Abstract
Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 15 140 genome samples collected up to June 1, 2020, we report that SARS-CoV-2 has undergone 8309 single mutations which can be clustered into six subtypes. We introduce mutation ratio and mutation h-index to characterize the protein conservativeness and unveil that SARS-CoV-2 envelope protein, main protease, and endoribonuclease protein are relatively conservative, while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like protease are relatively nonconservative. In particular, we have identified mutations on 40% of nucleotides in the nucleocapsid gene in the population level, signaling potential impacts on the ongoing development of COVID-19 diagnosis, vaccines, and antibody and small-molecular drugs.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Antibodies, Viral / metabolism
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COVID-19* / diagnosis
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COVID-19* / epidemiology
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COVID-19* / prevention & control
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COVID-19* / therapy
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Coronavirus 3C Proteases / chemistry
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Coronavirus 3C Proteases / genetics
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Coronavirus Envelope Proteins / chemistry
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Coronavirus Envelope Proteins / genetics
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Coronavirus Nucleocapsid Proteins / chemistry
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Coronavirus Nucleocapsid Proteins / genetics
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Coronavirus Papain-Like Proteases / chemistry
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Coronavirus Papain-Like Proteases / genetics
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Endoribonucleases / chemistry
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Endoribonucleases / genetics
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Genome, Viral
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Genotype
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Geography
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Humans
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Mutant Proteins / chemistry
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Mutant Proteins / genetics
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Mutation
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Phosphoproteins / chemistry
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Phosphoproteins / genetics
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Protein Conformation
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SARS-CoV-2 / classification*
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SARS-CoV-2 / metabolism*
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Spike Glycoprotein, Coronavirus / chemistry
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Spike Glycoprotein, Coronavirus / genetics
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Vaccines / metabolism
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Viral Nonstructural Proteins / chemistry
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Viral Nonstructural Proteins / genetics
Substances
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Antibodies, Viral
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Coronavirus Envelope Proteins
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Coronavirus Nucleocapsid Proteins
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Mutant Proteins
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Phosphoproteins
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Spike Glycoprotein, Coronavirus
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Vaccines
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Viral Nonstructural Proteins
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envelope protein, SARS-CoV-2
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nucleocapsid phosphoprotein, SARS-CoV-2
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spike protein, SARS-CoV-2
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Endoribonucleases
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nidoviral uridylate-specific endoribonuclease
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Coronavirus Papain-Like Proteases
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Coronavirus 3C Proteases