Characterization of recombinant genomes of the omicron variant of SARS-CoV-2 between 2022 and 2023 in the department of Antioquia, Colombia

Abstract

Introduction. Recombination is a mechanism that prevents the accumulation of noxious mutations. Recombination occurs between different sublineages of the same virus that are co-circulating and co-infecting the same host. Next-generation sequencing technologies have allowed the identification of recombinant sublineages of omicron. Objective. To describe how viral recombination in new omicron lineages has conferred important characteristics to this variant and allowed its prevalence. Materials and methods. A total of 338 genomes of recombinant lineages from positive samples of SARS-CoV-2 analyzed by the Laboratorio Departamental de Salud Pública de Antioquia were characterized, between November 9, 2022, and November 5, 2023. The genomes were obtained using Oxford Nanopore™ sequencing technology. Phylogenetic analysis identified different recombinant sublineages of omicron and predictors allowed the identification of regions in the SARS-CoV-2 genome that were the product of recombination events. Results. Twenty-six recombinant lineages of omicron were identified, and important amino acid changes were found involved in evasion of the immune response, infectivity and increased viral replication, N501Y, D614G and P681H. The F456L variant was also identified and was present in 55% of the XBB.1.5.72 genomes and is a biomarker for recognition of this sublineage. The analysis with recombination predictors allowed the identification of the potential parents of some recombinant genomes such as XBB.1.5 and XBB.1.5.77. Conclusion. The circulation of omicron sublineage recombinants shows important changes that impact their biology and have altered infection and virulence factors.