Analysis of Amino Acid Sequence of SARS-CoV, SARS-CoV-2, and MERS-CoV Spike Glycoproteins: Preliminary Study for Obtaining Universal Peptide Vaccine Candidates

In the manufacture of universal peptide vaccines, it is necessary to analyze the amino acids of the various candidates. Therefore, this study aims to examine the amino acids of the spike glycoproteins of SARS-CoV, SARS-CoV-2, and MERS CoV. The method used is the alignment of the amino acid spike glycoprotein between SARS-CoV with SARS-CoV-2, MERS CoV with SARS-CoV-2, and SARS-CoV with MERS-CoV using web-based software water emboss. The analysis result showed that SARS and SARS CoV-2 were very similar with 87% similarity and 76.4% identity values. In contrast, SARS CoV-2 with MERS and SARS with MERS were very different, having similarity and identity values less than 70%. Therefore, it is reasonable to conclude that spike glycoprotein's peptide is only useful from attacks by the SARS-CoV and SARS-CoV-2 viruses.

Vaccines for MERS, SARS and COVID-19 are yet to be discovered (Slamet et al., 2013) but the process continues to experience development. In addition, it consists of several amino acid residues (small proteins) (Subroto et al., 2013) and with the existence, it is possible to make a universal vaccine. This can serve a protective function against various types of antigens, which is primarily used for making peptide vaccines. Therefore, a strong similarity protein is needed to make a universal vaccine against coronaviruses (SARS, (Alouane et al., 2020;Khalaj-Hedayati, 2020;Wu et al., 2020).
There have been many research related to the manufacture of vaccine candidates, one of which is the HPV (Human Papillomavirus). This study shows that the promising vaccine peptide candidate of the E1 protein obtained from HPV genome is LLITSNINA, from E5 is VLLCVCLLI and from E7 is LLMGTLGIV (Aprilyanto & Sembiring, 2017). Furthermore, they have been tested in vitro, and the results are useful in activating the immune response.
One of the conditions for making a peptide vaccine is that the protein antigen should be located at the outer part of the virus in order to ease the purification process. The spike glycoprotein is used as a peptide vaccine candidate since its position is in the outer part, and it is possessed by all types of Coronavirus. Therefore, this protein is used as a candidate source for peptide vaccines for all kinds of Coronavirus.
Initially, the research was conducted to obtain an overview of its potential as a vaccine candidate. In addition, an explanation of their potential will be obtained by testing the similarity and identity for the amino acid sequence of spike glycoproteins.

MATERIALS AND METHODS
This research used the following materials; amino acid sequence of SARS-CoV-2, SARS-CoV (SARS), and MERS-CoV ( Table 1 represents the results of the alignment shown by the value of identity and similarity. The Identity is the percentage of identical matches between the two sequences over the reported aligned region (including any gaps in the length). The following are the results of alignment among the three viruses. The similarity is the percentage of matches between the two sequences over the reported aligned region (including any gaps in the length) (Taupiqurrohman et al., 2016). In addition, Identity value indicates the identical equation of the compared amino acids, while the similarity value indicates the conformity on chemical properties (Hui et al., 2020). Table 1 also shows that Coronaviruses of SARS and COVID-19 have a high similarity with an identity value of 76.4% and 87%. On the contrary, the comparison of MERS and COVID-19 is relatively not similar because the alignment results are below 70%. The low result is also shown by the comparison between SARS with MERS having 31.6% identity, and 47.3% similarity. This is consistent with the explanation of Andriani (2016) and , where it was stated that the coronaviruses of SARS and COVID-19 are very close based on evolution tree. According to Rice et al. (2000), phylogenetic results (evolutionary kinship) cannot be concluded because of the type of protein being compared. Therefore, this research has illustrated the great potential of spike glycoprotein to be the source of peptide vaccine candidates for the SARS and COVID-19 diseases. Below is the structure of the spike glycoprotein of SARS-CoV, SARS-CoV-2, and MERS based on the database (pdb.org).

Work Principles of Universal Peptide
Vaccine. The sequential analysis shows that spike glycoprotein can only be used as the source of peptide vaccine candidates for SARS and COVID-19. This should be properly conducted since the working principle of peptide vaccine is based on the immune system. The two common parts when a virus infects are the outside (specific body tissue) and the inside of an infected cell (body cell). When a part of the tissue is infected, the immune cells in the region begin to respond (Mothes et al., 2010;Mallapaty, 2020). This is evident in macrophages, which is one type of immune cell that is responsible for initiating the formation of antibodies through the activation of helper T cells. To activate this cells, macrophages will phagocytize the incoming antigen protein. Furthermore, the results of phagocytosis (small peptides) are raised to the surface of the body by major histocompatibility (MHC) class II protein to be recognized by helper T cell receptors . Andriani (2016) stated the predicted part and made into a peptide vaccine.
During an internal cellular infection, the cell responds through a series of reactions (Fig.  4). An important part of this response in relation to the peptide vaccine is that the cell will attempt to bring the virus part to the surface. This is conducted by the MHC class I and recognized by cytotoxic T cells, which functions to reduce infection . The part of the virus raised by MHC I and II is another peptide vaccine candidate that is predicted by using the spike glycoprotein (marked in the box in the picture). This protein is a potential candidate for peptide vaccine since it is found on the outer part of the virus spike glycoprotein is also in the outer part of the virus, thus it is a potential candidate for peptide vaccine. Initially, it is recognized or attached to the cell surface, and the location is given below.
Every disease has a cure. If the right medicine is found for a disease, the disease will be cured with the permission of Allah Azza wa Jalla (Sahih Muslim No. 4084). Based on this hadith, we can learn that there is no disease on this earth that was created by Allah swt. without a cure. As at present, many kinds of research have been carried out by scientists to find the most appropriate vaccine candidates for use in the prevention of infectious diseases caused by the coronavirus. The success of finding a vaccine candidate with the highest level of effectiveness is also inseparable from the power of Allah Almighty, as His word in QS. Ash-Shu'ara verse 80 (Kementerian Agama RI, 2019). This verse explains that it is Allah swt. who heals a man when he is sick. Allah has the power to heal any disease that a person has. But man, through the use of the mind by studying science, must also find out how to obtain this healing. Through science, humans can find out Vol 8(2), December 2020 Biogenesis: Jurnal Ilmiah Biologi 193 the types of amino acids from the glycoprotein spike of various types of coronaviruses that are most appropriate to be used in the production of universal peptide vaccines for various types of infectious diseases caused by various types of coronaviruses. The lesson that can be taken from this verse is that diseases experienced by humans are the result of human actions themselves, including infection with diseases caused by the coronavirus, one of which is the lack of a clean lifestyle. Through the efforts made by humans and by the will of Allah swt. diseases suffered by humans can be cured. Diseases that occur in humans can also be a reminder to always be grateful for the various blessings from Allah swt. One of which is the favor of healing from an illness.

CONCLUSION
SARS CoV-2 (COVID-19) and SARS are very similar with 87% similarity and 76.4% identity values. In contrast, covid-19 with MERS and SARS with MERS are very different because of their reduced similarity and identity values below 70%. Therefore, the spike glycoprotein can only be used as the peptide vaccine candidate for COVID-19 and SARS.