5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus
The spread of Zika virus (ZIKV) from the African continent to the Americas promoted its molecular evolution, as reflected by mutations in its RNA genome. Most of the ZIKV genome sequences in the GenBank database have incomplete 5' and 3' UTR sequences, reflecting the deficiency of whole-ge...
- Autores:
-
Álvarez Díaz, Diego Alejandro
Usme Ciro, José Aldemar
Corchuelo, Sheryll
Naizaque, Julián Ricardo
Rivera, Jorge Alonso
Castiblanco Martínez, Hernán Darío
Torres Fernández, Orlando
Rengifo, Aura Caterine
- Tipo de recurso:
- Article of journal
- Fecha de publicación:
- 2023
- Institución:
- Universidad Cooperativa de Colombia
- Repositorio:
- Repositorio UCC
- Idioma:
- eng
- OAI Identifier:
- oai:repository.ucc.edu.co:20.500.12494/55526
- Acceso en línea:
- https://hdl.handle.net/20.500.12494/55526
- Palabra clave:
- 610 - Medicina y salud
Zika virus
RNA genome
ZIKV genome
UTR sequences
- Rights
- openAccess
- License
- http://creativecommons.org/licenses/by-nc-nd/4.0/
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5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| title |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| spellingShingle |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus 610 - Medicina y salud Zika virus RNA genome ZIKV genome UTR sequences |
| title_short |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| title_full |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| title_fullStr |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| title_full_unstemmed |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| title_sort |
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus |
| dc.creator.fl_str_mv |
Álvarez Díaz, Diego Alejandro Usme Ciro, José Aldemar Corchuelo, Sheryll Naizaque, Julián Ricardo Rivera, Jorge Alonso Castiblanco Martínez, Hernán Darío Torres Fernández, Orlando Rengifo, Aura Caterine |
| dc.contributor.author.none.fl_str_mv |
Álvarez Díaz, Diego Alejandro Usme Ciro, José Aldemar Corchuelo, Sheryll Naizaque, Julián Ricardo Rivera, Jorge Alonso Castiblanco Martínez, Hernán Darío Torres Fernández, Orlando Rengifo, Aura Caterine |
| dc.contributor.researchgroup.none.fl_str_mv |
CIST-Centro de Investigación en Salud para el Trópico |
| dc.subject.ddc.none.fl_str_mv |
610 - Medicina y salud |
| topic |
610 - Medicina y salud Zika virus RNA genome ZIKV genome UTR sequences |
| dc.subject.proposal.none.fl_str_mv |
Zika virus RNA genome ZIKV genome UTR sequences |
| description |
The spread of Zika virus (ZIKV) from the African continent to the Americas promoted its molecular evolution, as reflected by mutations in its RNA genome. Most of the ZIKV genome sequences in the GenBank database have incomplete 5' and 3' UTR sequences, reflecting the deficiency of whole-genome sequencing technologies to resolve the sequences of the genome ends. We modified a protocol for rapid amplification of cDNA ends (RACE) to determine the complete sequences of the 5' and 3' UTRs of a previously reported ZIKV isolate (GenBank no. MH544701.1). This strategy is useful for determining 5' and 3' UTR sequences of ZIKV isolates and will be useful for comparative genomics applications. |
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2023 |
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2023-07-10 |
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2024-05-06T20:43:48Z |
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2024-05-06T20:43:48Z |
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Artículo |
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info:eu-repo/semantics/article |
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Álvarez-Díaz, D.A., Usme-Ciro, J.A., Corchuelo, S. et al. 5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus. Arch Virol 168, 204 (2023). doi: 10.1007/s00705-023-05820-8. |
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0304-8608 |
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https://hdl.handle.net/20.500.12494/55526 |
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doi.org/10.1007/s00705-023-05820-8 |
| dc.identifier.eissn.none.fl_str_mv |
1432-8798 |
| identifier_str_mv |
Álvarez-Díaz, D.A., Usme-Ciro, J.A., Corchuelo, S. et al. 5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus. Arch Virol 168, 204 (2023). doi: 10.1007/s00705-023-05820-8. 0304-8608 doi.org/10.1007/s00705-023-05820-8 1432-8798 |
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https://hdl.handle.net/20.500.12494/55526 |
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eng |
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eng |
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204 |
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8 |
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8 |
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1 |
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168 |
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Archives of Virology |
| dc.relation.references.none.fl_str_mv |
Akiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS (2016) Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science 354:1148–1152 Alvarez DE, Lodeiro MF, Ludueña SJ, Pietrasanta LI, Gamarnik AV (2005) Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79:6631–6643 Bellaousov S, Mathews DH (2010) ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA 16:1870–1880 Besnard M, Eyrolle-Guignot D, Guillemette-Artur P, Lastère S, Bost-Bezeaud F, Marcelis L, Abadie V, Garel C, Moutard ML, Jouannic JM, Rozenberg F, Leparc-Goffart I, Mallet HP (2016) Congenital cerebral malformations and dysfunction in fetuses and newborns following the 2013–2014 Zika virus epidemic in French Polynesia. Euro Surveill 21:30181 Bryant JE, Vasconcelos PF, Rijnbrand RC, Mutebi JP, Higgs S, Barrett AD (2005) Size heterogeneity in the 3' noncoding region of South American isolates of yellow fever virus. J Virol 79:3807–3821 Cao-Lormeau V-M, Blake A, Mons S, Lastère S, Roche C, Vanhomwegen J, Dub T, Baudouin L, Teissier A, Larre P, Vial A-L, Decam C, Choumet V, Halstead SK, Willison HJ, Musset L, Manuguerra J-C, Despres P, Fournier E, Mallet H-P, Musso D, Fontanet A, Neil J, Ghawché F (2016) Guillain–Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study. The Lancet 387:1531–1539 Chen YS, Fan YH, Tien CF, Yueh A, Chang RY (2018) The conserved stem-loop II structure at the 3’ untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA. PLoS One 13:e0201250 de Borba L, Villordo SM, Marsico FL, Carballeda JM, Filomatori CV, Gebhard LG, Pallarés HM, Lequime S, Lambrechts L, Sánchez Vargas I, Blair CD, Gamarnik AV (2019) RNA Structure Duplication in the Dengue Virus 3’ UTR. Redundancy or Host Specificity? mBio 10:e02506 Dong H, Zhang B, Shi PY (2008) Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein. Virology 381:123–135 Duffy MR, Chen TH, Hancock WT, Powers AM, Kool JL, Lanciotti RS, Pretrick M, Marfel M, Holzbauer S, Dubray C, Guillaumot L, Griggs A, Bel M, Lambert AJ, Laven J, Kosoy O, Panella A, Biggerstaff BJ, Fischer M, Hayes EB (2009) Zika virus outbreak on Yap Island, Federated States of Micronesia. N Engl J Med 360:2536–2543 |
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info:eu-repo/semantics/openAccess |
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Attribution-NonCommercial-NoDerivatives 4.0 International |
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8 páginas |
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application/pdf |
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Universidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina, Santa Marta |
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Universidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina, Santa Marta |
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Álvarez Díaz, Diego AlejandroUsme Ciro, José AldemarCorchuelo, SheryllNaizaque, Julián RicardoRivera, Jorge AlonsoCastiblanco Martínez, Hernán DaríoTorres Fernández, OrlandoRengifo, Aura CaterineCIST-Centro de Investigación en Salud para el Trópico2024-05-06T20:43:48Z2024-05-06T20:43:48Z2023-07-10Álvarez-Díaz, D.A., Usme-Ciro, J.A., Corchuelo, S. et al. 5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus. Arch Virol 168, 204 (2023). doi: 10.1007/s00705-023-05820-8.0304-8608https://hdl.handle.net/20.500.12494/55526doi.org/10.1007/s00705-023-05820-81432-8798The spread of Zika virus (ZIKV) from the African continent to the Americas promoted its molecular evolution, as reflected by mutations in its RNA genome. Most of the ZIKV genome sequences in the GenBank database have incomplete 5' and 3' UTR sequences, reflecting the deficiency of whole-genome sequencing technologies to resolve the sequences of the genome ends. We modified a protocol for rapid amplification of cDNA ends (RACE) to determine the complete sequences of the 5' and 3' UTRs of a previously reported ZIKV isolate (GenBank no. MH544701.1). This strategy is useful for determining 5' and 3' UTR sequences of ZIKV isolates and will be useful for comparative genomics applications.8 páginasapplication/pdfengUniversidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina, Santa MartaExternohttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://purl.org/coar/access_right/c_abf2https://link.springer.com/article/10.1007/s00705-023-05820-8#:~:text=The%20use%20of%205'%2F,assembly%20of%20complete%20genome%20sequences.610 - Medicina y saludZika virusRNA genomeZIKV genomeUTR sequences5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virusArtículohttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1http://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion204881168Archives of VirologyAkiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS (2016) Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science 354:1148–1152Alvarez DE, Lodeiro MF, Ludueña SJ, Pietrasanta LI, Gamarnik AV (2005) Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79:6631–6643Bellaousov S, Mathews DH (2010) ProbKnot: fast prediction of RNA secondary structure including pseudoknots. RNA 16:1870–1880Besnard M, Eyrolle-Guignot D, Guillemette-Artur P, Lastère S, Bost-Bezeaud F, Marcelis L, Abadie V, Garel C, Moutard ML, Jouannic JM, Rozenberg F, Leparc-Goffart I, Mallet HP (2016) Congenital cerebral malformations and dysfunction in fetuses and newborns following the 2013–2014 Zika virus epidemic in French Polynesia. Euro Surveill 21:30181Bryant JE, Vasconcelos PF, Rijnbrand RC, Mutebi JP, Higgs S, Barrett AD (2005) Size heterogeneity in the 3' noncoding region of South American isolates of yellow fever virus. J Virol 79:3807–3821Cao-Lormeau V-M, Blake A, Mons S, Lastère S, Roche C, Vanhomwegen J, Dub T, Baudouin L, Teissier A, Larre P, Vial A-L, Decam C, Choumet V, Halstead SK, Willison HJ, Musset L, Manuguerra J-C, Despres P, Fournier E, Mallet H-P, Musso D, Fontanet A, Neil J, Ghawché F (2016) Guillain–Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study. The Lancet 387:1531–1539Chen YS, Fan YH, Tien CF, Yueh A, Chang RY (2018) The conserved stem-loop II structure at the 3’ untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA. PLoS One 13:e0201250de Borba L, Villordo SM, Marsico FL, Carballeda JM, Filomatori CV, Gebhard LG, Pallarés HM, Lequime S, Lambrechts L, Sánchez Vargas I, Blair CD, Gamarnik AV (2019) RNA Structure Duplication in the Dengue Virus 3’ UTR. Redundancy or Host Specificity? mBio 10:e02506Dong H, Zhang B, Shi PY (2008) Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein. Virology 381:123–135Duffy MR, Chen TH, Hancock WT, Powers AM, Kool JL, Lanciotti RS, Pretrick M, Marfel M, Holzbauer S, Dubray C, Guillaumot L, Griggs A, Bel M, Lambert AJ, Laven J, Kosoy O, Panella A, Biggerstaff BJ, Fischer M, Hayes EB (2009) Zika virus outbreak on Yap Island, Federated States of Micronesia. 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