COVID-2019 Genome Sequence Analysis: Phylogenetic Molecular Evolution and Docking of Structural Modelling of Receptor Binding Domain of S Protein in Active Site of ACE2

Meanwhile the outbreak of the Covid-19 since December, 2019 in China, it has killed more than a hundred thousand of people of all ages and sex across the globe in a short span of time. On the bases of this study the nearest family member of the virus and its receptor binding domain of S protein including its model structure and function of its active sites were naked through Multiple Sequence Alignment, modelling and molecular docking software accordingly its repository genome databases. The virus was genetically associated and molecular evolutionary related with (RaTG13) and it scores 96.12% homology with 99% query coverage followed by bat-SL-CoVZC45 and bat-SL-CoVZXC21 notch 89.12% and 88.65% respectively. However, SARS and MERS corona type virus those outbreak earlier respectively less likely family members of 2019-nCoV. Though the virus has a close genetic association with those previous SARS coronaviruses, and certainly the spike protein used as a binding receptor to fight against human receptor protein of ACE 2, but on the basis of FRODOC and HDOCK server analysis multi favorable active sites of S protein was discovered such GLN493 shown as a finest key in both model and possessed a unique traits on it resulting unexpected rate of transmission and number of people died while compared to the previous distance divergence between wild type novel coronavirus which was risen from China against to the genomes from Lebanon, India, Italy, and USA and so on. Thus, the World Health Organization and its researchers should focus on immunologic research and effective drug and vaccine development that will help to address the epidemiology of the virus, which can provide a long-term solution.


Introduction
Novel Coronavirus (2019-nCoV) according to the world report, the virus was discovered in a seafood market in the Chinese state of Wuhan, Hubei since late December, 2019 and now the virus classified a pandemic as the outbreak has spread to around the world and is currently infected in over 188 countries. Thus, up-to-date Agust-05-/2020, approximately 18.5 million total confirmed cases and 701,455 fatality cases have been verified (https://coronavirus.jhu.edu/map.html).
Coronavirus causes pathogenicity for the various of animals and including humankind, and resulting sever lethal respiratory associated cases were recorded against to pigs, dogs, avian, bovine, masked palm civet, camels horse as well humans for the last decades [1] [2]. Primarily coronavirus incidence as SARS in 2002 and HKU3-1 to HKU3-3 were identified in the horseshoe bats (rhinolophus-non-cave species) in 2005 from Hong Kong and was thought as reservoir of the virus and will be responsible for future epidemic [3] [4]. Himalayan masked palm civets (paguma larvata) also and it was considered to be the natural reservoir of the virus and may has served as intermediate host between bat and the first human cases.
Consequently, remarkably two of corona virus SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome) are going to invasive the human population across as epidemic in world. In November 2002, SARS coronavirus was outbreak in Guangdong, southern part of china and then spread to 29 countries in 2003. Due to this adverse plague, more than 774 fatalities was recorded out of 8000 confirmed cases and noted low transmission rate against to its high 9.5% mortality rate. Followed by, since 2012 the outbreak of MERS originally from Saudi Arabia and cause for the sever death of 858 out of total 2494 total confirmed cases and were registered as high 35% mortality rate in the world [5] [6] [7]. But (2019-nCoV) with a 3.8% fatality cases rate even high transmission proportion has been recorded globally [8].
We did not find it easy to know the meticulous origin of the virus, the receptor binding proteins (RBD) and its mutational change to talk about the distinc- If takes a trajectory of genomes sequence deposited from Lebanon, India, Taiwan, Uganda, Bangladesh, USA and so on countries had shown high S protein amino acid mutation took place and more than 15% significance divergent of genome sequence was analyzed through next strains hCoV-2019 virtual platform in dataset of epidemiology center ( Figure 1). Figure 1. Up-to-date of 22-Apr-2020, Over 4000 novel coronavirus genome sample and its phylogeny and genetically mutational divergent across geographical locations, over elapsed time and host human genetic diversity globally. In particular, the countries whose names appear on the graph are taken as a sample where the virus genetically changed in fast.

Prevalence of COVID-19 and Its Vaccine Development Program
Due to its rapid genetic variation, the distribution of Covid-19 across the world is so exceptional and unprecedented numbers of cases are going on reporting from different countries into world health organizations (WHO). Except a few countries, almost all countries has suffered from this pandemic as a map presented in Figure 2. Evidence suggests that it has been growing rapidly since 2020-June in contradiction of in the first few months. On the basis of WHO reports, Today, the number has risen to 18.5 million cases and at around 0.7 million fatality cases was verified at all age, sex and any genetic variations (exceptional study is needed). Although diagnostic capabilities and diagnosis kits have been increasing over time, it has not been able to stop the spread of the virus because it has allowed it to spread rapidly with its genetic properties. Therefore, researches into the urgency of the development of effective vaccine ought to be considered and should be took as the main solution [12]. There are currently no Food and Drug Autho-

Phylogenetic and Molecular Evaluation Genetic Analysis
Phylogenic and molecular evolutionary genetic analysis were conducted using MEGA software (version 10.1.7) using neighbor-joining statistical approaches and a single amino acid substitution [13].

Multiple Sequence Alignment (MSA) of COVID-19
High quality of 25 genome sequence of COVID-19 and including corona type those were happened as plague around the world for the last years were selected for further analysis. Each selected genome sequence of 2019-nCoV against to any corona type targeted multiple sequence alignment (MSA) was performed through ClustalX software (version 2.0.10) [15].

Targeted S Spike-Surface Glycoprotein of COVID-19
Amongst all notable genes, S-gene translated and expressed into S or spike surface glycoproteins which support the binding affinity and fusion of the virus to pass in to the surface of host cells particular where a receptor protein Angiotensin Converting Enzyme II (ACE2) which expressed in alveolar cells of the lung, esophagus upper and stratified epithelial cells, absorptive entrecotes from ilium and colon [16]. 13

Conserved Regions of Receptor Binding Domain (RBD) of S Proteins
S-spike protein of coronavirus is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing host antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into two parts an amino or N-terminal S1 subunit and carboxyl or C-terminal S2 subunit that mediates attachment and membrane fusion, respec-  and VAL445 were added into 2019-nCoV. It is difficult to say that this change was arbitrary and there was no definitive study yet to be confirmed the mechanism of this chaos amino acid change and this study should confirmed through in vitro laboratory using animal model and continue study the expression of mutational S gene for its phenotype trait.

Homology Modeling of S Protein and Protein-Protein Interactions
Sequence of spike protein of 2019-nCoV (Acc: YP_009724390.1) which sample was collected from Wuhan sea food market positive patient as a reference and its homology modeling predictions and analysis were performed through Phyre2 server (Protein Homology/analogY Recognition Engine V 2.0) and high quality and ≥90% confidence score of eight alignment was selected based on heuristics to maximise confidence, percentage identity and alignment coverage [19].
Such that out of them template c6xr8C_ of PDB: viral protein was scored 100% confidence and 99% alignment coverage and be candidate for further structural and functional analysis through protein-protein docking. The candidate of S spike protein of 2019-nCoV was characterized based on modeling prediction analysis and used for docking between S protein and ACE2. Out of hundred prediction, 10 paramount docking model predictions was generated from HDOCK online server [20].  Figure 7(a). The surface of S pike protein in accessible to solvent at (1.4 Angstrom probe) was done using FRODOCK server (Job ID 5613947) as the parameters published on [21] and the surface of area of the protein and its hydrophobic effects was shown in Figure   7(b).

Methods
Open biological big genomic data of 2019-nCoV and any corona type virus vir-

Conclusions and Discussions
Since the virus started in December 2019 in China, millions of people have been infected throughout the world, and hundreds thousands of deaths have resulted in deaths. While there are some deletions, substitutions and mutations that are generalized to the virus, the coding region genome of the virus is already in ancestral relationship with some of the previously created types of coronavirus, such as SARS, MERS and bat SRAS-like like CoV. In particular, it is strongly associated with the bat SARS-like corona virus (Rhinolophus affinis, Rhinolophs sinicus and SL-bat strain) based on evolutionary analysis through mega software.
In addition to that the spike glycol surface protein used for adhesion and binding receptor into ACE2 has a high similarity to the previous RaTG13 and SL strains of coronavirus as well synthetic spike proteins over finding of mafft Multiple Sequence Analysis. After all, though, it is believed that the bat SARS-like coronavirus will eventually become a pandemic in the world [14] and the present problem shows a lack of focus on early researches and a lack of preparedness. Bat SARS coronavirus eventually mutated and cause for amino acid change at site of S surface protein specifically GLN493 had strong bond while it was flipping the side in different position. Even though bat is not purchased or sold at market now, the people who used to play with it or consumed animal and its products should care on exclusively, but we strongly have suggested to keep on physical distance until full potential and official vaccine development because the virus already has adapted a human serology too much and able transmit easily rather than in animated. Altering of active amino acid of the binding protein makes the virus more contagious since it will have rotatable attachment or adherence capacity for human receptor protein. As a result the virus getting unconstrained chance to entry to the human cells and being contagious from human to human within fast transmission rate. Hence, the study's facts indicate that the current distribution of the virus should be examined in terms of genomic diversity to realize its distance divergence across the world. Particularly, the mutation that takes place on S-gene would be complicated the viral for vaccine development program since its hot spot to be multivalent against to ACE2. The wild genome, which originally originated from Wuhan sea food market, China on the basis of geographical location, relapsed time, and host human genetic variation, is currently undergoing significant divergence, specifically, up to 25% of the variance in India, Italy and the United States has been documented through epidemiology dataset online analysis platforms. If it continues with its virulence severity, the next most likely robust viral strain, SARS-3 coronavirus, is likely to be broader. It is therefore a major way to curb the spread by concentrating on the types of severe strains that are highly concentrated and studied in a comprehensive manner worldwide. Next, an unprecedented amount of financial and technical support should be made for researches undertaken globally to find the best drugs and vaccines internationally, with great emphasis on the World Health Organization. Somehow, we suggested to investigate the crystallography of spike proteins and would be proofed through in vitro lab and understand the whole genetic materials machinery process particularly those participated on RNA transcription, protein translations, surface binding and cell division as per its progressive mutations and reveled the exact common active binding sites or epitopes for drug design and vaccine development.