Loading…

In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack

The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search....

Full description

Saved in:
Bibliographic Details
Published in:Viruses 2022-02, Vol.14 (2), p.385
Main Authors: Hussein, Mouraya, Andrade Dos Ramos, Zaria, Berkhout, Ben, Herrera-Carrillo, Elena
Format: Article
Language:English
Subjects:
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233
cites cdi_FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233
container_end_page
container_issue 2
container_start_page 385
container_title Viruses
container_volume 14
creator Hussein, Mouraya
Andrade Dos Ramos, Zaria
Berkhout, Ben
Herrera-Carrillo, Elena
description The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.
doi_str_mv 10.3390/v14020385
format article
fullrecord <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_f7a6097c750544bc903631668072c684</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_f7a6097c750544bc903631668072c684</doaj_id><sourcerecordid>2633201294</sourcerecordid><originalsourceid>FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233</originalsourceid><addsrcrecordid>eNpdkktvEzEURkcIREthwR9AltjQxYBf48cGKYpoiVQBagpby_bcSZ1O7OJxIvHvcZsStaxsXx8dfb6-TfOW4I-MafxpRzimmKnuWXNMtNYt16R7_mh_1LyapjXGQmgsXzZHrKOk01IeNzeLiJZhDD6hHxn64EtIEdnYoyWMsD-lAV3ZvIJSa7-3ED1MKERUrgEtZ5fLdp5-tRRdfpuhc4hpA2hIuSrQLJawC9mOaFaK9TevmxeDHSd487CeND_PvlzNv7YX388X89lF67nQpVXKciAUCFa4lyAwUMe9U66nUggnuXRMMiuY0KJ3nFtCO-qJG_zgKKWMnTSLvbdPdm1uc9jY_MckG8x9IeWVsbkEP4IZpBVYSy873HHuvMZMMCKEwpJ6oXh1fd67brduA72HWOqDnkif3sRwbVZpZ5RSmFJRBR8eBDnV5k3FbMLkYRxthLSdTEWYElyIrqLv_0PXaZtjbdU9RTGh-i7R6Z7yOU1ThuEQhmBzNw7mMA6Vffc4_YH89__sL6pErG4</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2633201294</pqid></control><display><type>article</type><title>In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack</title><source>Publicly Available Content (ProQuest)</source><source>PubMed Central</source><source>Coronavirus Research Database</source><creator>Hussein, Mouraya ; Andrade Dos Ramos, Zaria ; Berkhout, Ben ; Herrera-Carrillo, Elena</creator><creatorcontrib>Hussein, Mouraya ; Andrade Dos Ramos, Zaria ; Berkhout, Ben ; Herrera-Carrillo, Elena</creatorcontrib><description>The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.</description><identifier>ISSN: 1999-4915</identifier><identifier>EISSN: 1999-4915</identifier><identifier>DOI: 10.3390/v14020385</identifier><identifier>PMID: 35215977</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Antiviral agents ; Computer Simulation ; Conserved sequence ; Coronaviridae ; Coronaviruses ; COVID-19 ; CRISPR ; CRISPR-Cas Systems ; CRISPR-Cas13d ; Design ; Disease transmission ; Drug development ; FDA approval ; Gene expression ; Genome, Viral ; Genomes ; Humans ; Middle East respiratory syndrome ; Nucleotide sequence ; Pandemics ; Pathogens ; Pneumonia ; Proteins ; RNA, Viral - genetics ; RNA-mediated interference ; SARS-CoV-2 - genetics ; SARS-CoV-2 genome ; Severe acute respiratory syndrome coronavirus 2 ; Spike Glycoprotein, Coronavirus - genetics ; Viruses ; Zoonoses</subject><ispartof>Viruses, 2022-02, Vol.14 (2), p.385</ispartof><rights>2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 by the authors. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233</citedby><cites>FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233</cites><orcidid>0000-0001-9986-8552</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2633201294?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2633201294?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,38516,43895,44590,53791,53793,74412,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35215977$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hussein, Mouraya</creatorcontrib><creatorcontrib>Andrade Dos Ramos, Zaria</creatorcontrib><creatorcontrib>Berkhout, Ben</creatorcontrib><creatorcontrib>Herrera-Carrillo, Elena</creatorcontrib><title>In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack</title><title>Viruses</title><addtitle>Viruses</addtitle><description>The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.</description><subject>Antiviral agents</subject><subject>Computer Simulation</subject><subject>Conserved sequence</subject><subject>Coronaviridae</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>CRISPR</subject><subject>CRISPR-Cas Systems</subject><subject>CRISPR-Cas13d</subject><subject>Design</subject><subject>Disease transmission</subject><subject>Drug development</subject><subject>FDA approval</subject><subject>Gene expression</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>Humans</subject><subject>Middle East respiratory syndrome</subject><subject>Nucleotide sequence</subject><subject>Pandemics</subject><subject>Pathogens</subject><subject>Pneumonia</subject><subject>Proteins</subject><subject>RNA, Viral - genetics</subject><subject>RNA-mediated interference</subject><subject>SARS-CoV-2 - genetics</subject><subject>SARS-CoV-2 genome</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Spike Glycoprotein, Coronavirus - genetics</subject><subject>Viruses</subject><subject>Zoonoses</subject><issn>1999-4915</issn><issn>1999-4915</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>COVID</sourceid><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNpdkktvEzEURkcIREthwR9AltjQxYBf48cGKYpoiVQBagpby_bcSZ1O7OJxIvHvcZsStaxsXx8dfb6-TfOW4I-MafxpRzimmKnuWXNMtNYt16R7_mh_1LyapjXGQmgsXzZHrKOk01IeNzeLiJZhDD6hHxn64EtIEdnYoyWMsD-lAV3ZvIJSa7-3ED1MKERUrgEtZ5fLdp5-tRRdfpuhc4hpA2hIuSrQLJawC9mOaFaK9TevmxeDHSd487CeND_PvlzNv7YX388X89lF67nQpVXKciAUCFa4lyAwUMe9U66nUggnuXRMMiuY0KJ3nFtCO-qJG_zgKKWMnTSLvbdPdm1uc9jY_MckG8x9IeWVsbkEP4IZpBVYSy873HHuvMZMMCKEwpJ6oXh1fd67brduA72HWOqDnkif3sRwbVZpZ5RSmFJRBR8eBDnV5k3FbMLkYRxthLSdTEWYElyIrqLv_0PXaZtjbdU9RTGh-i7R6Z7yOU1ThuEQhmBzNw7mMA6Vffc4_YH89__sL6pErG4</recordid><startdate>20220214</startdate><enddate>20220214</enddate><creator>Hussein, Mouraya</creator><creator>Andrade Dos Ramos, Zaria</creator><creator>Berkhout, Ben</creator><creator>Herrera-Carrillo, Elena</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>COVID</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-9986-8552</orcidid></search><sort><creationdate>20220214</creationdate><title>In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack</title><author>Hussein, Mouraya ; Andrade Dos Ramos, Zaria ; Berkhout, Ben ; Herrera-Carrillo, Elena</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Antiviral agents</topic><topic>Computer Simulation</topic><topic>Conserved sequence</topic><topic>Coronaviridae</topic><topic>Coronaviruses</topic><topic>COVID-19</topic><topic>CRISPR</topic><topic>CRISPR-Cas Systems</topic><topic>CRISPR-Cas13d</topic><topic>Design</topic><topic>Disease transmission</topic><topic>Drug development</topic><topic>FDA approval</topic><topic>Gene expression</topic><topic>Genome, Viral</topic><topic>Genomes</topic><topic>Humans</topic><topic>Middle East respiratory syndrome</topic><topic>Nucleotide sequence</topic><topic>Pandemics</topic><topic>Pathogens</topic><topic>Pneumonia</topic><topic>Proteins</topic><topic>RNA, Viral - genetics</topic><topic>RNA-mediated interference</topic><topic>SARS-CoV-2 - genetics</topic><topic>SARS-CoV-2 genome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Spike Glycoprotein, Coronavirus - genetics</topic><topic>Viruses</topic><topic>Zoonoses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hussein, Mouraya</creatorcontrib><creatorcontrib>Andrade Dos Ramos, Zaria</creatorcontrib><creatorcontrib>Berkhout, Ben</creatorcontrib><creatorcontrib>Herrera-Carrillo, Elena</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Virology and AIDS Abstracts</collection><collection>Health &amp; Medical Collection (ProQuest Medical &amp; Health Databases)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Biological Science Database</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Viruses</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hussein, Mouraya</au><au>Andrade Dos Ramos, Zaria</au><au>Berkhout, Ben</au><au>Herrera-Carrillo, Elena</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack</atitle><jtitle>Viruses</jtitle><addtitle>Viruses</addtitle><date>2022-02-14</date><risdate>2022</risdate><volume>14</volume><issue>2</issue><spage>385</spage><pages>385-</pages><issn>1999-4915</issn><eissn>1999-4915</eissn><abstract>The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>35215977</pmid><doi>10.3390/v14020385</doi><orcidid>https://orcid.org/0000-0001-9986-8552</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1999-4915
ispartof Viruses, 2022-02, Vol.14 (2), p.385
issn 1999-4915
1999-4915
language eng
recordid cdi_doaj_primary_oai_doaj_org_article_f7a6097c750544bc903631668072c684
source Publicly Available Content (ProQuest); PubMed Central; Coronavirus Research Database
subjects Antiviral agents
Computer Simulation
Conserved sequence
Coronaviridae
Coronaviruses
COVID-19
CRISPR
CRISPR-Cas Systems
CRISPR-Cas13d
Design
Disease transmission
Drug development
FDA approval
Gene expression
Genome, Viral
Genomes
Humans
Middle East respiratory syndrome
Nucleotide sequence
Pandemics
Pathogens
Pneumonia
Proteins
RNA, Viral - genetics
RNA-mediated interference
SARS-CoV-2 - genetics
SARS-CoV-2 genome
Severe acute respiratory syndrome coronavirus 2
Spike Glycoprotein, Coronavirus - genetics
Viruses
Zoonoses
title In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T12%3A12%3A35IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=In%20Silico%20Prediction%20and%20Selection%20of%20Target%20Sequences%20in%20the%20SARS-CoV-2%20RNA%20Genome%20for%20an%20Antiviral%20Attack&rft.jtitle=Viruses&rft.au=Hussein,%20Mouraya&rft.date=2022-02-14&rft.volume=14&rft.issue=2&rft.spage=385&rft.pages=385-&rft.issn=1999-4915&rft.eissn=1999-4915&rft_id=info:doi/10.3390/v14020385&rft_dat=%3Cproquest_doaj_%3E2633201294%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c469t-88a4e12e1080d7e60e2b4cb8bd2766b747b373a63696db44a1252c1bfcfb22233%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2633201294&rft_id=info:pmid/35215977&rfr_iscdi=true