Osman Mutluhan UGUREL, Oguz ATA, Dilek TURGUT-BALİK

4024

An updated analysis of variations in SARS-CoV-2 genome

A novel pathogen, named SARS-CoV-2, has caused an unprecedented worldwide pandemic in the first half of 2020. As the SARS-CoV-2 genome sequences have become available, one of the important focus of scientists has become tracking variations in the viral genome. In this study, 30366 SARS-CoV-2 isolate genomes were aligned using the software developed by our group (ODOTool) and 11 variations in SARS-CoV-2 genome over 10% of whole isolates were discussed. Results indicated that, frequency rates of these 11 variations change between 3.56%-88.44 % and these rates differ greatly depending on the continents they have been reported. Despite some variations being in low frequency rate in some continents, C14408T and A23403G variations on Nsp12 and S protein, respectively, observed to be the most prominent variations all over the world, in general, and both cause missense mutations. It is also notable that most of isolates carry C14408T and A23403 variations simultaneously and also nearly all isolates carrying the G25563T variation on ORF3a, also carry C14408T and A23403 variations, although their location distributions are not similar. All these data should be considered towards development of vaccine and antiviral treatment strategies as well as tracing diversity of virus in all over the world.
Keywords:

SARS-CoV-2, COVID-19 genomic diversity, codon bias, multiple sequence alignment,

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  • Angelini MM, 2013, MBIO, V4, DOI 10.1128/mBio.00524-13
  • Azhar EI, 2014, NEW ENGL J MED, V370, P2499, DOI 10.1056/NEJMoa1401505
  • Bardou P, 2014, BMC BIOINFORMATICS, V15, DOI 10.1186/1471-2105-15-293
  • Belalov IS, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0056642
  • Brian DA, 2005, CURR TOP MICROBIOL, V287, P1, DOI 10.1007/3-540-26765-4_1
  • Briguglio I, 2011, INT J MED CHEM, V2011, DOI 10.1155/2011/213135
  • BULMER M, 1987, NATURE, V325, P728, DOI 10.1038/325728a0
  • CARNEIRO JS, 1995, J GEN VIROL, V76, P1189, DOI 10.1099/0022-1317-76-5-1189
  • Chen Y, 2020, J MED VIROL, V92, P418, DOI 10.1002/jmv.25681
  • Cheng VCC, 2007, CLIN MICROBIOL REV, V20, P660, DOI 10.1128/CMR.00023-07
  • Chew Suok Kai, 2007, Bull World Health Organ, V85, P324
  • Cock PJA, 2009, BIOINFORMATICS, V25, P1422, DOI 10.1093/bioinformatics/btp163
  • Cui J, 2019, NAT REV MICROBIOL, V17, P181, DOI 10.1038/s41579-018-0118-9
  • de Groot RJ, 2013, J VIROL, V87, P7790, DOI 10.1128/JVI.01244-13
  • De Lorenzo G, 2016, PLOS ONE, V11, DOI 10.1371/journal.pone.0166719
  • de-Dios T, 2020, INFECT GENET EVOL, V80, DOI 10.1016/j.meegid.2020.104209
  • DUNCAN BK, 1980, NATURE, V287, P560, DOI 10.1038/287560a0
  • Elbe S, 2017, GLOB CHALL, V1, P33, DOI 10.1002/gch2.1018
  • Fang SG, 2007, VIROLOGY, V358, P136, DOI 10.1016/j.virol.2006.08.020
  • Frick DN, 2006, CURR PHARM DESIGN, V12, P1315, DOI 10.2174/138161206776361147
  • Gadlage MJ, 2008, J VIROL, V82, P11964, DOI 10.1128/JVI.01126-07
  • Gallagher TM, 2001, VIROLOGY, V279, P371, DOI 10.1006/viro.2000.0757
  • Ge XY, 2013, NATURE, V503, P535, DOI 10.1038/nature12711
  • Gorbalenya AE, 2006, VIRUS RES, V117, P17, DOI 10.1016/j.virusres.2006.01.017
  • Gorbalenya AE, 2020, NAT MICROBIOL, V5, P536, DOI 10.1038/s41564-020-0695-z
  • Graham RL, 2005, J VIROL, V79, P13399, DOI 10.1128/JVI.79.21.13399-13411.2005
  • Guan Y, 2003, SCIENCE, V302, P276, DOI 10.1126/science.1087139
  • Hadfield J, 2018, BIOINFORMATICS, V34, P4121, DOI 10.1093/bioinformatics/bty407
  • Issa E, 2020, MSYSTEMS, V5, DOI 10.1128/mSystems.00266-20
  • Jang KJ, 2008, BIOCHEM BIOPH RES CO, V366, P738, DOI 10.1016/j.bbrc.2007.12.020
  • Kang SS, 2020, ACTA PHARMACOL SIN B, V10, P1228, DOI 10.1016/j.apsb.2020.04.009
  • Katoh K, 2019, BRIEF BIOINFORM, V20, P1160, DOI 10.1093/bib/bbx108
  • KIMURA M, 1977, NATURE, V267, P275, DOI 10.1038/267275a0
  • Kiyotani K, 2020, J HUM GENET, V65, P569, DOI 10.1038/s10038-020-0771-5
  • Kocherhans R, 2001, VIRUS GENES, V23, P137, DOI 10.1023/A:1011831902219
  • Kuraku S, 2013, NUCLEIC ACIDS RES, V41, pW22, DOI 10.1093/nar/gkt389
  • Kwong AD, 2005, NAT REV DRUG DISCOV, V4, P845, DOI 10.1038/nrd1853
  • Lei J, 2018, ANTIVIR RES, V149, P58, DOI 10.1016/j.antiviral.2017.11.001
  • Li F, 2016, ANNU REV VIROL, V3, P237, DOI 10.1146/annurev-virology-110615-042301
  • Li WH, 2003, NATURE, V426, P450, DOI 10.1038/nature02145
  • Li WH, 2005, EMBO J, V24, P1634, DOI 10.1038/sj.emboj.7600640
  • Liu P, 2019, VIRUSES-BASEL, V11, DOI 10.3390/v11110979
  • Lu W, 2010, MOL BIOL SARS CORONA .
  • Madhugiri R, 2016, ADV VIRUS RES, V96, P127, DOI 10.1016/bs.aivir.2016.08.007
  • Ng WC, 2017, VIRUSES-BASEL, V9, DOI 10.3390/v9060137
  • Ou XY, 2020, NAT COMMUN, V11, DOI 10.1038/s41467-020-15562-9
  • Pachetti M, 2020, J TRANSL MED, V18, DOI 10.1186/s12967-020-02344-6
  • PEABODY DS, 1989, J BIOL CHEM, V264, P5031
  • Peiris JSM, 2003, LANCET, V361, P1319, DOI 10.1016/S0140-6736(03)13077-2
  • Perlman S, 2009, NAT REV MICROBIOL, V7, P439, DOI 10.1038/nrmicro2147
  • Pyrc K, 2004, VIROL J, V1, DOI 10.1186/1743-422X-1-7
  • Raj VS, 2013, NATURE, V495, P251, DOI 10.1038/nature12005
  • Sanchez CM, 1999, J VIROL, V73, P7607 .
  • SHARP PM, 1993, BIOCHEM SOC T, V21, P835, DOI 10.1042/bst0210835
  • Shu YL, 2017, EUROSURVEILLANCE, V22, P2, DOI 10.2807/1560-7917.ES.2017.22.13.30494
  • Snijder EJ, 2016, ADV VIRUS RES, V96, P59, DOI 10.1016/bs.aivir.2016.08.008
  • Su S, 2016, TRENDS MICROBIOL, V24, P490, DOI 10.1016/j.tim.2016.03.003
  • Tai WB, 2020, CELL MOL IMMUNOL, V17, P613, DOI 10.1038/s41423-020-0400-4
  • Phan T, 2020, INFECT GENET EVOL, V81, DOI 10.1016/j.meegid.2020.104260
  • Wang CT, 2020, J MED VIROL, V92, P667, DOI 10.1002/jmv.25762
  • Wang Z, 2011, FEBS J, V278, P383, DOI 10.1111/j.1742-4658.2010.07961.x
  • Waterhouse AM, 2009, BIOINFORMATICS, V25, P1189, DOI 10.1093/bioinformatics/btp033
  • Wong SK, 2004, J BIOL CHEM, V279, P3197, DOI 10.1074/jbc.C300520200
  • Woo PCY, 2007, VIROLOGY, V369, P431, DOI 10.1016/j.virol.2007.08.010
  • Wu AP, 2020, CELL HOST MICROBE, V27, P325, DOI 10.1016/j.chom.2020.02.001
  • Wu CR, 2020, ACTA PHARMACOL SIN B, V10, P766, DOI 10.1016/j.apsb.2020.02.008
  • Yang D, 2015, VIRUS RES, V206, P120, DOI 10.1016/j.virusres.2015.02.025
  • Yin YD, 2018, RESPIROLOGY, V23, P130, DOI 10.1111/resp.13196
  • Zaki AM, 2012, NEW ENGL J MED, V367, P1814, DOI 10.1056/NEJMoa1211721
  • Zhong NS, 2003, LANCET, V362, P1353, DOI 10.1016/S0140-6736(03)14630-2
  • Zhou YD, 2020, CELL DISCOV, V6, DOI 10.1038/s41421-020-0153-3
Turkish Journal of Biology-Cover
  • ISSN: 1300-0152
  • Yayın Aralığı: Yılda 6 Sayı
  • Yayıncı: TÜBİTAK
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