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Simas MCDC, Costa SM, Gomes PDSFC, Cruz NVGD, Corrêa IA, de Souza MRM, Dornelas-Ribeiro M, Nogueira TLS, Santos CGMD, Hoffmann L, Tanuri A, Moura-Neto RSD, Damaso CR, Costa LJD, Silva R. Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture. Viruses 2023; 15:v15030801. [PMID: 36992509 PMCID: PMC10051148 DOI: 10.3390/v15030801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper function; however, isolated viruses with partial deletion of ORF7a can replicate in culture cells similarly to wild-type viruses at 24 hpi, but with less infectious particles after 48 hpi. These findings on deleted ORF7a accessory protein gene, contribute to understanding SARS-CoV-2 phenotypes such as replication, immune evasion and evolutionary fitness as well insights into the role of SARS-CoV-2_ORF7a in the mechanism of virus-host interactions.
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Affiliation(s)
- Maria Clara da Costa Simas
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Sara Mesquita Costa
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Priscila da Silva Figueiredo Celestino Gomes
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Physics Department, Auburn University, Auburn, AL 36849, USA
| | | | - Isadora Alonso Corrêa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Marcos Dornelas-Ribeiro
- Laboratório de Biodefesa, Instituto de Biologia do Exército, Rio de Janeiro 20911-270, Brazil
| | | | | | - Luísa Hoffmann
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Clarissa R Damaso
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Luciana Jesus da Costa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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Monnerat G, Evaristo GPC, Evaristo JAM, Dos Santos CGM, Carneiro G, Maciel L, Carvalho VO, Nogueira FCS, Domont GB, Campos de Carvalho AC. Metabolomic profiling suggests systemic signatures of premature aging induced by Hutchinson-Gilford progeria syndrome. Metabolomics 2019; 15:100. [PMID: 31254107 DOI: 10.1007/s11306-019-1558-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/15/2019] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Hutchinson-Gilford Progeria Syndrome (HGPS) is an extremely rare genetic disorder. HGPS children present a high incidence of cardiovascular complications along with altered metabolic processes and an accelerated aging process. No metabolic biomarker is known and the mechanisms underlying premature aging are not fully understood. OBJECTIVES The present work aims to evaluate the metabolic alterations in HGPS using high resolution mass spectrometry. METHODS The present study analyzed plasma from six HGPS patients of both sexes (7.7 ± 1.4 years old; mean ± SD) and eight controls (8.6 ± 2.3 years old) by LC-MS/MS in high-resolution non-targeted metabolomics (Q-Exactive Plus). Targeted metabolomics was used to validate some of the metabolites identified by the non-targeted method in a triple quadrupole (TSQ-Quantiva). RESULTS We found several endogenous metabolites with statistical differences between control and HGPS children. Multivariate statistical analysis showed a clear separation between groups. Potential novel metabolic biomarkers were identified using the multivariate area under ROC curve (AUROC) based analysis, showing an AUC value higher than 0.80 using only two metabolites, and tending to 1.00 when increasing the number of metabolites in the AUROC model. Taken together, changed metabolic pathways involve sphingolipids, amino acids, and oxidation of fatty acids, among others. CONCLUSION Our data show significant alterations in cellular energy use and availability, in signal transduction, and lipid metabolites, adding new insights on metabolic alterations associated with premature aging and suggesting novel putative biomarkers.
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Affiliation(s)
- Gustavo Monnerat
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho 373 - CCS - Bloco G, Rio de Janeiro, 21941-902, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Gabriel Carneiro
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Maciel
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho 373 - CCS - Bloco G, Rio de Janeiro, 21941-902, Brazil
| | | | - Fábio César Sousa Nogueira
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho 373 - CCS - Bloco G, Rio de Janeiro, 21941-902, Brazil
| | - Gilberto Barbosa Domont
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho 373 - CCS - Bloco G, Rio de Janeiro, 21941-902, Brazil.
| | - Antonio Carlos Campos de Carvalho
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho 373 - CCS - Bloco G, Rio de Janeiro, 21941-902, Brazil.
- National Institute of Cardiology, Rio de Janeiro, Brazil.
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