Analysis of SNPs
The genome-wide SNPs are reported in Table 1 (positions referred respect
to the reference sequence; GenBank accession number: NC_045512.2). The
corresponding amino-acid positions and variations inside the proteins
are shown in Table 2. The genome sequence from the Bangladesh differed
in nine nucleotide positions from that of the COVID-19 patient in Wuhan
(NC_045512.2), while with the genome sequence isolated from the Indian
patient showed 15 nucleotide variations followed by Italian patient 11
nucleotide variations (Table 1). Among all of the 11 nt mutation 2
mutation at position 1162 and 17019 reveled the novel mutation in
comparison of the all submitted sequences in the NCBI database (Figure
2). Table 2 that depicts overall five Nonsynonymous mutations that was
observed compared to the reference Wuhan sequence. The sequence of the
Bangladeshi female patient (EPI_ISL_437912) presented a mutation 388F
with respect to the reference Wuhan genome (L) (Table 3). In addition,
this EPI_ISL_437912 also presented EP mutation 4803L, 5673D, 6508G,
9627K and 9628R with respect to the reference Wuhan genome P,E, D, R,G
respectively with 2 amino acid changes (Figure 2 & Table 3). In
comparison with the most close neighboring country India sequences,
EPI_ISL_437912 presented 11 mutation at 388F,607G,2104T,3694L,4808L,
5673I,6508G,9503P,9516R,9627K,9628R with respect to the Indian patient
genome I, S, K, F, S, D, L, S, R, G respectively (Table 3). Meanwhile,
the sequence of the Russia patient (EPI_ISL_430111) presented I and S
at amino acidic position 388 and 5673 with respect to the Bangladeshi
sequence (F and I)( Table 3).Furthermore, predicted 3D structures of
NSP13-261E and NSP13-261D were >90% confident. These
structures were identical and completely overlapped with each other when
aligned using PyMOL. The predicted secondary structures were similar,
both 261E and 261D were localized in α -helix (Figure 3a). Based on
these findings, it can be concluded that the E261D mutation in NSP13 has
no effect on protein structure and hence the function. Nonetheless,
amino acid 261 is not a part of NSP13 active site. However, the
predicted structures of both NSP2-120I and NSP-120F were around 46%
confident. These structures failed to align, but the phenylalanine
reside of the NSP-120F was in a α -helix (Figure 3b) whereas the
isoleucine reside of the NSP2-120I was not. Despite the reliability of
Phyre2 structures, predicted secondary structures also showed the same
thing with high confidence. Such findings suggest that the I120F
mutation in NSP2 could affect the structure and function of NSP2. The
structure and function of NSP2 is yet to explore, but current prediction
suggests that there is no known functional domain spanning this mutation
site (Figure 3a & Figure 3b).