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. 2020 Dec 28;60(12):5853-5865.
doi: 10.1021/acs.jcim.0c00501. Epub 2020 Jun 25.

Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine

Rui Wang  1 , Yuta Hozumi  1 , Changchuan Yin  2 , Guo-Wei Wei  1   3   4
Affiliations

Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine

Rui Wang et al. J Chem Inf Model. .

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.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Pie chart plot of six distinct clusters in the world. The light blue, dark blue, green, red, purple, and yellow represent clusters I, II, III, IV, V, and VI, respectively. The base color of each country is decided by the color of the dominant cluster.
Figure 2
Figure 2
Pie chart plot of four distinct clusters in the US. The blue, red, yellow, and green colors represent clusters A, B, C, and D. The base color of each state corresponds to its dominant cluster.
Figure 3
Figure 3
Distribution of SNP mutations of SARS-CoV-2 isolates from 15 140 genome samples in the world with respect to the reference genome of January 5, 2020 (GenBank access number: NC_045512.2).
Figure 4
Figure 4
Frequencies of the single SNP mutations of SARS-CoV-2 on the genome samples in the world with respect to the reference genome of January 5, 2020 (GenBank access number: NC_045512.2).
Figure 5
Figure 5
Illustration of SARS-CoV-2 spike protein mutations using 6VXX as a template.
Figure 6
Figure 6
Illustration of SARS-CoV-2 spike-protein receptor binding domain (RBD) mutation using 6M0J as a template. It is noted that nearly half of the residues in RBD have undergone mutations in the few months.
Figure 7
Figure 7
Illustration of SARS-CoV-2 main protease mutations using 6LU7 as a template.
Figure 8
Figure 8
Illustration of SARS-CoV-2 main protease binding domain (BD) mutations of 6LU7.
Figure 9
Figure 9
Illustration of SARS-CoV-2 papain-like protease mutations using 6W9C as a template.
Figure 10
Figure 10
Illustration of SARS-CoV-2 RNA-polymerase mutations using 6M71 as a template.
Figure 11
Figure 11
Illustration of SARS-CoV-2 Endoribo-nuclease protein mutations using 6VWW as a template.
Figure 12
Figure 12
Illustration of SARS-CoV-2 envelope protein mutations using 5X29 as a template.
Figure 13
Figure 13
Illustration of SARS-CoV-2 nucleocapsid phosphoprotein mutations using 6VYO as a template.
See this image and copyright information in PMC

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