The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants

Autor: Carolina Campos, Sergi Colomer-Castell, Damir Garcia-Cehic, Josep Gregori, Cristina Andrés, Maria Piñana, Alejandra González-Sánchez, Blanca Borràs, Oleguer Parés-Badell, Caroline Melanie Adombi, Marta Ibañez-Lligoña, Juliana Esperalba, Maria Gema Codina, Ariadna Rando-Segura, Narcis Saubí, Juan Ignacio Esteban, Francisco Rodriguez-Frías, Tomàs Pumarola, Andrés Antón, Josep Quer
Přispěvatelé: Institut Català de la Salut, [Campos C, Quer J] Grup de Recerca de les Malalties Hepàtiques, Unitat Hepàtica, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. 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. Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain. [Colomer-Castell S] Grup de Recerca de les Malalties Hepàtiques, Unitat Hepàtica, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Vall d’Hebron Hospital Universitari, Barcelona, Spain. Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain. [Garcia-Cehic D, Gregori J] Grup de Recerca de les Malalties Hepàtiques, Unitat Hepàtica, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. 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. [ndrés C, Piñana M, González-Sánchez A, Esperalba J, Codina MG, Rando-Segura A, Saubí N] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Borràs B, Parés-Badell O] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Medicina Preventiva, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Adombi CM, Ibañez-Lligoña M] Grup de Recerca de les Malalties Hepàtiques, Unitat Hepàtica, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Esteban JI] Grup de Recerca de les Malalties Hepàtiques, Unitat Hepàtica, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. 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. Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. [Rodriguez-Frías F] Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain. Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain. Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Bioquímica, Vall d’Hebron Hospital Universitari, Barcelona, Spain. [Pumarola T, Antón A] Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain. Servei de Microbiologia, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Departament de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain, Vall d'Hebron Barcelona Hospital Campus
Rok vydání: 2022
Předmět:
mezclas complejas::productos biológicos::vacunas::vacunas víricas [COMPUESTOS QUÍMICOS Y DROGAS]
Multidisciplinary
Evolution
Molecular biology
Genetics
virosis::infecciones por virus ARN::infecciones por Nidovirales::infecciones por Coronaviridae::infecciones por Coronavirus [ENFERMEDADES]
Virus Diseases::RNA Virus Infections::Nidovirales Infections::Coronaviridae Infections::Coronavirus Infections [DISEASES]
Complex Mixtures::Biological Products::Vaccines::Viral Vaccines [CHEMICALS AND DRUGS]
Amino Acids
Peptides
and Proteins::Proteins::Blood Proteins::Immunoproteins::Immunoglobulins::Antibodies::Antibodies
Neutralizing [CHEMICALS AND DRUGS]
Immunoglobulines
aminoácidos
péptidos y proteínas::proteínas::proteínas sanguíneas::inmunoproteínas::inmunoglobulinas::anticuerpos::anticuerpos neutralizantes [COMPUESTOS QUÍMICOS Y DROGAS]
Microbiology
COVID-19 (Malaltia) - Vacunació
Zdroj: Scientia
ISSN: 2045-2322
DOI: 10.1038/s41598-022-24918-8
Popis: Evolution; Genetics; Molecular biology Evolució; Genètica; Biologia molecular Evolución; Genética; Biología molecular The SARS-CoV-2 Omicron variant emerged showing higher transmissibility and possibly higher resistance to current COVID-19 vaccines than other variants dominating the global pandemic. In March 2020 we performed a study in clinical samples, where we found that a portion of genomes in the SARS-CoV-2 viral population accumulated deletions immediately before the S1/S2 cleavage site (furin-like cleavage site, PRRAR/S) of the spike gene, generating a frameshift and appearance of a premature stop codon. The main aim of this study was to determine the frequency of defective deletions in prevalent variants from the first to sixth pandemic waves in our setting and discuss whether the differences observed might support epidemiological proposals. The complete SARS-CoV-2 spike gene was deeply studied by next-generation sequencing using the MiSeq platform. More than 90 million reads were obtained from respiratory swab specimens of 78 COVID-19 patients with mild infection caused by the predominant variants circulating in the Barcelona city area during the six pandemic waves: B.1.5, B.1.1, B.1.177, Alpha, Beta, Delta, and Omicron. The frequency of defective genomes found in variants dominating the first and second waves was similar to that seen in Omicron, but differed from the frequencies seen in the Alpha, Beta and Delta variants. The changing pattern of mutations seen in the various SARS-CoV-2 variants driving the pandemic waves over time can affect viral transmission and immune escape. Here we discuss the putative biological effects of defective deletions naturally occurring before the S1/S2 cleavage site during adaption of the virus to human infection. This study was partially supported by Pla Estratègic de Recerca i Innovació en Salut (PERIS) – Direcció General de Recerca i Innovació en Salut (DGRIS), Catalan Health Ministry, Generalitat de Catalunya; the Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016/0003) from the European Regional Development Fund (ERDF); Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297; Grant PI19/00301 from Instituto de Salud Carlos III cofinanced by the European Regional Development Fund (ERDF), and Gilead’s biomedical research project GLD21/00006. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCov Database on which this research is based.
Databáze: OpenAIRE
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