Introduction
Novel coronavirus SARS-COV2 created pandemic by creating Covid-19 disease and believed to be originated in Wuhan, China in 2019. SARS-COV2 bears genomic identity to earlier SARS-COV virus with 79.8% and with MERS-COV virus with 59.1% (1, 2). Although Bat (Rhinolophus affinis from Wunnan) could be considered as a natural reservoir for this group of Coronavirus, an intermediate host of SARS-COV2 is much expected in between bat and human host. Genomic similarities from isolate of SARS-COV2 like virus from pangolin suggests that it could serve as an intermediate host (3). With a detail study comparing the genomic sequences that bears highest identities to related virus of Bat (ZC-45 (87.7%), RaTG13 (96.3%)), Pangolin (Pan-SL_CoV_GD (Guangdong, China) (91.2%), Pan_SL_CoV_GX (Guanxhi) (85.4%)) with SARS-COV2(4), they proposed that SARS-COV2 arose from Bat RaTG13 and gained three insertions in the vicinity of RBM (Receptor Binding Motif) at RBD (Receptor Binding Domain) in S1 region by exchanged recombination with Pan_SL_COV_GD genome of pangolin from Guangdong. However, due to higher dissimilarities with Pan-COV genomic sequences, they suggested that pangolin could not be an intermediate host of SARS-COV2 but RatG13 is the most probable ancestors of SARS-COV2 of human.
S (spike) protein of the SARS-COV2 virus resides on their protein coat membrane and is cleaved into two small proteins S1 and S2 by the human host enzymes. S1 forms a claw like structure and attaches with the host ACE2 (Angiotensin Converting Enzyme 2) receptor with five key entry point residues whereas S2 mediates membrane fusion with the host cell. The cleavage of the S protein occurs at the two sites: one in between S1/S2 site by furin and other in S2 site by a serine protease, TMPRSS2 (5, 6). The critical residues 449Y, 455L, 486F, 489Y, 493Q, 500T and 501N at the RBM in RBD in S1 of SARS-COV2 binds with K31, E35, D38, M82 and K353 of human ACE2 (7). Among these residues K31-493Q and K353-501N interactions are most important for SARS-COV2 infection to human host and provide more chemically favorable interaction than SARS-COV K31-479L/N (homologue of SARS-COV2 493Q) and K353-487S/T (homologue of 501N) binding, which gave SARS-COV2 more infection power over SARS-COV (4, 7). Recently, another mutation D614G is observed only in more virulent SARS-COV2 strain that is believed to be the cause of a widespread pandemic in Europe and USA with much more infectivity(8, 9). This mutation creates an extra serine protease cleavage site at the S1/S2 junction of the spike protein and facilitate further infectivity in Caucasians with a Del C (rs35074065) genotypic background in the intergenic region between TMPRSS2 and MX1 gene (9). Zhang et al (2020) showed that 614G mutated protein reduces S1 shedding and increase infectivity (10).
Until now, it is believed that SARS-COV2 is originated in bat and gained three insertions by recombination with interchanging genetic materials from Pan_SL_COV_GD of Guangdong. For the evolution of SARS-COV2 three hypothesis can be predicted, 1) SARS-COV2 entered human early without all required mutation at these key entry-point residues at RBD with a poor efficiency and then spent silently long time in human host, adapted to evade host immune system with slower mutation rate, eventually perfected its entry-point residues and attained widespread infectivity; or 2) it gained all required mutations in those entry-point residues to infect human efficiently with widespread infectivity then adapted to evade the immune system with higher mutation rate ; or 3) entered an intermediate host from bat that have human like conditions, then entered human and adapted easily without spending long time. Here we will discuss all these possibilities by comparing their genomic sequence identities, and the existence of probable intermediate host by tracking the evolution of key entry-point residues in RBD in S1 protein. We estimated the mutation rate of SARS-COV2 in human host and calculated the time frame for evolution of SARS-COV2 from bat RaTG13 and its mutational constraints that led to select them to infect, survive and become virulent in human.