In silicoidentification of conservedcis-acting RNA elements in the SARS-CoV-2 genome

被引：11

作者：

Alhatlani, Bader Y. ^{[1
]}

机构：

[1] Qassim Univ, Unayzah Community Coll, Dept Med Appl Sci, Unayzah, Saudi Arabia

来源：

FUTURE VIROLOGY | 2020年 / 15卷 / 07期

关键词：

cis-acting RNA elements; RNA structure; RNA virus; SARS-CoV-2; PACKAGING SIGNAL; 5'-UNTRANSLATED REGION; STEM-LOOP; CORONAVIRUS; IDENTIFICATION; ALPHACORONAVIRUS; REPLICATION;

D O I：

10.2217/fvl-2020-0163

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

Aim:The aim of this study was to computationally predict conserved RNA sequences and structures known ascis-acting RNA elements (CREs) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome.Materials & methods:Bioinformatics tools were used to analyze and predict CREs by obtaining viral sequences from available databases.Results:Computational analysis revealed the presence of RNA stem-loop structures within the 3 ' end of the ORF1ab region analogous to previously identified SARS-CoV genomic packaging signals. Alignment-based RNA secondary structure predictions of the 5 ' end of the SARS-CoV-2 genome also identified conserved CREs.Conclusion:These CREs may be potential vaccine and/or antiviral therapeutic targets; however, further studies are warranted to confirm their roles in the SARS-CoV-2 life cycle.

引用

页码：409 / 417

页数：9

共 33 条

[1] Functions of the 5′ and 3′ ends of calicivirus genomes [J].

Alhatlani, Bader ;

Vashist, Surender ;

Goodfellow, Ian .

VIRUS RESEARCH, 2015, 206 :134-143

[2] The proximal origin of SARS-CoV-2 [J].

Andersen, Kristian G. ;

Rambaut, Andrew ;

Lipkin, W. Ian ;

Holmes, Edward C. ;

Garry, Robert F. .

NATURE MEDICINE, 2020, 26 (04) :450-452

[3] New structure model for the packaging signal in the genome of group IIa coronaviruses [J].

Chen, Shih-Cheng ;

van den Born, Erwin ;

van den Worm, Sjoerd H. E. ;

Pleij, Cornelis W. A. ;

Snijder, Eric J. ;

Olthoorn, Ren C. L. .

JOURNAL OF VIROLOGY, 2007, 81 (12) :6771-6774

[4] Group-specific structural features of the 5′-proximal sequences of coronavirus genomic RNAs [J].

Chen, Shih-Cheng ;

Olsthoorn, Rene C. L. .

VIROLOGY, 2010, 401 (01) :29-41

[5] VARNA: Interactive drawing and editing of the RNA secondary structure [J].

Darty, Kevin ;

Denise, Alain ;

Ponty, Yann .

BIOINFORMATICS, 2009, 25 (15) :1974-1975

[6] Identification of a novel coronavirus in patients with severe acute respiratory syndrome [J].

Drosten, C ;

Günther, S ;

Preiser, W ;

van der Werf, S ;

Brodt, HR ;

Becker, S ;

Rabenau, H ;

Panning, M ;

Kolesnikova, L ;

Fouchier, RAM ;

Berger, A ;

Burguière, AM ;

Cinatl, J ;

Eickmann, M ;

Escriou, N ;

Grywna, K ;

Kramme, S ;

Manuguerra, JC ;

Müller, S ;

Rickerts, V ;

Stürmer, M ;

Vieth, S ;

Klenk, HD ;

Osterhaus, ADME ;

Schmitz, H ;

Doerr, HW .

NEW ENGLAND JOURNAL OF MEDICINE, 2003, 348 (20) :1967-1976

[7] Transmissible gastroenteritis coronavirus packaging signal is located at the 5′ end of the virus genome [J].

Escors, D ;

Izeta, A ;

Capiscol, C ;

Enjuanes, L .

JOURNAL OF VIROLOGY, 2003, 77 (14) :7890-7902

[8] IDENTIFICATION AND CHARACTERIZATION OF A CORONAVIRUS PACKAGING SIGNAL [J].

FOSMIRE, JA ;

HWANG, K ;

MAKINO, S .

JOURNAL OF VIROLOGY, 1992, 66 (06) :3522-3530

[9] Identification of a cis-acting replication element within the poliovirus coding region [J].

Goodfellow, I ;

Chaudhry, Y ;

Richardson, A ;

Meredith, J ;

Almond, JW ;

Barclay, W ;

Evans, DJ .

JOURNAL OF VIROLOGY, 2000, 74 (10) :4590-4600

[10] The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 [J].

Gorbalenya, Alexander E. ;

Baker, Susan C. ;

Baric, Ralph S. ;

de Groot, Raoul J. ;

Drosten, Christian ;

Gulyaeva, Anastasia A. ;

Haagmans, Bart L. ;

Lauber, Chris ;

Leontovich, Andrey M. ;

Neuman, Benjamin W. ;

Penzar, Dmitry ;

Perlman, Stanley ;

Poon, Leo L. M. ;

Samborskiy, Dmitry V. ;

Sidorov, Igor A. ;

Sola, Isabel ;

Ziebuhr, John .

NATURE MICROBIOLOGY, 2020, 5 (04) :536-544

← 1 2 3 4 →