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

Journal of Chemical Information and Modeling
Rui WangGuo-Wei Wei

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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Citations

Nov 11, 2020·Biochemical Society Transactions·Jiayue-Clara Jiang, Yan Zhang
Oct 20, 2020·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Anwar MohammadFahd Al-Mulla
Dec 17, 2020·Heliyon·Shweta JakhmolaHem Chandra Jha
Jan 29, 2021·Journal of Theoretical Biology·Changchuan Yin
Oct 1, 2020·Viruses·Rui WangGuo-Wei Wei
Mar 2, 2021·Computers in Biology and Medicine·Yuta HozumiGuo-Wei Wei
Mar 3, 2021·NPJ Science of Learning·Mengzhou LiGe Wang
Apr 3, 2021·Journal of Biomolecular Structure & Dynamics·Neha PeriwalVikas Sood
Apr 21, 2021·Communications Biology·Hajime ShinodaRikiya Watanabe
May 22, 2021·Viral Immunology·Noha A KamelKhaled M Aboshanab
Jul 3, 2021·Biology·Nancy FayadJad Abdallah
Jul 9, 2021·Frontiers in Molecular Biosciences·Santosh K Ghosh, Aaron Weinberg
Jul 27, 2021·Journal of Biomolecular Structure & Dynamics·G Mahaboob BashaYasinalli Tamboli
Jan 1, 2021·Journal of Chemical Information and Modeling·Adrian J Mulholland, Rommie E Amaro
Nov 13, 2020·The Journal of Physical Chemistry Letters·Rui WangGuo-Wei Wei
Jul 18, 2020·ACS Infectious Diseases·Xi YuanPeiwu Qin
Aug 28, 2021·Cells·Marianna SorokaAnna Rymaszewska
Sep 18, 2021·Analytical and Bioanalytical Chemistry·Christian MannKevin M Downard
Sep 22, 2021·Methods : a Companion to Methods in Enzymology·Nimisha GhoshNikhil Sharma

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Methods Mentioned

BETA
genotyping
PCR
GISAID
PCA

Software Mentioned

PLPro
GISAID
Clustal Omega

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