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

Öz

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.

Anahtar Kelimeler

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

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

Öz

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.

Anahtar Kelimeler

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

Kaynakça

1. 1.T.C. Ministry Of Health General Directorate Of Public Health, Covid-19 (Sars-Cov2 Infection)Directory, Coronavirus Scientific Advisory Board, Turkey. [accessed 9.09.2023]. https://covid19bilgi.saglik.gov.tr/tr/.
2. 2.Xu Y, Xiao M, Liu X, et al. Significance of serology testing to assist timely diagnosis of SARSCoV-2 infections: implication from a family cluster. Emerg Microbes Infect 2020;9(1):924-7.
3. 3.Adebali O, Bircan A, Çirci D, et al. Phylogenetic analysis of SARS-CoV-2 genomes in Turkey. Turk J Biol. 2020 Jun 21;44(3):146-156.
4. 4.Virological.org. Novel 2019 Coronavirus Genome 2020. http://virological.org/t/novel-2019-coronavirus-genome/319. (Accessed 1.2.2020.)
5. 5.World Health Organization.covid19.who.int (Accessed 9.09.2023)
6. 6.Global Initiative's database on Sharing All Influenza Data (GISAID). https://www.epicov.org/epi3/frontend# (Accessed 9.09.2023)
7. 7.Rothe C, Schunk M, Sothmann P, et al. Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med 2020;382(10):970-1.
8. 8.Kepenek Kurt E, Kandemir B, Erayman İ, et al. Comparison of Clinical and Laboratory Findings and Computed Tomography Findings of SARS-CoV-2 Infected Patients Followed-up in a Tertiary University Hospital. Mediterr J Infect Microb Antimicrob. 2021;10:37

9. 9.COVID-19 weekly epidemiological update, 22 June 2021. World Health Organization. https:// www.who.int/publications/m/ item/weeklyepidemiological-update-on-covid-19)
10. 10.Singhal T. A review of coronavirus disease-2019 (COVID-19). Indian J Pediatr. 2020;87:281-6.
11. 11.Pourbagheri-Sigaroodi A, Bashash D, Fateh F, Abolghasemi H. Laboratory findings in COVID-19 diagnosis and prognosis. Clin Chim Acta 2020;510:475-82
12. 12.Demir AB, Bulgurcu A, Appak Ö, Sayıner AA. Analysis of Nucleotide Changes in RT-PCR Primer/Probe Binding Regions in SARS-CoV-2 Isolates Reported from Turkey. Mikrobiyol Bul 2021; 55(3):311-326.
13. 13.Karamese M, Ozgur D, Tutuncu EE. Molecular Characterization, Phylogenetic and Variation Analyzes of SARS-CoV-2 strains in Turkey. Future Microbiol 2021:1209-1214.
14. 14.Khailany RA, Safdar M, Ozaslan M. Genomic characterization of a novel SARS-CoV-2. Gene Rep. 2020:100682
15. 15.Wang C, Liu Z, Chen Z, et al. The establishment of reference sequence for SARS-CoV-2 and variation analysis. J Med Virol 2020;92(6):667-74.
16. 16.PANGO lineages. https://cov-lineages.org/global_report.html, (accessed 27.10.2021)
17. 17.Pangolin lineages. https://cov-lineages.org/global_report.html,(accessed 27.10.2021).
18. 18.Bhattacharyya C, Das C, Ghosh A, et al. Global spread of SARS-CoV-2 subtype with spike protein mutation D614G is shaped by human genomic variations that regulate expression of TMPRSS2 and MX1 genes. BioRxiv.2020 May 5
19. 19.Koyama T, Weeraratne D, Snowdon JL, Parida L. Emergence of drift variants that may affect COVID-19 vaccine development and antibody treatment. Pathogens 2020 Apr 26;9(5):324.
20. 20.Koyama T, Platt D, Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organ 2020 Jul 1;98(7):495-504.
21. 21.Esenkaya Taşbent F, Özdemir M, Metin Akçan Ö, Kepenek Kurt E. SARS-CoV-2 Genome Analysis of Pediatric Patients in Konya Region, Turkey. J Pediatr Infect Dis 2021;6(16):296-302.
22. 22.Biswas SK, Mudi SR. Spike protein D614G and RdRp P323L: the SARS‐CoV‐2 mutations associated with severity of COVID‐19. Genomics Inform. 2020;18(4):e44.
23. 23.Maison DP, Ching LL, Shikuma CM, Nerurkar VR. Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation. Hawaii J Health Soc Welf 2021;80(3):52-61.
24. 24.Sahin E, Bozdayi G, Yigit S, Muftah H, Dizbay M, Tunccan OG. Genomic characterization of SARS‐CoV‐2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins. J Med Virol. 2021;93:6016–6026.
25. 25.Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. J Virol.2020;94(7):e00127-20. doi: 10.1128/JVI.00127-20.
26. 26.Soyak F. Relatıonshıp Between SARS-CoV-2 Full Genome Analysis and Clinical Findings in Patients Diagnosed with COVID-19 (the thesis). Denizli: Pamukkale University Medical Faculty; 2023.