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Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine.
J Chem Inf Model. 2020 12 28; 60(12):5853-5865.JC

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.

Authors+Show Affiliations

Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States.Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States.Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, Illinois 60607, United States.Department of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States. Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

32530284

Citation

Wang, Rui, et al. "Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine." Journal of Chemical Information and Modeling, vol. 60, no. 12, 2020, pp. 5853-5865.
Wang R, Hozumi Y, Yin C, et al. Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. J Chem Inf Model. 2020;60(12):5853-5865.
Wang, R., Hozumi, Y., Yin, C., & Wei, G. W. (2020). Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. Journal of Chemical Information and Modeling, 60(12), 5853-5865. https://doi.org/10.1021/acs.jcim.0c00501
Wang R, et al. Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. J Chem Inf Model. 2020 12 28;60(12):5853-5865. PubMed PMID: 32530284.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. AU - Wang,Rui, AU - Hozumi,Yuta, AU - Yin,Changchuan, AU - Wei,Guo-Wei, Y1 - 2020/06/25/ PY - 2020/6/13/pubmed PY - 2021/1/26/medline PY - 2020/6/13/entrez SP - 5853 EP - 5865 JF - Journal of chemical information and modeling JO - J Chem Inf Model VL - 60 IS - 12 N2 - 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. SN - 1549-960X UR - https://www.unboundmedicine.com/medline/citation/32530284/Decoding_SARS_CoV_2_Transmission_and_Evolution_and_Ramifications_for_COVID_19_Diagnosis_Vaccine_and_Medicine_ L2 - https://doi.org/10.1021/acs.jcim.0c00501 DB - PRIME DP - Unbound Medicine ER -