Computational analysis of a species D human adenovirus provides evidence of a novel virus

Espínola, Emilio E. - Barrios, Julio C. - Russomando, Graciela - Mirazo, Santiago - Arbiza, Juan

Resumen:

A human adenovirus (HAdV) species D, was isolated from a hospitalised child with severe lower respiratory infection. It was initially detected in the nasopharyngeal aspirate of the child followed by conventional PCR amplification of the hexon, penton base, and fibre genes. Sanger DNA sequencing and phylogenetic analyses showed characteristics of a recombinant genome not described before. Next Generation Sequencing analysis was performed to reconstruct its complete DNA genome after viral isolation in adenocarcinoma human cell line (A549). A complete genomic sequence of 35.2 kb in length, with a G +C content of 57 % was obtained, related to HAdV-D29 (96 % identity). Imputed serology analysis demonstrated its novel type with a nucleotide sequence identity of 95.3 % (hexon loop 1) and 96 % (hexon loop 2) to HAdV-D9. The penton base gene showed a novel sequence, distantly related to HAdV-D44. The E3 and E4 regions evolved significantly from their ancestors. The fibre gene was almost identical to the knob region of HAdV-D15 but showed an unrelated shaft sequence. In conclusion the genomics of this novel HAdV, designated the HAdV-D83 [P83H9F15] prototype and bearing a new penton base gene, supports the importance of viral evolution to understand modified tissue tropism, nhanced transmission, or altered virulence.


Detalles Bibliográficos
2017
Adenovirus
Recombination
DNA sequencing
Bioinformatics
Inglés
Universidad de la República
COLIBRI
https://hdl.handle.net/20.500.12008/34077
Acceso abierto
Licencia Creative Commons Atribución (CC - By 4.0)
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author Espínola, Emilio E.
author2 Barrios, Julio C.
Russomando, Graciela
Mirazo, Santiago
Arbiza, Juan
author2_role author
author
author
author
author_facet Espínola, Emilio E.
Barrios, Julio C.
Russomando, Graciela
Mirazo, Santiago
Arbiza, Juan
author_role author
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collection COLIBRI
dc.contributor.filiacion.none.fl_str_mv Espínola Emilio E.
Barrios Julio C.
Russomando Graciela
Mirazo Santiago, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.
Arbiza Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.
dc.creator.none.fl_str_mv Espínola, Emilio E.
Barrios, Julio C.
Russomando, Graciela
Mirazo, Santiago
Arbiza, Juan
dc.date.accessioned.none.fl_str_mv 2022-10-11T13:03:39Z
dc.date.available.none.fl_str_mv 2022-10-11T13:03:39Z
dc.date.issued.none.fl_str_mv 2017
dc.description.abstract.none.fl_txt_mv A human adenovirus (HAdV) species D, was isolated from a hospitalised child with severe lower respiratory infection. It was initially detected in the nasopharyngeal aspirate of the child followed by conventional PCR amplification of the hexon, penton base, and fibre genes. Sanger DNA sequencing and phylogenetic analyses showed characteristics of a recombinant genome not described before. Next Generation Sequencing analysis was performed to reconstruct its complete DNA genome after viral isolation in adenocarcinoma human cell line (A549). A complete genomic sequence of 35.2 kb in length, with a G +C content of 57 % was obtained, related to HAdV-D29 (96 % identity). Imputed serology analysis demonstrated its novel type with a nucleotide sequence identity of 95.3 % (hexon loop 1) and 96 % (hexon loop 2) to HAdV-D9. The penton base gene showed a novel sequence, distantly related to HAdV-D44. The E3 and E4 regions evolved significantly from their ancestors. The fibre gene was almost identical to the knob region of HAdV-D15 but showed an unrelated shaft sequence. In conclusion the genomics of this novel HAdV, designated the HAdV-D83 [P83H9F15] prototype and bearing a new penton base gene, supports the importance of viral evolution to understand modified tissue tropism, nhanced transmission, or altered virulence.
dc.format.extent.es.fl_str_mv 11 h.
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dc.identifier.citation.es.fl_str_mv Espínola, E, Barrios, J, Russomando, G. [y otros autores]. "Computational analysis of a species D human adenovirus provides evidence of a novel virus". Journal of General Virology. [en línea] 2017, 98, 2810–2820. 11 h.
dc.identifier.doi.none.fl_str_mv 10.1099/jgv.0.000947
dc.identifier.issn.none.fl_str_mv 0022-1317
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12008/34077
dc.language.iso.none.fl_str_mv en_US
eng
dc.publisher.es.fl_str_mv Microbiology Society
dc.relation.ispartof.es.fl_str_mv Journal of General Virology, 2017, 98: 2810–2820.
dc.rights.license.none.fl_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.rights.uri.*.fl_str_mv An error occurred getting the license - uri.
dc.source.none.fl_str_mv reponame:COLIBRI
instname:Universidad de la República
instacron:Universidad de la República
dc.subject.es.fl_str_mv Adenovirus
Recombination
DNA sequencing
Bioinformatics
dc.title.none.fl_str_mv Computational analysis of a species D human adenovirus provides evidence of a novel virus
dc.type.es.fl_str_mv Artículo
dc.type.none.fl_str_mv info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description A human adenovirus (HAdV) species D, was isolated from a hospitalised child with severe lower respiratory infection. It was initially detected in the nasopharyngeal aspirate of the child followed by conventional PCR amplification of the hexon, penton base, and fibre genes. Sanger DNA sequencing and phylogenetic analyses showed characteristics of a recombinant genome not described before. Next Generation Sequencing analysis was performed to reconstruct its complete DNA genome after viral isolation in adenocarcinoma human cell line (A549). A complete genomic sequence of 35.2 kb in length, with a G +C content of 57 % was obtained, related to HAdV-D29 (96 % identity). Imputed serology analysis demonstrated its novel type with a nucleotide sequence identity of 95.3 % (hexon loop 1) and 96 % (hexon loop 2) to HAdV-D9. The penton base gene showed a novel sequence, distantly related to HAdV-D44. The E3 and E4 regions evolved significantly from their ancestors. The fibre gene was almost identical to the knob region of HAdV-D15 but showed an unrelated shaft sequence. In conclusion the genomics of this novel HAdV, designated the HAdV-D83 [P83H9F15] prototype and bearing a new penton base gene, supports the importance of viral evolution to understand modified tissue tropism, nhanced transmission, or altered virulence.
eu_rights_str_mv openAccess
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identifier_str_mv Espínola, E, Barrios, J, Russomando, G. [y otros autores]. "Computational analysis of a species D human adenovirus provides evidence of a novel virus". Journal of General Virology. [en línea] 2017, 98, 2810–2820. 11 h.
0022-1317
10.1099/jgv.0.000947
instacron_str Universidad de la República
institution Universidad de la República
instname_str Universidad de la República
language eng
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publishDate 2017
reponame_str COLIBRI
repository.mail.fl_str_mv mabel.seroubian@seciu.edu.uy
repository.name.fl_str_mv COLIBRI - Universidad de la República
repository_id_str 4771
rights_invalid_str_mv An error occurred getting the license - uri.
Licencia Creative Commons Atribución (CC - By 4.0)
spelling Espínola Emilio E.Barrios Julio C.Russomando GracielaMirazo Santiago, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Arbiza Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.2022-10-11T13:03:39Z2022-10-11T13:03:39Z2017Espínola, E, Barrios, J, Russomando, G. [y otros autores]. "Computational analysis of a species D human adenovirus provides evidence of a novel virus". Journal of General Virology. [en línea] 2017, 98, 2810–2820. 11 h.0022-1317https://hdl.handle.net/20.500.12008/3407710.1099/jgv.0.000947A human adenovirus (HAdV) species D, was isolated from a hospitalised child with severe lower respiratory infection. It was initially detected in the nasopharyngeal aspirate of the child followed by conventional PCR amplification of the hexon, penton base, and fibre genes. Sanger DNA sequencing and phylogenetic analyses showed characteristics of a recombinant genome not described before. Next Generation Sequencing analysis was performed to reconstruct its complete DNA genome after viral isolation in adenocarcinoma human cell line (A549). A complete genomic sequence of 35.2 kb in length, with a G +C content of 57 % was obtained, related to HAdV-D29 (96 % identity). Imputed serology analysis demonstrated its novel type with a nucleotide sequence identity of 95.3 % (hexon loop 1) and 96 % (hexon loop 2) to HAdV-D9. The penton base gene showed a novel sequence, distantly related to HAdV-D44. The E3 and E4 regions evolved significantly from their ancestors. The fibre gene was almost identical to the knob region of HAdV-D15 but showed an unrelated shaft sequence. In conclusion the genomics of this novel HAdV, designated the HAdV-D83 [P83H9F15] prototype and bearing a new penton base gene, supports the importance of viral evolution to understand modified tissue tropism, nhanced transmission, or altered virulence.Submitted by Farías Verónica (vfarias@fcien.edu.uy) on 2022-09-27T15:24:39Z No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1099jgv.0.000947.pdf: 1312484 bytes, checksum: 407353c319463bb5a5034bc6f7dcb44b (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2022-10-11T12:54:02Z (GMT) No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1099jgv.0.000947.pdf: 1312484 bytes, checksum: 407353c319463bb5a5034bc6f7dcb44b (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2022-10-11T13:03:39Z (GMT). No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1099jgv.0.000947.pdf: 1312484 bytes, checksum: 407353c319463bb5a5034bc6f7dcb44b (MD5) Previous issue date: 201711 h.application/pdfen_USengMicrobiology SocietyJournal of General Virology, 2017, 98: 2810–2820.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)An error occurred getting the license - uri.info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)AdenovirusRecombinationDNA sequencingBioinformaticsComputational analysis of a species D human adenovirus provides evidence of a novel virusArtículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaEspínola, Emilio E.Barrios, Julio C.Russomando, GracielaMirazo, SantiagoArbiza, JuanLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/34077/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; charset=utf-844http://localhost:8080/xmlui/bitstream/20.500.12008/34077/2/license_urla0ebbeafb9d2ec7cbb19d7137ebc392cMD52license_textlicense_texttext/html; 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- Universidad de la Repúblicafalse
spellingShingle Computational analysis of a species D human adenovirus provides evidence of a novel virus
Espínola, Emilio E.
Adenovirus
Recombination
DNA sequencing
Bioinformatics
status_str publishedVersion
title Computational analysis of a species D human adenovirus provides evidence of a novel virus
title_full Computational analysis of a species D human adenovirus provides evidence of a novel virus
title_fullStr Computational analysis of a species D human adenovirus provides evidence of a novel virus
title_full_unstemmed Computational analysis of a species D human adenovirus provides evidence of a novel virus
title_short Computational analysis of a species D human adenovirus provides evidence of a novel virus
title_sort Computational analysis of a species D human adenovirus provides evidence of a novel virus
topic Adenovirus
Recombination
DNA sequencing
Bioinformatics
url https://hdl.handle.net/20.500.12008/34077