Genomic analysis and comparative multiple sequences of SARS-CoV2

Background: China announced an outbreak of new coronavirus in the city of Wuhan on December 31, 2019; lash to now, the virus transmission has become pandemic worldwide. Severe cases from the Huanan Seafood Wholesale market in Wuhan were confirmed pneumonia with a novel coronavirus (2019-nCoV). Understanding the molecular mechanisms of genome selection and packaging is critical for developing antiviral strategies. Thus, we defined the correlation in 10 severe acute respiratory syndrome coronavirus (SARS-CoV2) sequences from different countries to analyze the genomic patterns of disease origin and evolution aiming for developing new control pandemic processes. Methods: We apply genomic analysis to observe SARS-CoV2 sequences from GenBank (http://www.ncbi.nim.nih.gov/genebank/): MN 908947 (China, C1), MN985325 (USA: WA, UW), MN996527 (China, C2), MT007544 (Australia: Victoria, A1), MT027064 (USA: CA, UC), MT039890 (South Korea, K1), MT066175 (Taiwan, T1), MT066176 (Taiwan, T2), LC528232 (Japan, J1), and LC528233 (Japan, J2) for genomic sequence alignment analysis. Multiple Sequence Alignment by Clustalw (https://www.genome.jp/tools-bin/clustalw) web service is applied as our alignment tool. Results: We analyzed 10 sequences from the National Center for Biotechnology Information (NCBI) database by genome alignment and found no difference in amino acid sequences within M and N proteins. There are two amino acid variances in the spike (S) protein region. One mutation found from the South Korea sequence is verified. Two possible “L” and “S” SNPs found in ORF1ab and ORF8 regions are detected. Conclusion: We performed genomic analysis and comparative multiple sequences of SARS-CoV2. Studies about the biological symptoms of SARS-CoV2 in clinic animals and humans will manipulate an understanding on the origin of pandemic crisis.

[1]  S. Harrison,et al.  Structure of SARS Coronavirus Spike Receptor-Binding Domain Complexed with Receptor , 2005, Science.

[2]  Yi Shi,et al.  Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 , 2013, Nature.

[3]  G. Herrler,et al.  SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor , 2020, Cell.

[4]  L. Enjuanes,et al.  The Membrane M Protein Carboxy Terminus Binds to Transmissible Gastroenteritis Coronavirus Core and Contributes to Core Stability , 2001, Journal of Virology.

[5]  S. Perlman,et al.  Middle East Respiratory Syndrome: Emergence of a Pathogenic Human Coronavirus. , 2017, Annual review of medicine.

[6]  B. Fielding,et al.  Coronavirus envelope protein: current knowledge , 2019, Virology Journal.

[7]  G. Gao,et al.  MERS-CoV spike protein: Targets for vaccines and therapeutics , 2016, Antiviral Research.

[8]  Obi L. Griffith,et al.  The Genome Sequence of the SARS-Associated Coronavirus , 2003, Science.

[9]  A. Debnath,et al.  Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors , 2004, The Lancet.

[10]  C. Hsiao,et al.  The SARS coronavirus nucleocapsid protein – Forms and functions , 2014, Antiviral Research.

[11]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[12]  S. Perlman,et al.  Coronaviruses: An Overview of Their Replication and Pathogenesis , 2015, Methods in molecular biology.

[13]  Y. Hu,et al.  Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China , 2020, The Lancet.

[14]  Christian Drosten,et al.  Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome , 2003, Science.

[15]  D. Falzarano,et al.  SARS and MERS: recent insights into emerging coronaviruses , 2016, Nature Reviews Microbiology.

[16]  S. Shen,et al.  A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature , 2004, Virology.

[17]  E. Holmes,et al.  The proximal origin of SARS-CoV-2 , 2020, Nature Medicine.

[18]  Huachen Zhu,et al.  Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China , 2020, bioRxiv.

[19]  K. To,et al.  Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan , 2020, Emerging microbes & infections.

[20]  S. Lo,et al.  A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster , 2020, The Lancet.

[21]  Xiang Li,et al.  On the origin and continuing evolution of SARS-CoV-2 , 2020, National science review.

[22]  Shibo Jiang,et al.  Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine , 2020, Cellular & Molecular Immunology.

[23]  I. Wilson,et al.  A structural analysis of M protein in coronavirus assembly and morphology , 2010, Journal of Structural Biology.

[24]  Christian Drosten,et al.  Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC , 2013, Nature.