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KMID : 1143420230160080215
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Public Health Weekly Report
2023 Volume.16 No. 8 p.215 ~ p.229
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Characterization of COVID-19 Diagnosis Based on Whole Genome Sequencing in Gyeongbuk Region
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Yun Hae-Sun
Park Jeon-Joo
Chae Ha-Gyeong
Kim Hyo-Jin
Oh Seong-Hee
Lee Yong-Pyo
Moon Gyeong-Ran
Sohn Chang-Kyu
Lee Chang-Il
Choi Woo-Young
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Abstract
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In order to analyze the differences between the results of coronavirus disease 2 019 (COVID-19) diagnostic tests in Gyeongbuk, Republic of Korea, this study was performed full length genome analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) used by Ion Torrent Genexus Integrated Sequencer and dedicated analysis program. Full-length genomic sequences of the SARS-CoV-2 were obtained from specimen of 13 confirmed cases of COVID-19. As a result of the analysis, the Omicron sub-lineages were BA.1.1 (n=5), BA.2 (n=4), and BA.2.3 (n=4). In detail, R61C or R61H were confirmed in the E gene, meanwhile L142W and 166?178 nucleotide sequences were deleted in the ORF1ab NSP3 region. In the analysis using a computer program, mutations in the E gene region (R61H) were not useful as a target region for COVID-19 Real-time RT-PCR. Amino acid mutation (L142W) and nucleotide deletion (166?178) in the ORF1ab NSP3 region have been identified to affect diagnosis of COVID-19 with specific diagnostic kits. Thus, these results suggest that the detailed lineage and genetic mutations of the SARS-CoV-2 using the whole genome sequencing could be a critical tool for the COVID-19 diagnosis.
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KEYWORD
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Coronavirus Disease-19, Severe acute respiratory syndrome coronavirus 2, Whole genome sequencing, SARSCoV-2 variant, Molecular diagnostic test
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