Genomic epidemiology of SARS-CoV-2 delta sublineages of the second wave of 2021 in Antioquia, Colombia Vigilancia genómica de SARS-CoV-2

Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, Colombia, epidemiological peaks related to the Alfa, Gamma, Beta, Mu, Lambda and, Delta variants were presented, where Delta had the highest incidence and prevalence. This lineage is considered of concern and has proven to be relevant due to its clinical manifestations that it triggers and its epidemiological characteristics. A total of 253 Delta sublineages have been reported in the PANGOLIN database. The identification of these sublineages through genomic analysis has made it possible to trace their evolution and propagation. Objetive. To characterize the genetic diversity of the different SARS-CoV-2 Delta sublineages in Antioquia, and to describe its prevalence. Material and methods. Information was collected 2675 sociodemographic data and 1,115 genomes from GISAID database between July 12, 2021 and January 18, 2022. Of the genomes analyzed, 515 were selected due to their high coverage values (>90%) to perform phylogenetic analysis and inference of allele frequencies of mutations of interest. Results. We characterized 24 sublineages where it was observed that the most prevalent was AY.25. Mutations of interest as L452R, P681R and P681H were identified in this sublineage, which comprise a frequency close to 0.99. Conclusions. This study allowed us to identify that the AY_25 sublineage has a transmission advantage compared to the other Delta sublineages. This may be related to the presence of the L452R and P681R mutations that have been associated in other studies with greater transmissibility, evasion of the immune system, and less efficacy of drugs against SARS-CoV-2.