[Clinical Impact of Current Variants in COVID-19 Patients: Clinical Characteristics in Variant EG.5]

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has mutated at a high rate since the beginning of the pandemic, leading to the formation of different variants. Alpha, Beta, Gamma, Delta and Omicron have emerged as concerning variants identified by the World Health Organization (WHO). The Omicron variant and its sublineages became dominant worldwide in 2022. EG.5, a sublineage of Omicron, was associated with increased cases recently. In this study, we aimed to investigate the relationship between SARS-CoV-2 variants and the severity of the disease by using the whole genome sequence analysis method in patient samples diagnosed with coronavirus diseases 2019 (COVID-19) in our hospital and to contribute to SARS-CoV-2 surveillance in our country, in the period until the end of 2023, after the announcement of the EG.5 variant. The study included 68 patient samples that were found to be SARS-CoV-2 positive by polymerase chain reaction. Nasopharyngeal/oropharyngeal swab samples obtained from the patients were analysed by syndromic multiplex viral polymerase chain reaction panel. Whole genome sequence analysis was performed on SARS-CoV-2 positive patient samples with high viral load. Barcoded sequencing library was prepared and extracted DNA was sequenced on the Illumina next generation sequencing platform using COVIDSeq test kits (Illumina, USA). The library was loaded into a NextSeq 500/550 high output reagent cartridge v2 75 cycle, NextSeq 500/550 high output flow cell on the NextSeq 550 instrument (Illumina, USA). The DRAGEN COVID lineage programme available in the core domain was used to analyse the sequence data. The resulting combined fasta files were loaded into Nexclade and Pangolin COVID-19 Lineage Assigner programmes and class assignment, mutation calls and sequence quality checks were performed. Statistical evaluation was performed using Statistical Package for Social Sciences (Windows v20.0, Armonk, NY) programme. Sequence results of a total of 68 patients whose SARS-CoV-2 positivity was confirmed in our laboratory and whose samples were suitable for sequence study were analysed with clinical data. While EG.5 variant was detected in 15 (22.1%) of the samples included in the study, different sub-variants other than EG.5 were detected in 53 (77.9%) samples. The first three most frequently detected variants were XBB.1.16, EG.5.1 and FL.1.5.1, respectively. The subtypes of the EG.5 variant were determined as EG.5.1.1, EG.5.1.3, EG.5.1.6 and EG.5.1. Of the patients included in the study, 20 (29.4%) were hospitalised and followed up, 14 of whom had moderate to severe clinical conditions. Four hospitalised patients with comorbidities at an advanced age resulted in exitus. In the statistical evaluation, no significant difference was found between EG.5 and nonEG.5 Omicron variants in terms of age group, clinical symptoms and disease severity. It is recommended to continue genomic surveillance for the timely identification of SARS-CoV-2 and changes in the clinical spectrum and implementation of appropriate countermeasures.