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Park A, Lee C, Lee JY. Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis. J Microbiol 2024; 62:393-407. [PMID: 38451451 DOI: 10.1007/s12275-024-00112-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 03/08/2024]
Abstract
Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.
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Affiliation(s)
- Anyeseu Park
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Chanhee Lee
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea
| | - Jeong Yoon Lee
- The Laboratory of Viromics and Evolution, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54531, Republic of Korea.
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Flynn TG, Olortegui MP, Kosek MN. Viral gastroenteritis. Lancet 2024; 403:862-876. [PMID: 38340741 DOI: 10.1016/s0140-6736(23)02037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/17/2023] [Accepted: 09/18/2023] [Indexed: 02/12/2024]
Abstract
Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.
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Affiliation(s)
- Thomas G Flynn
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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3
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Lan W, Quan L, Li Y, Ou J, Duan B, Mei T, Tan X, Chen W, Feng L, Wan C, Zhao W, Chodosh J, Seto D, Zhang Q. Isolation of novel simian adenoviruses from macaques for development of a vector for human gene therapy and vaccines. J Virol 2023; 97:e0101423. [PMID: 37712705 PMCID: PMC10617444 DOI: 10.1128/jvi.01014-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/16/2023] [Indexed: 09/16/2023] Open
Abstract
IMPORTANCE Adenoviruses are widely used in gene therapy and vaccine delivery. Due to the high prevalence of human adenoviruses (HAdVs), the pre-existing immunity against HAdVs in humans is common, which limits the wide and repetitive use of HAdV vectors. In contrast, the pre-existing immunity against simian adenoviruses (SAdVs) is low in humans. Therefore, we performed epidemiological investigations of SAdVs in simians and found that the SAdV prevalence was as high as 33.9%. The whole-genome sequencing and sequence analysis showed SAdV diversity and possible cross species transmission. One isolate with low level of pre-existing neutralizing antibodies in humans was used to construct replication-deficient SAdV vectors with E4orf6 substitution and E1/E3 deletion. Interestingly, we found that the E3 region plays a critical role in its replication in human cells, but the absence of this region could be compensated for by the E4orf6 from HAdV-5 and the E1 expression intrinsic to HEK293 cells.
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Affiliation(s)
- Wendong Lan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Lulu Quan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yiqiang Li
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Junxian Ou
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Biyan Duan
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Ting Mei
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Xiao Tan
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
| | - Weiwei Chen
- The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Liqiang Feng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Chengsong Wan
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - James Chodosh
- Department of Ophthalmology and Visual Sciences, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Qiwei Zhang
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, Guangdong, China
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Mancuso DM, Gainor K, Dore KM, Gallagher CA, Cruz K, Beierschmitt A, Malik YS, Ghosh S. Detection and Molecular Characterization of Adenoviruses in Captive and Free-Roaming African Green Monkeys ( Chlorocebus sabaeus): Evidence for Possible Recombination and Cross-Species Transmission. Viruses 2023; 15:1605. [PMID: 37515291 PMCID: PMC10385324 DOI: 10.3390/v15071605] [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: 06/14/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
In the present study, 31 samples (12 fecal, 9 nasal and 10 rectal swabs) from 28/92 (30.43%, 10 captive and 18 free-roaming African green monkeys (AGMs, Chlorocebus sabaeus)) apparently healthy AGMs in the Caribbean Island of St. Kitts tested positive for adenoviruses (AdVs) by DNA-dependent DNA polymerase (pol)-, or hexon-based screening PCR assays. Based on analysis of partial deduced amino acid sequences of Pol- and hexon- of nine AGM AdVs, at least two AdV genetic variants (group-I: seven AdVs with a Simian mastadenovirus-F (SAdV-F)/SAdV-18-like Pol and hexon, and group-II: two AdVs with a SAdV-F/SAdV-18-like Pol and a Human mastadenovirus-F (HAdV-F)/HAdV-40-like hexon) were identified, which was corroborated by analysis of the nearly complete putative Pol, complete hexon, and partial penton base sequences of a representative group-I (strain KNA-08975), and -II (KNA-S6) AdV. SAdV-F-like AdVs were reported for the first time in free-roaming non-human primates (NHPs) and after ~six decades from captive NHPs. Molecular characterization of KNA-S6 (and the other group-II AdV) indicated possible recombination and cross-species transmission events involving SAdV-F-like and HAdV-F-like viruses, corroborating the hypothesis that the evolutionary pathways of HAdVs and SAdVs are intermingled, complicated by recombination and inter-species transmission events, especially between related AdV species, such as HAdV-F and SAdV-F. To our knowledge, this is the first report on detection and molecular characterization of AdVs in AGMs.
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Affiliation(s)
- Diana M Mancuso
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Kerry Gainor
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Kerry M Dore
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- National Coordinator, CABI/GEF/UNEP Regional Project-'Preventing the COSTS of Invasive Alien Species in Barbados and OECS Countries' in St. Kitts, Ministry of Environment, Climate Action and Constituency Development, Basseterre 00265, Saint Kitts and Nevis
| | - Christa A Gallagher
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Katalina Cruz
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Amy Beierschmitt
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- Behavioral Science Foundation, Estridge Estate, Basseterre P.O. Box 428, Saint Kitts and Nevis
| | - Yashpal S Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141012, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
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Bots STF, Kemp V, Dautzenberg IJC, Hoeben RC. Genome Analyses of Ten New Ape Adenoviruses with Similarity to Human Mastadenovirus C. Int J Mol Sci 2022; 23:ijms23179832. [PMID: 36077230 PMCID: PMC9456536 DOI: 10.3390/ijms23179832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/27/2022] [Indexed: 12/01/2022] Open
Abstract
The adenoviruses (AdVs) isolated from humans are taxonomically grouped in seven different species in the Mastadenovirus genus (HAdV-A through G). AdVs isolated from apes are often included in one of the human AdV species. Here we describe the sequence analyses of ten new AdVs that are related to the HAdV-C species and that were isolated from healthy western lowland gorillas, bonobos, chimpanzees, and orangutans kept in Dutch zoos. We analyzed these viruses and compared their genome sequences to those of human- and ape-derived AdV sequences in the NCBI GenBank database. Our data demonstrated that the ape-derived viruses clustering to HAdV-C are markedly distinct from the human HAdV-C species in the size and nucleotide composition (%GC) of their genome, differ in the amino-acid sequence of AdV proteins, and have longer RGD-loops in their penton-base proteins. The viruses form three well-separated clades (the human, the gorilla, and the combined group of the bonobo and chimpanzee viruses), and we propose that these should each be given species-level ranks. The Ad-lumc005 AdV isolated from orangutans was found to be very similar to the gorilla AdVs, and bootstrap inference provided evidence of recombination between the orangutan AdV and the gorilla AdVs. This suggests that this virus may not be a genuine orangutan AdV but may have been transferred from a gorilla to an orangutan host.
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Lockhart A, Mucida D, Parsa R. Immunity to enteric viruses. Immunity 2022; 55:800-818. [PMID: 35545029 PMCID: PMC9257994 DOI: 10.1016/j.immuni.2022.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
Pathogenic enteric viruses are a major cause of morbidity and mortality, particularly among children in developing countries. The host response to enteric viruses occurs primarily within the mucosa, where the intestinal immune system must balance protection against pathogens with tissue protection and tolerance to harmless commensal bacteria and food. Here, we summarize current knowledge in natural immunity to enteric viruses, highlighting specialized features of the intestinal immune system. We further discuss how knowledge of intestinal anti-viral mechanisms can be translated into vaccine development with particular focus on immunization in the oral route. Research reveals that the intestine is a complex interface between enteric viruses and the host where environmental factors influence susceptibility and immunity to infection, while viral infections can have lasting implications for host health. A deeper mechanistic understanding of enteric anti-viral immunity with this broader context can ultimately lead to better vaccines for existing and emerging viruses.
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Affiliation(s)
- Ainsley Lockhart
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA.
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Rajaiya J, Saha A, Zhou X, Chodosh J. Human Adenovirus Species D Interactions with Corneal Stromal Cells. Viruses 2021; 13:2505. [PMID: 34960773 PMCID: PMC8709199 DOI: 10.3390/v13122505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Notable among the many communicable agents known to infect the human cornea is the human adenovirus, with less than ten adenoviruses having corneal tropism out of more than 100 known types. The syndrome of epidemic keratoconjunctivitis (EKC), caused principally by human adenovirus, presents acutely with epithelial keratitis, and later with stromal keratitis that can be chronic and recurrent. In this review, we discuss the current state of knowledge regarding the molecular biology of adenovirus infection of corneal stromal cells, among which the fibroblast-like keratocyte is the most predominant, in order to elucidate basic pathophysiologic mechanisms of stromal keratitis in the human patient with EKC.
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Affiliation(s)
- Jaya Rajaiya
- Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (A.S.); (X.Z.)
| | | | | | - James Chodosh
- Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (A.S.); (X.Z.)
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Mendonça SA, Lorincz R, Boucher P, Curiel DT. Adenoviral vector vaccine platforms in the SARS-CoV-2 pandemic. NPJ Vaccines 2021; 6:97. [PMID: 34354082 PMCID: PMC8342436 DOI: 10.1038/s41541-021-00356-x] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Adenoviral vectors have been explored as vaccine agents for a range of infectious diseases, and their ability to induce a potent and balanced immune response made them logical candidates to apply to the COVID-19 pandemic. The unique molecular characteristics of these vectors enabled the rapid development of vaccines with advanced designs capable of overcoming the biological challenges faced by early adenoviral vector systems. These successes and the urgency of the COVID-19 situation have resulted in a flurry of candidate adenoviral vector vaccines for COVID-19 from both academia and industry. These vaccines represent some of the lead candidates currently supported by Operation Warp Speed and other government agencies for rapid translational development. This review details adenoviral vector COVID-19 vaccines currently in human clinical trials and provides an overview of the new technologies employed in their design. As these vaccines have formed a cornerstone of the COVID-19 global vaccination campaign, this review provides a full consideration of the impact and development of this emerging platform.
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Affiliation(s)
- Samir Andrade Mendonça
- Washington University in Saint Louis, School of Medicine, Biologic Therapeutics Center, Radiation Oncology Department. 660 South Euclid Avenue, St. Louis, MO, USA
| | - Reka Lorincz
- Washington University in Saint Louis, School of Medicine, Biologic Therapeutics Center, Radiation Oncology Department. 660 South Euclid Avenue, St. Louis, MO, USA
| | - Paul Boucher
- Washington University in Saint Louis, School of Medicine, Biologic Therapeutics Center, Radiation Oncology Department. 660 South Euclid Avenue, St. Louis, MO, USA
| | - David T Curiel
- Washington University in Saint Louis, School of Medicine, Biologic Therapeutics Center, Radiation Oncology Department. 660 South Euclid Avenue, St. Louis, MO, USA.
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Allard MW, Brown EW. Epidemiology needs more interdisciplinary teams with expertise in molecular systematics, public health and food safety. Cladistics 2020; 36:345-347. [DOI: 10.1111/cla.12428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 01/30/2023] Open
Affiliation(s)
- Marc W. Allard
- Center of Food Safety and Applied NutritionU. S. Food and Drug Administration College Park MD 20740 USA
| | - Eric W. Brown
- Center of Food Safety and Applied NutritionU. S. Food and Drug Administration College Park MD 20740 USA
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