The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants
Campos, Carolina (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Colomer-Castell, Sergi (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Garcia-Cehic, D. (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas)
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Andrés, Cristina (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Piñana, Maria (Hospital Universitari Vall d'Hebron. Institut de Recerca)
González-Sánchez, Alejandra (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Borras Bermejo, Blanca (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Parés-Badell, Oleguer (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Adombi, Caroline Melanie (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Ibañez-Lligoña, Marta (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Esperalba, Juliana (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Codina, María Gema (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Rando-Segura, Ariadna (Hospital Universitari Vall d'Hebron)
Saubí, Narcis (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Esteban Mur, Juan Ignacio (Universitat Autònoma de Barcelona. Departament de Medicina)
Rodríguez Frías, Francisco (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Pumarola Suñé, Tomàs (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Antón, Andrés (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Quer, Josep 1963- (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)

Date:	2022
Abstract:	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.
Grants:	Ministerio de Economía y Competitividad RD16/0016/0003 Instituto de Salud Carlos III PI19/00301
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Evolution ; Genetics ; Microbiology ; Molecular biology
Published in:	Scientific reports, Vol. 12 (december 2022) , ISSN 2045-2322

DOI: 10.1038/s41598-022-24918-8
PMID: 36581627

11 p, 1.5 MB

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