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3 results on '"Garcia-Cehic, D."'

1. Host-dependent editing of SARS-CoV-2 in COVID-19 patients

Author

Tomás Pumarola, Elena Sulleiro, Narcís Saubi, Mari Carmen Martin, Ariadna Rando, Juliana Esperalba, Juan Ignacio Esteban, Josep F. Abril, Joan Joseph, Josep Gregori, Francisco Rodriguez-Frias, Maria Piñana, Josep Quer, Sergi Colomer-Castell, Andrés Antón, Cristina Andrés, Carla Castillo, Carolina Campos, Damir Garcia-Cehic, Maria Francesca Cortese, Maria Gema Codina, Institut Català de la Salut, [Gregori J] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Malalties Hepàtiques-Hepatitis Viral, Unitat del Fetge, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. Roche Diagnostics SL, Barcelona, Spain. [Cortese MF, Saubí N] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Bioquímica i Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Piñana M, Andrés C, Martin MC, Castillo C] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Unitat de Virus Respiratoris, Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Campos C, Garcia-Cehic D, Quer J] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Malalties Hepàtiques-Hepatitis Viral, Unitat del Fetge, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. [Codina MG, Rando A, Esperalba J, Sulleiro E, Joseph J] Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Colomer-Castell S, Esteban JI] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Malalties Hepàtiques-Hepatitis Viral, Unitat del Fetge, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Pumarola T] Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Universitat Autònoma de Barcelona, Bellaterra, Spain. [Rodriguez-Frias F ] Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Bioquímica i Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Universitat Autònoma de Barcelona, Bellaterra, Spain. [Antón A] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Unitat de Virus Respiratoris, Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Universitat Autònoma de Barcelona, Bellaterra, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Male, Virologia, Epidemiology, Protein Conformation, viruses, Genoma humà, Virus Replication, COVID-19 (Malaltia), Chemical Phenomena::Biochemical Phenomena::Molecular Structure::Amino Acid Sequence [PHENOMENA AND PROCESSES], Protein structure, Drug Discovery, virosis::infecciones por virus ARN::infecciones por Nidovirales::infecciones por Coronaviridae::infecciones por Coronavirus [ENFERMEDADES], Peptide sequence, Genetics, Virus Diseases::RNA Virus Infections::Nidovirales Infections::Coronaviridae Infections::Coronavirus Infections [DISEASES], General Medicine, Middle Aged, Infectious Diseases, Host-Pathogen Interactions, Spike Glycoprotein, Coronavirus, Female, Research Article, Adult, Other subheadings::Other subheadings::Other subheadings::/virology [Other subheadings], Immunology, Viral quasispecies, Biology, Microbiology, Seqüència d'aminoàcids, Virology, Genetic variation, ADAR1, Humans, Genetic variability, Amino Acid Sequence, Human genome, Otros calificadores::Otros calificadores::Otros calificadores::/virología [Otros calificadores], Base Sequence, Host (biology), SARS-CoV-2, editing, Mutació (Biologia), RNA, COVID-19, Genetic Variation, quasispecies, Mutation (Biology), mutations, Viral replication, fenómenos químicos::fenómenos bioquímicos::estructura molecular::secuencia de aminoácidos [FENÓMENOS Y PROCESOS], Parasitology
Abstract

SARS-CoV-2; Mutacions; Quasiespècie SARS-CoV-2; Mutaciones; Cuasiespecie SARS-CoV-2; Mutations; Quasispecies A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants. This study was supported by the Direcció General de Recerca i Innovació en Salut (DGRIS) of the Catalan Health Ministry, Generalitat de Catalunya, through the Vall d’Hebron Institut de Recerca (VHIR); the European Regional Development Fund (ERDF) “A way to achieve Europe” by the Spanish Network for Research in Infectious Diseases [grant number REIPI RD16/0016/0003]; Instituto de Salud Carlos III [grant number FIS PI19/00301]; and Centro para el Desarrollo Tecnologico Industrial (CDTI) from the Ministry of Economic Affairs and Digital Transformation [grant number IDI-20200297].

Published
2021

2. Host-dependent editing of SARS-CoV-2 in COVID-19 patients.

Author

Gregori J, Cortese MF, Piñana M, Campos C, Garcia-Cehic D, Andrés C, Abril JF, Codina MG, Rando A, Esperalba J, Sulleiro E, Joseph J, Saubí N, Colomer-Castell S, Martin MC, Castillo C, Esteban JI, Pumarola T, Rodriguez-Frias F, Antón A, and Quer J

Subjects
Adult, Amino Acid Sequence, Base Sequence, Female, Host-Pathogen Interactions, Humans, Male, Middle Aged, Protein Conformation, SARS-CoV-2 physiology, Virus Replication, COVID-19 virology, Genetic Variation, SARS-CoV-2 genetics, Spike Glycoprotein, Coronavirus genetics
Abstract

A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants.

Published
2021
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3. Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients.

Author

Andrés C, Garcia-Cehic D, Gregori J, Piñana M, Rodriguez-Frias F, Guerrero-Murillo M, Esperalba J, Rando A, Goterris L, Codina MG, Quer S, Martín MC, Campins M, Ferrer R, Almirante B, Esteban JI, Pumarola T, Antón A, and Quer J

Subjects
Adult, Aged, COVID-19, Computational Biology, Female, Gene Deletion, High-Throughput Nucleotide Sequencing, Humans, Male, Middle Aged, Pandemics, RNA Cleavage, SARS-CoV-2, Sequence Analysis, RNA, Betacoronavirus genetics, Coronavirus Infections virology, Genome, Viral genetics, Pneumonia, Viral virology, Quasispecies genetics, Respiratory Tract Infections virology, Spike Glycoprotein, Coronavirus genetics
Abstract

The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.

Published
2020
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