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.