Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

Keynote webinar | Spotlight on medication adherence

LIVE: Thursday 27th June 2024, 18:00-19:30 (CEST)
Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.
ADVANCED SEARCH
Log in
Top
Archives of Virology
Published in: Archives of Virology 8/2023

01-08-2023 | Zika Virus | Brief Report

5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus

Authors: Diego Alejandro Álvarez-Díaz, José Aldemar Usme-Ciro, Sheryll Corchuelo, Julián Ricardo Naizaque, Jorge Alonso Rivera, Hernán Darío Castiblanco-Martínez, Orlando Torres-Fernández, Aura Caterine Rengifo

Published in: Archives of Virology | Issue 8/2023

Login to get access

Abstract

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.
Appendix
Available only for authorised users
Literature
1.
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 354:1148–1152CrossRefPubMedPubMedCentral
2.
Alvarez DE, Lodeiro MF, Ludueña SJ, Pietrasanta LI, Gamarnik AV (2005) Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol 79:6631–6643CrossRefPubMedPubMedCentral
3.
4.
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 21:30181CrossRef
5.
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 79:3807–3821CrossRefPubMedPubMedCentral
6.
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 387:1531–1539CrossRef
7.
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:e0201250CrossRefPubMedPubMedCentral
8.
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:e02506CrossRefPubMedPubMedCentral
9.
Dong H, Zhang B, Shi PY (2008) Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein. Virology 381:123–135CrossRefPubMed
10.
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 360:2536–2543CrossRefPubMed
11.
Filomatori CV, Lodeiro MF, Alvarez DE, Samsa MM, Pietrasanta L, Gamarnik AV (2006) A 5' RNA element promotes dengue virus RNA synthesis on a circular genome. Genes Dev 20:2238–2249CrossRefPubMedPubMedCentral
12.
Foy BD, Kobylinski KC, Chilson Foy JL, Blitvich BJ, Travassos da Rosa A, Haddow AD, Lanciotti RS, Tesh RB (2011) Probable non-vector-borne transmission of Zika virus, Colorado, USA. Emerg Infect Dis 17:880–882CrossRefPubMedPubMedCentral
13.
Göertz GP, Abbo SR, Fros JJ, Pijlman GP (2018) Functional RNA during Zika virus infection. Virus Res 254:41–53CrossRefPubMed
14.
Hamel R, Liégeois F, Wichit S, Pompon J, Diop F, Talignani L, Thomas F, Desprès P, Yssel H, Missé D (2016) Zika virus: epidemiology, clinical features and host-virus interactions. Microbes Infect 18:441–449CrossRefPubMed
15.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549CrossRefPubMedPubMedCentral
16.
17.
Laiton-Donato K, Álvarez-Díaz DA, Rengifo AC, Torres-Fernández O, Usme-Ciro JA, Rivera JA, Santamaría G, Naizaque J, Monroy-Gómez J, Sarmiento L, Gunturiz ML, Muñoz A, Vanegas R, Rico A, Pardo L, Peláez-Carvajal D (2019) Complete genome sequence of a Colombian Zika Virus strain obtained from BALB/c mouse brain after intraperitoneal inoculation. Microbiol Resour Announc 8:e01719CrossRefPubMedPubMedCentral
18.
Li P, Wei Y, Mei M, Tang L, Sun L, Huang W, Zhou J, Zou C, Zhang S, Qin CF, Jiang T, Dai J, Tan X, Zhang QC (2018) Integrative analysis of Zika virus genome RNA structure reveals critical determinants of viral infectivity. Cell Host Microbe 24:875-886e875CrossRefPubMed
19.
Lin HH, Yip BS, Huang LM, Wu SC (2018) Zika virus structural biology and progress in vaccine development. Biotechnol Adv 36:47–53CrossRefPubMed
20.
Liu Y, Liu J, Du S, Shan C, Nie K, Zhang R, Li XF, Zhang R, Wang T, Qin CF, Wang P, Shi PY, Cheng G (2017) Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes. Nature 545:482–486CrossRefPubMedPubMedCentral
21.
Manokaran G, Finol E, Wang C, Gunaratne J, Bahl J, Ong EZ, Tan HC, Sessions OM, Ward AM, Gubler DJ, Harris E, Garcia-Blanco MA, Ooi EE (2015) Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness. Science 350:217–221CrossRefPubMedPubMedCentral
22.
Mlakar J, Korva M, Tul N, Popović M, Poljšak-Prijatelj M, Mraz J, Kolenc M, Resman Rus K, Vesnaver Vipotnik T, Fabjan Vodušek V, Vizjak A, Pižem J, Petrovec M, Avšič Županc T (2016) Zika virus associated with microcephaly. N Engl J Med 374:951–958CrossRefPubMed
23.
24.
Pallarés HM, Costa Navarro GS, Villordo SM, Merwaiss F, de Borba L, Gonzalez Lopez Ledesma MM, Ojeda DS, Henrion-Lacritick A, Morales MA, Fabri C, Saleh MC, Gamarnik AV (2020) Zika virus subgenomic flavivirus RNA generation requires cooperativity between duplicated RNA structures that are essential for productive infection in human cells. J Virol 94:e00343CrossRefPubMedPubMedCentral
25.
Proutski V, Gould EA, Holmes EC (1997) Secondary structure of the 3' untranslated region of flaviviruses: similarities and differences. Nucleic Acids Res 25:1194–1202CrossRefPubMedPubMedCentral
26.
Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform 11:129CrossRef
27.
Rosales-Munar A, Alvarez-Diaz DA, Laiton-Donato K, Peláez-Carvajal D, Usme-Ciro JA (2020) Efficient method for molecular characterization of the 5’ and 3’ ends of the dengue virus genome. Viruses 12:496CrossRefPubMedPubMedCentral
28.
Song Y, Mugavero J, Stauft CB, Wimmer E (2019) Dengue and Zika virus 5’ untranslated regions harbor internal ribosomal entry site functions. mBio 10:e00459CrossRefPubMedPubMedCentral
29.
Song Y, Mugavero J, Stauft CB, Wimmer E (2019b) Dengue and Zika virus 5’-UTRs harbor IRES functions. 557942
30.
Whitehead SS, Durbin AP, Pierce KK, Elwood D, McElvany BD, Fraser EA, Carmolli MP, Tibery CM, Hynes NA, Jo M, Lovchik JM, Larsson CJ, Doty EA, Dickson DM, Luke CJ, Subbarao K, Diehl SA, Kirkpatrick BD (2017) In a randomized trial, the live attenuated tetravalent dengue vaccine TV003 is well-tolerated and highly immunogenic in subjects with flavivirus exposure prior to vaccination. PLoS Negl Trop Dis 11:e0005584CrossRefPubMedPubMedCentral
31.
Yu L, Nomaguchi M, Padmanabhan R, Markoff L (2008) Specific requirements for elements of the 5' and 3' terminal regions in flavivirus RNA synthesis and viral replication. Virology 374:170–185CrossRefPubMed
32.
Yuan L, Huang XY, Liu ZY, Zhang F, Zhu XL, Yu JY, Ji X, Xu YP, Li G, Li C, Wang HJ, Deng YQ, Wu M, Cheng ML, Ye Q, Xie DY, Li XF, Wang X, Shi W, Hu B, Shi PY, Xu Z, Qin CF (2017) A single mutation in the prM protein of Zika virus contributes to fetal microcephaly. Science 358:933–936CrossRefPubMed
Metadata
Title
5'/3' RACE method for sequencing the 5' and 3' untranslated regions of Zika virus
Authors
Diego Alejandro Álvarez-Díaz
José Aldemar Usme-Ciro
Sheryll Corchuelo
Julián Ricardo Naizaque
Jorge Alonso Rivera
Hernán Darío Castiblanco-Martínez
Orlando Torres-Fernández
Aura Caterine Rengifo
Publication date
01-08-2023
Publisher
Springer Vienna
Keyword
Zika Virus
Published in
Archives of Virology / Issue 8/2023
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI
https://doi.org/10.1007/s00705-023-05820-8

Other articles of this Issue 8/2023

Archives of Virology 8/2023 Go to the issue

Brief Report

Detection of mpox virus in ambient air in a sexual health clinic

Review

Role of Tim-3 in COVID-19: a potential biomarker and therapeutic target

Brief Report

Evidence of insufficient genetic data and lack of regular genetic research on rabies virus in the Russian Federation: a study of the recent epizootic situation

Brief Report

Molecular evolution of dengue virus: a Bayesian approach using 1581 whole-genome sequences from January 1944 to July 2022

Brief Report

Genomic analysis and characterization of bacteriophage vB_SpuS_NX263 infecting Salmonella enterica subsp. enterica serovar Pullorum

ORIGINAL ARTICLE

Clinical and molecular epidemiologic features of enterovirus D68 infection in children with acute lower respiratory tract infection in China
Live Webinar | 27-06-2024 | 18:00 (CEST)

Keynote webinar | Spotlight on medication adherence

Reserve your place

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

WHO estimates that half of all patients worldwide are non-adherent to their prescribed medication. The consequences of poor adherence can be catastrophic, on both the individual and population level.

Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.

Prof. Kevin Dolgin
Prof. Florian Limbourg
Prof. Anoop Chauhan
Developed by: Springer Medicine
Obesity Clinical Trial Summary

At a glance: The STEP trials

Read more

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Pediatric Cardiology Video

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

Cardiopulmonary Comorbidity Video

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Valvular Heart Disease Video

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Heart Failure Video

Watch this official video from ACC.24. Dr. Biykem Bozkurt discusses last year's major advances in heart failure and cardiomyopathies.

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Heart Failure Video

Watch this official video from ACC.24. Dr. Biykem Bozkurt discusses last year's major advances in heart failure and cardiomyopathies.

Watch now

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

16-04-2024 Type 2 Diabetes News

Incentivised to exercise

11-04-2024 Lifestyle Modifications News

New intervention for STEMI-related cardiogenic shock

10-04-2024 Myocardial Infarction News

» View more highlights on the ACC 2024 congress hub page

Image Credits