Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Ping-Hsing Tsai; Mong-Lien Wang; De-Ming Yang; Kung-How Liang; Shih-Jie Chou; Shih-Hwa Chiou; Ta-Hsien Lin; Chin-Tien Wang; Tai-Jay Chang

doi:10.1097/JCMA.0000000000000387

Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

J Chin Med Assoc. 2020 Aug;83(8):725-732. doi: 10.1097/JCMA.0000000000000387.

Authors

Ping-Hsing Tsai^{1

2}, Mong-Lien Wang^{3

4}, De-Ming Yang^{5

6

7}, Kung-How Liang^{4

8}, Shih-Jie Chou^{2

9}, Shih-Hwa Chiou^{2

10

11}, Ta-Hsien Lin^{12

13}, Chin-Tien Wang^{11

14}, Tai-Jay Chang^{15

16}

Affiliations

¹ Cell Therapy Innovation Center, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
² Institute of Pharmacology, School of Pharmaceutical Science, National Yang-Ming University, Taipei, Taiwan, ROC.
³ Laboratory of Molecular Oncology, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
⁴ Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan, ROC.
⁵ Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
⁶ Institute of Biophotonics, School of Medical Technology & Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
⁷ Biophotonics and Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, Taiwan, ROC.
⁸ Laboratory of Systems Biomedical Science, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
⁹ Laboratory of Gene & Nanomedicine, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
¹⁰ Laboratory of Stem Cell II, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
¹¹ Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC.
¹² Laboratory of Nuclear Magnetic Resonance, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
¹³ Institute of BioMedical Informatics, School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC.
¹⁴ Laboratory of Molecular Virology, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
¹⁵ Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC.
¹⁶ School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.

Abstract

Background: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused severe pneumonia at December 2019. Since then, it has been wildly spread from Wuhan, China, to Asia, European, and United States to become the pandemic worldwide. Now coronavirus disease 2019 were globally diagnosed over 3 084 740 cases with mortality of 212 561 toll. Current reports variants are found in SARS-CoV-2, majoring in functional ribonucleic acid (RNA) to transcribe into structural proteins as transmembrane spike (S) glycoprotein and the nucleocapsid (N) protein holds the virus RNA genome; the envelope (E) and membrane (M) alone with spike protein form viral envelope. The nonstructural RNA genome includes ORF1ab, ORF3, ORF6, 7a, 8, and ORF10 with highly conserved information for genome synthesis and replication in ORF1ab.

Methods: We apply genomic alignment analysis to observe SARS-CoV-2 sequences from GenBank (http://www.ncbi.nim.nih.gov/genebank/): MN 908947 (China, C1); MN985325 (United States: WA, UW); MN996527 (China, C2); MT007544 (Australia: Victoria, A1); MT027064 (United States: CA, UC); MT039890 (South Korea, K1); MT066175 (Taiwan, T1); MT066176 (Taiwan, T2); LC528232 (Japan, J1); and LC528233 (Japan, J2) and Global Initiative on Sharing All Influenza Data database (https://www.gisaid.org). We adopt Multiple Sequence Alignments web from Clustalw (https://www.genome.jp/tools-bin/clustalw) and Geneious web (https://www.geneious.com.

Results: We analyze database by genome alignment search for nonstructural ORFs and structural E, M, N, and S proteins. Mutations in ORF1ab, ORF3, and ORF6 are observed; specific variants in spike region are detected.

Conclusion: We perform genomic analysis and comparative multiple sequence of SARS-CoV-2. Large scaling sequence alignments trace to localize and catch different mutant strains in United possibly to transmit severe deadly threat to humans. Studies about the biological symptom of SARS-CoV-2 in clinic animal and humans will be applied and manipulated to find mechanisms and shield the light for understanding the origin of pandemic crisis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Betacoronavirus / genetics*
Genome, Viral*
Humans
Open Reading Frames*
Phylogeny
Point Mutation
SARS-CoV-2
Spike Glycoprotein, Coronavirus / genetics
Spike Glycoprotein, Coronavirus / physiology*

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2