The Chemical Mechanism of Pestilences or Coronavirus Disease 2019 (COVID-19)

Abstract

In this paper, the chemical mechanism of the coronavirus disease 2019 (COVID-19) has been explored and clearly revealed.

Share and Cite:

Zhang, D. , Fang, L. , Wang, L. , Pan, Z. , Lai, Z. , Wu, M. , Tang, K. , Lei, L. , Qian, D. , Huang, Z. , Wang, X. , Chen, H. and Chou, K. (2020) The Chemical Mechanism of Pestilences or Coronavirus Disease 2019 (COVID-19). Natural Science, 12, 717-725. doi: 10.4236/ns.2020.1211063.

1. INTRODUCTION

Around the end of 2019, a new viral species caused large-scale transmissions and infections, discovered in Wuhan (WHO Emergencies Preparedness, Response, 2020) and subsequently around the world (WHO COVID-19 Disease Dashboard, 2020). Symptoms caused include coughing, shortness of breath, and fever. Around 1% to 5% (Worldometer, 2020) of confirmed infections have resulted in deaths, mainly due to severe respiratory failure (CDC, 2020). Genealogical tree studies of the new virus strains have later revealed them to be phylogenetically intimate relatives of the Severe Acute Respiratory Syndrome Coronavirus, namely (SARS-CoV), first identified in 2003 [1]. This new virus has been named SARS-CoV-2 by the International Committee on Taxonomy of Viruses (ICTV) (Gorbalenya et al., 2020) on February 11th, 2020 [2 - 29].

2. MATERIALS AND METHOD

For the materials used in this study, see Figure 1 and Figure 2.

Figure 1. The alignment of the amino acid sequences of the S proteins from 4 coronaviruses and the phylogenetic tree of the genes of the receptor binding proteins from 8 different single strand RNA viruses with the MEGA software. Top: The alignment of the amino acid sequences of the S proteins from 4 coronaviruses, namely Bat Coronavirus RaTG13, Pangolin CoV (GX), SARS-CoV (NC_004718) and SARS-CoV-2 (NC_045512). Receptor Binding Domain (RBD) is labeled with the color boxes and the black arrows indicate the beginning and the end of RBD.

Figure 2. The alignment of the spike (S) protein of 3 strains of SARS-CoV-2 and 1 strain of SARS-CoV (NC_004718.3), SARS-CoV-2 (NC_045512), MT415375 and MT415377. Important functional regions, such as the Signal Peptide (SP), Receptor Binding Motif (RBM), Fusion Peptide (FP) and the inserted amino acid (amino acids PRRA)/host protease recognition site and cleavage site (amino acids RRAR)/cleavage site (between amino acids 685R and 686S) have been marked on the CA pictures. SP: green Box (the green arrows showing the beginning and end of the SP); RBM: blue box (the blue arrows showing the beginning and end of the RBM); PRRAR: black box (the black arrows showing the beginning and end of the inserted/host protease recognition amino acid sites; the red arrow showing the host protease cleavage site between amino acids 685R and 686S) (T. Meng, et al.); FP: yellow box.

The “Chou’s 5-step rules” or “Chou’s 5-steps rule” has also been applied because it has been widely and increasingly used by many scientists to study biological sequence analyses [2 - 56].

To develop a really useful predictor for a biological system, one needs to go through the following five steps: 1) select or construct a valid benchmark dataset to train and test the predictor; 2) represent the samples with an effective formulation that can truly reflect their intrinsic correlation with the target to be predicted; 3) introduce or develop a powerful algorithm to conduct the prediction; 4) properly perform cross-validation tests to objectively evaluate the anticipated prediction accuracy; 5) establish a user-friendly web-server for the predictor that is accessible to the public. Papers presented for developing a new sequence-analyzing method or statistical predictor by observing the guidelines of Chou’s 5-step rules have the following notable merits: 1) crystal clear in logic development, 2) completely transparent in operation, 3) easily to repeat the reported results by other investigators, 4) with high potential in stimulating other sequence-analyzing methods, and 5) very convenient to be used by the majority of experimental scientists.

Accordingly, the webserver for the current paper has been currently underway; once done, it will be announced through the addendum of this paper.

3. CONCLUSION

The chemical principle proposed in this paper is extremely useful in fighting against the pandemic COVID-19, particularly in developing very powerful vaccine against this kind of horrible disease.

Conflicts of Interest

The authors declare no conflicts of interest regarding the publication of this paper.

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