory settings shows stability as well. HAdV genome stability and evolution are considerations for applications as vaccines and as vectors for gene delivery. In the annotation analysis, a single sequencing error in the HAdV-C5_ARM (Adenovirus Reference Material) genome is noted and may lead to erroneous annotation and biological interpretations.
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Affiliation(s)
- Jason Seto
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA 20110, USA.
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Torres S, Chodosh J, Seto D, Jones MS. The revolution in viral genomics as exemplified by the bioinformatic analysis of human adenoviruses. Viruses 2010; 2:1367-1381. [PMID: 21994684 PMCID: PMC3185712 DOI: 10.3390/v2071367] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 06/24/2010] [Indexed: 12/23/2022] Open
Abstract
Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV), HAdV-C2 and HAdV-C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910) within the hexon gene, of which HAdV-C2 and HAdV-C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.
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Affiliation(s)
- Sarah Torres
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, CA 94535, USA; E-Mail:
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, 02114 MA, USA; E-Mail:
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110, USA; E-Mail:
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, CA 94535, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-415-279-1869; Fax: +1-707-423-7267
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Halstead DC, Gray GC, Meyer KS, Stanciu SR, Gorospe WC. Recombinant Adenovirus (AdV) Type 3 and Type 14 Isolated From a Fatal Case of Pneumonia. REVIEWS IN MEDICAL MICROBIOLOGY : A JOURNAL OF THE PATHOLOGICAL SOCIETY OF GREAT BRITAIN AND IRELAND 2010; 21:28-30. [PMID: 21461125 PMCID: PMC3066448 DOI: 10.1097/mrm.0b013e3283393523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
We report a fatal case of pneumonia apparently due to adenovirus infection in a 53-year-old male who had recently returned from Iraq. The isolate was identified by sequence analysis as AdV3 and AdV14. Based on restriction analysis (REA), the virus appeared to be a recombinant virus containing properties of both AdV3 and AdV14 rather than a coinfection with these two viruses.
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Affiliation(s)
- Diane C. Halstead
- Jacksonville Pathology Consultants, P.A./Baptist Health Infectious Disease Laboratories, Jacksonville, Florida
| | - Gregory C. Gray
- University of Iowa College of Public Health, Coralville, Iowa
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Mahadevan P, Seto J, Tibbetts C, Seto D. Natural variants of human adenovirus type 3 provide evidence for relative genome stability across time and geographic space. Virology 2010; 397:113-8. [DOI: 10.1016/j.virol.2009.10.052] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 09/23/2009] [Accepted: 10/30/2009] [Indexed: 10/20/2022]
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45
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Genomic characterization of human adenovirus 36, a putative obesity agent. Virus Res 2010; 149:152-61. [PMID: 20109503 DOI: 10.1016/j.virusres.2010.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/20/2010] [Accepted: 01/21/2010] [Indexed: 02/08/2023]
Abstract
Increased levels of serum antibody titers against human adenovirus 36 (HAdV-D36) are associated with human obesity and experimental obesity in laboratory animals. While HAdV-D36 has been studied as an infectious agent implicated in obesity for over a decade, the complete genome sequence and its analysis have yet to be reported. A detailed analysis of the genome sequence of HAdV-D36 may be important to understand its role in obesity. Genomic and bioinformatic comparisons with other HAdVs identified differences that suggested unique functions. Global pairwise genome alignment with all sequenced human adenovirus D (HAdV-D) genomes revealed areas of nonconserved sequences in the hexon, E3 CR1 beta, E3 CR1 gamma, and fiber genes. Phylogenetic analysis of all HAdV-D36 proteins confirmed that this virus belongs to species Human adenovirus D. This genomic analysis of HAdV-D36 provides an important tool for comprehending the role that this unique adenovirus may play in human obesity. Low amino acid sequence identity in the E3 CR1 beta and CR1 gamma genes may suggest distinctive roles for these proteins. Furthermore, the predicted molecular models of the HAdV-D36 fiber protein seem to implicate a unique tissue tropism for HAdV-D36.
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Applying genomic and bioinformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery. Viruses 2010; 2:1-26. [PMID: 21994597 PMCID: PMC3185558 DOI: 10.3390/v2010001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 12/05/2009] [Accepted: 12/17/2009] [Indexed: 12/25/2022] Open
Abstract
Technological advances and increasingly cost-effect methodologies in DNA sequencing and computational analysis are providing genome and proteome data for human adenovirus research. Applying these tools, data and derived knowledge to the development of vaccines against these pathogens will provide effective prophylactics. The same data and approaches can be applied to vector development for gene delivery in gene therapy and vaccine delivery protocols. Examination of several field strain genomes and their analyses provide examples of data that are available using these approaches. An example of the development of HAdV-B3 both as a vaccine and also as a vector is presented.
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47
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Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J Clin Microbiol 2009; 48:991-3. [PMID: 20042633 DOI: 10.1128/jcm.01694-09] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel human adenoviruses (HAdVs) arise from genome recombination. Analysis of HAdV type 55 from an outbreak in China shows a hexon recombination between HAdV-B11 and HAdV-B14, resulting in a genome that is 97.4% HAdV-B14. Sporadic appearances as a re-emergent pathogen and misidentification as "HAdV-B11a" are due to this partial hexon.
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