GENOMIC CHARACTERIZATION OF SARS CoV-2 BY NEXT GENERATION SEQUENCE ANALYSIS

Project no. 23076 · Status: Kapanmış (Yayın bekleniyor) · 2022

Summary

PURPOSE: The coronavirus disease (COVID-19) outbreak emerged in December 2019 in Wuhan, China's Hubei province. The pathogen has been identified as SARS-CoV-2. On March 11, 2020, the World Health Organization (WHO) declared a global epidemic. Information gathered from next-generation sequencing (YND), ıt provides knowledge, including the development of therapeutics and vaccines, monitoring of changes in the virus. In this study, it was aimed to detect genetic changes by whole genome sequencing, to perform "clade" and "lineage" analyzes, and to examine clinical features of samples with SARS-CoV-2 detected in two different date ranges belonging to the period when variants were dominant in the pandemicMATERİALS AND METHODS: Among the respiratory tract samples sent to Ege University Faculty of Medicine Medical Microbiology Laboratory for SARS-CoV-2 polymerase chain reaction (PCR) test, 39 respiratory samples (nine in September 2021, thirty in March-April 2022) that were working with real time PCR were estimated to have SARS-CoV-2 positive and high viral load were selected [cycle threshold (CT) <20] for whole genome NGS analysis. The DNA library prepared after viral RNA extraction, reverse transcription and PCR from patient samples was loaded into the flow cell, and data analysis was performed after sequencing with the MinKNOW program. These 39 examples are also; the age, gender, comorbid diseases of the patients, severity of the clinic (mild-moderate-severe), length of stay in the hospital, and presence of reproduction if there is a simultaneous bacterial culture were also examined.RESULTS: Thirty-three of the thirty-nine sequences yielded high-quality genomic data reaching ≥90% genome coverage. Delta in 9 samples sequenced in September 2021, Omicron variant was detected in thirty samples sequenced between March-April 2022. According to the Nextstrain classification, 9 strings were found as 21J and 30 strings as 21L. According to Pango classification, BA.2 (n=26), BA.2.9 (n=3), AY.122 (n=2), BA.2.5 (n=1), AY.46 (n=1), AY. 46.2 (n=1), AY.121 (n=1), AY.126 (n=1), AY.78 (n=1), B.1617.2 (n=1), AY.4.6 (n=1) has been found. In our study, moderate severity was observed in 33.3% of patients with Delta variant, and severe clinic was observed in 3.3% of patients with Omicron variant.CONCLUSİON: The variants detected in our study were found to be temporally consistent with the dominant variants in the global GISAID data. Common lineages in our country and lineages related to Turkey were observed. While more pathogenic mutations are observed in the sequences with delta variant; In the sequences with the omicron variant, more transmission, and more mutations for escape from the immune system were observed. The results of the study once again highlight the need for continuous sequencing-based surveillance of SARS-CoV-2 strains for public health decision-making and healthcare.

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