[Genomic Characterization of SARS-CoV-2 by Next-Generation Sequencing Analysis].

Authors

Tansu Gülbahar Aydoğan, Memnune Selda Erensoy, İlkin Çankayali, Yusuf Ali Altunci, Şaziye Rüçhan Sertöz

Published in

Mikrobiyoloji bulteni. Volume 60. Issue 3. Pages 301-317.

Abstract

The coronavirus disease-2019 pandemic has been shaped by successive waves of variants due to the high mutational capacity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Monitoring the genomic diversity and mutational profiles of these variants and their clinical impact is essential to inform public health measures as well as vaccine and treatment strategies. This study aimed to analyze clinical samples detected as SARS-CoV-2 positive by real-time reverse transcription polymerase chain reaction (rRT-PCR) during two different periods of the pandemic in Türkiye using next-generation sequencing to compare their genomic profiles, determine their phylogenetic positions and assess the relationship between mutations and clinical findings. A total of 39 rRT-PCR-positive respiratory samples (9 in September 2021 and 30 in March-April 2022) with cycle threshold <20 from our laboratory were included in the study.An amplicon-based Oxford Nanopore method was used for next-generation sequencing. The 22 high-quality sequences obtained were evaluated phylogenetically using MEGA software together with the sequences obtained from the Global Initiative on Sharing All Influenza Data and the reference genome in order to enrich the phylogenetic tree. Lineage and clade assignments were performed using Nextstrain and PANGO. According to the Nextstrain classification, nine of the sequences belonged to the 21J (Delta) clade and 30 to the 21L (Omicron) clade. In the PANGO analysis, sequences from the 2021 period mostly matched B.1.617.2 and its AY sublineages (AY.122, AY.46, AY.46.2, etc.), while sequences from the 2022 period mostly matched BA.2 and its sublineages (BA.2.9, BA.2.5). In the phylogenetic analysis, sequences from the two periods diverged significantly. The evolutionary distance between the reference genome and the Omicron variant was found to be greater than that to the Delta variant. In addition, the distance of Omicron to Delta exceeded its distance to the reference genome. In the phylogenetic tree including Alpha sequences from the previous predominant variant period, the Alpha variant clustered with Omicron. These results suggest that Omicron does not appear to have evolved from Delta. The mutational analysis revealed that the Omicron variant harbored a higher number of amino acid changes across multiple regions of the genome, particularly in the Spike protein; a substantial portion of these alterations included deletions in the NTD (L24/P25/P26), as well as point mutations such as S375F, E484A, Q493R, and N501Y in the receptor binding domain and H655Y and N679K in the fusion region, which are associated with host cell entry and immune evasion. In the Delta variant, substitutions P681R and L452R near the S1/S2 cleavage site of Spike and deletions Δ156/157 in the N-terminal domain predominated. Both variants retained common adaptive mutations that confer an infectious advantage, such as S:D614G, S:T478K, and ORF1b:P314L. Clinical evaluation showed that Omicron cases had a significantly milder course (p= 0.032), with similar age, comorbidity and vaccination profiles between the two groups. The results suggest that some Omicron-specific Spike mutations suppress membrane fusion by reducing TMPRSS2 usage, a feature that may contribute to the variant's low virulence. This study presents comprehensive regional genomic data from the Delta-Omicron transition period in Türkiye, including phylogenetic positions, Spike mutation profiles and clinical outcomes. The results emphasize that monitoring the molecular adaptations of variants in conjunction with clinical data is essential for early warning and control of rapidly evolving pathogens such as SARS-CoV-2.

PMID:
42583851
Bibliographic data and abstract were imported from PubMed on 12 Aug 2026.

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