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Liana, Delima Fajar, Novianry, Virhan, Andriani, Andriani, Mahyarudin, Mahyarudin, Astuti, Puji. (1402). Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia. سامانه مدیریت نشریات علمی, 49(3), 176-185. doi: 10.30476/ijms.2023.97513.2935
Delima Fajar Liana; Virhan Novianry; Andriani Andriani; Mahyarudin Mahyarudin; Puji Astuti. "Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia". سامانه مدیریت نشریات علمی, 49, 3, 1402, 176-185. doi: 10.30476/ijms.2023.97513.2935
Liana, Delima Fajar, Novianry, Virhan, Andriani, Andriani, Mahyarudin, Mahyarudin, Astuti, Puji. (1402). 'Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia', سامانه مدیریت نشریات علمی, 49(3), pp. 176-185. doi: 10.30476/ijms.2023.97513.2935
Liana, Delima Fajar, Novianry, Virhan, Andriani, Andriani, Mahyarudin, Mahyarudin, Astuti, Puji. Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia. سامانه مدیریت نشریات علمی, 1402; 49(3): 176-185. doi: 10.30476/ijms.2023.97513.2935

Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia

Iranian Journal of Medical Sciences
مقاله 5، دوره 49، شماره 3، خرداد 2024، صفحه 176-185    اصل مقاله (1.57 M)
نوع مقاله: Original Article(s)
شناسه دیجیتال (DOI): 10.30476/ijms.2023.97513.2935
نویسندگان
Delima Fajar Liana* 1؛ Virhan Novianry2؛ Andriani Andriani2؛ Mahyarudin Mahyarudin1؛ Puji Astuti2
1Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
2Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
چکیده
Background: The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia.
Methods: In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software.
Results: Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40. 
Conclusion: Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.
کلیدواژه‌ها
SARS-CoV-2؛ Indonesia؛ Mutation؛ COVID-19؛ Spike glycoprotein, coronavirus
سایر فایل های مرتبط با مقاله
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