Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences

Osman Mutluhan UĞUREL, (Yıldız Teknik Üniversitesi, Kimya ve Metalurji Mühendisliği Fakültesi, Biyomühendislik Bölümü, İstanbul, Türkiye)
Oğuz ATA, (Altınbaş Üniversitesi, Mühendislik ve Doğa Bilimleri Yüksekokulu, Temel Bilimler Bölümü, İstanbul, Türkiye)
Dilek TURGUT BALIK (Altınbaş Üniversitesi, Mühendislik ve Doğa Bilimleri Fakültesi, Yazılım Mühendisliği Bölümü, İstanbul, Türkiye)
Turkish Journal of Biology
9 0
Yıl: 2021 Cilt: 45 Sayı: 4 Sayfa Aralığı: 425 - 435 Metin Dili: İngilizce DOI: 10.3906/biy-2106-8 İndeks Tarihi: 17-06-2022

Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences

Öz:
Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed to reach 31.25 just in March 2021. The average variation number of isolates is increasing and compromising with total case numbers around the world. Remarkably, cytosine deamination, which is one of the most important biochemical processes in the evolutionary development of coronaviruses, accounts for 46% of all SNVs seen in SARS-CoV-2 genomes within 16 months. This study is one of the most comprehensive SARS-CoV-2 genomic analysis study in terms of number of genomes analysed in an academic publication so far, and reported results could be useful in monitoring the development of SARS-CoV-2.
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  • Agbehadji IE, Awuzie BO, Ngowi AB, Millham RC (2020). Review of big data analytics, artificial intelligence and nature-inspired computing models towards accurate detection of COVID-19 pandemic cases and contact tracing. International Journal of Environmental Research and Public Health 17 (15): 5330. doi: 10.3390/ijerph17155330
  • Alkhansa A, Ghayas L, Loubna EZ (2021). Mutational analysis of sars-cov-2 orf8 during six months of covid-19 pandemic. Gene Reports 23: 101024.
  • Behillil S, Enouf V, Maquart M, Smati-Lafarge M, Varon E et al. (2021). Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nature Medicine 27: 917-924. doi: 10.1038/s41591-021-01318-5. Advance online publication.
  • Belalov IS, Lukashev AN (2013). Causes and implications of codon usage bias in RNA viruses. PLoS One 8 (2).
  • Bulmer M (1987). Coevolution of codon usage and transfer RNA abundance. Nature 325 (6106): 728-730.
  • Chan C, Foster ST, Chan KG, Cacace MJ, Ladd SL et al. (2021). Repositioned drugs for COVID-19-the impact on multiple organs. SN Comprehensive Clinical Medicine 3: 1484-1501. doi: 10.1007/s42399-021-00874-8
  • Duncan BK, Miller JH (1980). Mutagenic deamination of cytosine residues in DNA. Nature 287: 560-561.
  • Eskier D, Akalp E, Dalan Ö, Karakülah G, Oktay Y (2021). Current mutatome of SARS-CoV-2 in Turkey reveals mutations of interest. Turkish Journal of Biology 45 (1): 104-113.
  • Golamari R, Kapoor N, Devaraj T, Sahu N, Kramer C et al. (2021). Experimental therapies under investigation for COVID-19. Journal of Community Hospital Internal Medicine Perspectives 11 (2): 187-193. doi: 10.1080/20009666.2021.1874093
  • Gorbalenya AE, Baker SC, Baric RS, de Groot R, Drosten C et al. (2020). The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology 5: 536-544. doi: 10.1038/ s41564-020-0695-z
  • Grubaugh ND, Hanage WP, Rasmussen AL (2020). Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear. Cell 182 (4): 794-795. doi: 10.1016/j. cell.2020.06.040
  • Hadfield J, Megill C, Bell SM, Huddleston J, Potter B et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics (Oxford, England) 34 (23): 4121- 4123. doi: 10.1093/bioinformatics/bty407
  • Hosseini SA, Zahedipour F, Mirzaei H, Kazemi Oskuee R (2021). Potential SARS-CoV-2 vaccines: Concept, progress, and challenges. International Immunopharmacology 97: 107622. Advance Online Publication. doi: 10.1016/j. intimp.2021.107622
  • Hou W (2020). Characterization of codon usage pattern in SARSCoV-2. Virology Journal 17: 138. doi: 10.1186/s12985-020- 01395-x
  • Isabel S, Graña-Miraglia L, Gutierrez JM, Bundalovic-Torma C, Groves HE et al. (2020). Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Scientific Reports 10 (1): 14031. doi: 10.1038/ s41598-020-70827-z
  • Kathiravan MK, Radhakrishnan S, Namasivayam V, Palaniappan S (2021). An overview of spike surface glycoprotein in severe acute respiratory syndrome-coronavirus. Frontiers in Molecular Biosciences 8: 637550. doi: 10.3389/fmolb.2021.637550
  • Mercatelli D, Giorgi FM (2020). Geographic and genomic distribution of SARS-CoV-2 mutations. Frontiers in Microbiology 11: 1800.
  • O’Toole Á, Hill V, Pybus OG, Watts A, Bogoch II et al. (2021). Tracking the international spread of SARS-CoV-2 lineages B. 1.1. 7 and B. 1.351/501Y-V2. Wellcome Open Research 6 (121): 121.
  • Ozono S, Zhang Y, Ode H, Sano K, Tan TS et al. (2021). SARSCoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nature Communications 12 (1): 1-9.
  • Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E et al. (2020). Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. Journal of Translational Medicine 18 (1): 179. doi: 10.1186/s12967-020- 02344-6.
  • Phan T (2020). Genetic diversity and evolution of SARSCoV-2. Infection, genetics and evolution. Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases 81: 104260. doi: 10.1016/j.meegid.2020.104260
  • Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I et al. (2020). Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. The New England Journal of Medicine 383 (27): 2603- 2615. doi: 10.1056/NEJMoa2034577
  • Pyrc K, Jebbink MF, Berkhout B, van der Hoek L (2004). Genome structure and transcriptional regulation of human coronavirus NL63. Virology Journal 17: 1-7.
  • Qin L, Ding X, Li Y, Chen Q, Meng J et al. (2021). Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2. Briefings in Bioinformatics 14: bbab222. doi: 10.1093/bib/bbab222
  • Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 5 (11): 1403-1407.
  • Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 5 (11): 1403-1407. doi: 10.1038/s41564-020-0770-5
  • Shaffaf T, Ghafar-Zadeh E (2021). COVID-19 Diagnostic Strategies. Part I: Nucleic Acid-Based Technologies. Bioengineering 8 (4): 49. MDPI AG. Retrieved from doi: 10.3390/ bioengineering8040049
  • Sharp PM, Stenico M, Peden JF, Lloyd AT (1993) Codon usage: mutational bias, translational selection, or both? Biochem Society Transactions 21: 835-841.
  • Ugurel OM, Ata O, Turgut-Balik D (2020). An updated analysis of variations in SARS-CoV-2 genome. Turkish Journal of Biology 44 (3): 157-167. doi: 10.3906/biy-2005-111
  • Volz E, Mishra S, Chand M, Barrett JC, Johnson R et al. (2021). Transmission of SARS-CoV-2 Lineage B. 1.1. 7 in England: Insights from linking epidemiological and genetic data. medRxiv 2020-12.
  • Wang C, Liu Z, Chen Z, Huang X, Xu M et al. (2020). The establishment of reference sequence for SARS‐CoV‐2 and variation analysis. Journal of Medical Virology 92 (6): 667-674.
  • Wang R, Chen J, Gao K, Hozumi Y, Yin C et al. (2021). Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Communications Biology 4 (1): 1-14.
  • Woo PC, Wong BH, Huang Y, Lau SK, Yuen KY (2007). Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Virology 369 (2): 431-442. doi: 10.1016/j.virol.2007.08.010
  • Wu A, Peng Y, Huang B, Ding X, Wang X et al. (2020). Genome composition and divergence of the novel coronavirus (2019- nCoV) originating in China. Cell Host Microbe 27: 325328. doi: 10.1016/j.chom.2020.02.001
  • Zehender G, Lai A, Bergna A, Meroni L, Riva A et al. (2020). Genomic characterization and phylogenetic analysis of SARS‐ COV‐2 in Italy. Journal of Medical Virology 92 (9): 1637-1640.
  • Zhang Y, Zeng G, Pan H, Li C, Hu Y et al. (2021). Safety, tolerability, and immunogenicity of an inactivated SARS-CoV-2 vaccine in healthy adults aged 18–59 years: a randomised, doubleblind, placebo-controlled, phase 1/2 clinical trial. The Lancet Infectious Diseases 21 (2): 181-192.
  • Zost SJ, Gilchuk P, Chen RE, Case JB, Reidy JX et al. (2020). Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein. Nature Medicine 26 (9): 1422-1427. doi: 10.1038/s41591-020-0998-x
APA Uğurel O, Ata O, Turgut Balık D (2021). Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. , 425 - 435. 10.3906/biy-2106-8
Chicago Uğurel Osman Mutluhan,Ata Oguz,Turgut Balık Dilek Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. (2021): 425 - 435. 10.3906/biy-2106-8
MLA Uğurel Osman Mutluhan,Ata Oguz,Turgut Balık Dilek Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. , 2021, ss.425 - 435. 10.3906/biy-2106-8
AMA Uğurel O,Ata O,Turgut Balık D Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. . 2021; 425 - 435. 10.3906/biy-2106-8
Vancouver Uğurel O,Ata O,Turgut Balık D Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. . 2021; 425 - 435. 10.3906/biy-2106-8
IEEE Uğurel O,Ata O,Turgut Balık D "Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences." , ss.425 - 435, 2021. 10.3906/biy-2106-8
ISNAD Uğurel, Osman Mutluhan vd. "Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences". (2021), 425-435. https://doi.org/10.3906/biy-2106-8
APA Uğurel O, Ata O, Turgut Balık D (2021). Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turkish Journal of Biology, 45(4), 425 - 435. 10.3906/biy-2106-8
Chicago Uğurel Osman Mutluhan,Ata Oguz,Turgut Balık Dilek Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turkish Journal of Biology 45, no.4 (2021): 425 - 435. 10.3906/biy-2106-8
MLA Uğurel Osman Mutluhan,Ata Oguz,Turgut Balık Dilek Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turkish Journal of Biology, vol.45, no.4, 2021, ss.425 - 435. 10.3906/biy-2106-8
AMA Uğurel O,Ata O,Turgut Balık D Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turkish Journal of Biology. 2021; 45(4): 425 - 435. 10.3906/biy-2106-8
Vancouver Uğurel O,Ata O,Turgut Balık D Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences. Turkish Journal of Biology. 2021; 45(4): 425 - 435. 10.3906/biy-2106-8
IEEE Uğurel O,Ata O,Turgut Balık D "Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences." Turkish Journal of Biology, 45, ss.425 - 435, 2021. 10.3906/biy-2106-8
ISNAD Uğurel, Osman Mutluhan vd. "Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences". Turkish Journal of Biology 45/4 (2021), 425-435. https://doi.org/10.3906/biy-2106-8
Sayfa Oluşturulma Tarihi
23-04-2024 23:16

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