Whole Genome Sequence Analysis of Six SARS-CoV-2 Positive Patients Followed in a Tertiary University Hospital

Abstract

Aims: In this study, we aimed to determine mutations in the gene sequence of this virus, by performing whole genome sequence analysis from patient samples found positive by actual RT-PCR (PCR) for SARS-CoV-2. Methods: The study included six adult patient samples with different clinical manifestations with positive PCR tests for SARS-CoV-2, between June 01, 2020, and March 12, 2021. Sequence knowledge of all samples/testers has been loaded into the GISEAD (Global Initiative on Sharing All Influenza Data) data system. Clade Analysis, Genome Analysis, Variant Analysis, and Phylogenetic Tree Analysis were conducted. Results: 3 of the patients were women (female), and three were men(male), with the mean age of 42.5 years old (between 20 - 61). Totally 71 mutations were specified in 6 adult patients. By the Pangolin lineage, three of the patients were B.1.177, two were B.1, one was of B1.36 lineage. By the Pango lineage, two of the patients were B.1.609, one was B.177, one was B.1.36. By the Nexstrain Clade, four of the patients were 20A and two were of 19A lineage. No D614G mutation was detected in any of the patients. While five patients recovered, one patient with metastatic lung adenocarcinoma died. Conclusion; The patients were detected in the commonly found 'Non-VOC' group. Therefore, variants could not be associated with the clinical status and prognosis of the patients. However, it is thought that the data obtained contribute to both global and national SARS-CoV-2 data.

Keywords

• Genome sequence analysis
• SARS-CoV-2
• Konya
• Mutation

Project Number

201218019

Üçüncü Basamak Üniversite Hastanesinde Takip Edilen Altı SARS-CoV-2 Pozitif Hastanın Tüm Genom Dizi Analizi

Abstract

Amaç: Bu çalışmada Gerçek RT-PCR (PCR) ile SARS-CoV-2 için pozitif bulunan hasta örneklerinden tam genom dizi analizi yaparak bu virüsün gen dizisindeki mutasyonları belirlemeyi amaçladık. Yöntem: Çalışma, 01 Haziran 2020 - 12 Mart 2021 tarihleri arasında SARS-CoV-2 için pozitif PCR testleri olan farklı klinik belirtilere sahip altı yetişkin hasta örneğini içermektedir. Tüm numunelerin/test edicilerin sekans bilgisi, GISEAD (Tüm İnfluenza Verilerini Paylaşma Küresel Girişimi) veri sistemine yüklenmiştir. Clade Analizi, Genom Analizi, Varyant Analizi ve Filogenetik Ağaç Analizi yapılmıştır. Bulgular: Hastaların 3'ü kadın (kadın), 3'ü erkek (erkek) olup, yaş ortalaması 42,5 (20 - 61 arası) idi. 6 yetişkin hastada toplam 71 mutasyon belirlendi. Pangolin soyuna göre, hastaların üçü B.1.177, ikisi B.1, biri B1.36 soyundandı. Pango soyuna göre hastaların ikisi B.1.609, biri B.177, biri B.1.36 idi. Nexstrain Clade'e göre hastaların dördü 20A ve ikisi 19A soyundandı. Hiçbir hastada D614G mutasyonu saptanmadı. Beş hasta iyileşirken, metastatik akciğer adenokarsinomu olan bir hasta hayatını kaybetti. Sonuç; Hastalar yaygın olarak bulunan 'VOC olmayan' grupta tespit edildi. Bu nedenle varyantlar, hastaların klinik durumu ve prognozu ile ilişkilendirilememiştir. Ancak elde edilen verilerin hem küresel hem de ulusal SARS-CoV-2 verilerine katkı sağladığı düşünülüyor.

Keywords

• Genom dizi analizi
• SARS-CoV-2
• Konya
• Mutasyon

Supporting Institution

Necmettin Erbakan Ünversitesi BAP

Project Number

201218019

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