Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1

Detalhes bibliográficos
Autor(a) principal: Benedetti, Francesca
Data de Publicação: 2020
Outros Autores: Snyder, Greg A., Giovanetti, Marta, Angeletti, Silvia, Gallo, Robert C., Ciccozzi, Massimo, Zella, Davide
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/45902
Resumo: Institute of Human Virology. School of Medicine. University of Maryland. Baltimore, USA / Department of Biochemistry and Molecular Biology. University of Maryland, Baltimore, USA
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spelling Benedetti, FrancescaSnyder, Greg A.Giovanetti, MartaAngeletti, SilviaGallo, Robert C.Ciccozzi, MassimoZella, Davide2021-02-01T15:53:52Z2021-02-01T15:53:52Z2020BENEDETTI, Francesca et al. Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1. Journal of Translational Medicine, v. 18, n. 329, p. 1-6, 2020.1479-5876https://www.arca.fiocruz.br/handle/icict/4590210.1186/s12967-020-02507-5porBMCSARS-CoV-2COVID-19nsp1Adaptação viralExclusãoPatogênicasSARS-CoV-2COVID-19Deletionnsp1PathogenicViral adaptationEmerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleInstitute of Human Virology. School of Medicine. University of Maryland. Baltimore, USA / Department of Biochemistry and Molecular Biology. University of Maryland, Baltimore, USAInstitute of Human Virology. School of Medicine. University of Maryland. Baltimore, USA / Department of Microbiology and Immunology, University of Maryland, Baltimore, USAFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Flavivírus. Rio de Janeiro, RJ, Brasil..Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.Institute of Human Virology. School of Medicine. University of Maryland. Baltimore, USA / Department of Medicine, University of Biomedical Campus. Rome, Italy / Global Virus Network, Baltimore, USA.Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.Institute of Human Virology. School of Medicine. University of Maryland. Baltimore, USA / Department of Biochemistry and Molecular Biology. University of Maryland, Baltimore, USA / Global Virus Network, Baltimore, USA.Background: The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼ 30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by (a) the presence of specific amino acid residues of nsp1 and (b) the interaction between the protein and the host’s small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects. Methods: A total of 17,928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER. Results: We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure. Conclusions: Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host’s gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: (i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and (ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/45902/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALBenedetti_Francesca_etal_IOC_2020_COVID-19.pdfBenedetti_Francesca_etal_IOC_2020_COVID-19.pdfapplication/pdf1045095https://www.arca.fiocruz.br/bitstream/icict/45902/2/Benedetti_Francesca_etal_IOC_2020_COVID-19.pdf3d9640d569230bd3da757952e64bb231MD52TEXTBenedetti_Francesca_etal_IOC_2020_COVID-19.pdf.txtBenedetti_Francesca_etal_IOC_2020_COVID-19.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
title Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
spellingShingle Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
Benedetti, Francesca
SARS-CoV-2
COVID-19
nsp1
Adaptação viral
Exclusão
Patogênicas
SARS-CoV-2
COVID-19
Deletion
nsp1
Pathogenic
Viral adaptation
title_short Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
title_full Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
title_fullStr Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
title_full_unstemmed Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
title_sort Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1
author Benedetti, Francesca
author_facet Benedetti, Francesca
Snyder, Greg A.
Giovanetti, Marta
Angeletti, Silvia
Gallo, Robert C.
Ciccozzi, Massimo
Zella, Davide
author_role author
author2 Snyder, Greg A.
Giovanetti, Marta
Angeletti, Silvia
Gallo, Robert C.
Ciccozzi, Massimo
Zella, Davide
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Benedetti, Francesca
Snyder, Greg A.
Giovanetti, Marta
Angeletti, Silvia
Gallo, Robert C.
Ciccozzi, Massimo
Zella, Davide
dc.subject.other.pt_BR.fl_str_mv SARS-CoV-2
COVID-19
nsp1
Adaptação viral
Exclusão
Patogênicas
topic SARS-CoV-2
COVID-19
nsp1
Adaptação viral
Exclusão
Patogênicas
SARS-CoV-2
COVID-19
Deletion
nsp1
Pathogenic
Viral adaptation
dc.subject.en.pt_BR.fl_str_mv SARS-CoV-2
COVID-19
Deletion
nsp1
Pathogenic
Viral adaptation
description Institute of Human Virology. School of Medicine. University of Maryland. Baltimore, USA / Department of Biochemistry and Molecular Biology. University of Maryland, Baltimore, USA
publishDate 2020
dc.date.issued.fl_str_mv 2020
dc.date.accessioned.fl_str_mv 2021-02-01T15:53:52Z
dc.date.available.fl_str_mv 2021-02-01T15:53:52Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv BENEDETTI, Francesca et al. Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1. Journal of Translational Medicine, v. 18, n. 329, p. 1-6, 2020.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/45902
dc.identifier.issn.pt_BR.fl_str_mv 1479-5876
dc.identifier.doi.none.fl_str_mv 10.1186/s12967-020-02507-5
identifier_str_mv BENEDETTI, Francesca et al. Emerging of a SARS‑CoV‑2 viral strain with a deletion in nsp1. Journal of Translational Medicine, v. 18, n. 329, p. 1-6, 2020.
1479-5876
10.1186/s12967-020-02507-5
url https://www.arca.fiocruz.br/handle/icict/45902
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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