deLemus

Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins

Spike Glycoprotein

The spike glycoprotein of SARS-CoV-2 is a trimeric type I viral fusion protein that binds the virus to the angiotensin-converting enzyme 2 (ACE2) receptor of a host cell. It is composed of 2 subunits: the N-terminal subunit 1 (S1) and C-terminal subunit 2 (S2), within which multiple domains lie. The S1 region facilitates ACE2 binding and is made up of an N-terminal domain (NTD), a receptor-binding domain (RBD), and 2 C-terminal subdomains (CTD1 and CTD2), while the downstream S2 region is responsible for mediating virus-host cell membrane fusion.

Update

The identified leading mutations in 2023 are listed as follows :

2023.082023.072023.062023.052023.042023.032023.022023.01

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.08.04 - 2023.08.22

Outlined Mutations	Confirmed in VOC/Emerging Variants
N185D	XBB.1.5
L212S	FY.4.2
V445A	XBC.1.6
L455F	EG.5.1.1
F456L	EG.5.1 (Eris)
E554Q	XBB.1.5.18
Q613H	XBB.1.16
T883I	XBB.1.16

*The reported mutations of detected variants are from Cov-Lineages

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.06.30 - 2023.07.05

Outlined Mutations	Confirmed in VOC/Emerging Variants
H146K	FL.2.3 (XBB.1.9.1.2.3)
S446N	FL.19
F456L	XBF

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.06.01 - 2023.06.13

Outlined Mutations	Confirmed in VOC/Emerging Variants
F490P	XBB.1.9.1
E554K	XBB.1.9.1 (sublineage)
Q675K	XBB.1.22.1
L858I	CH.1.1.1

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.05.01 - 2023.05.12

Outlined Mutations	Confirmed in VOC/Emerging Variants
F456L	FD.1.1 & EG.5.1 (2023.08)
S494P	XBB.2.3 & XBB.1.1
T572I	FY.1 ( XBB.1.22.1.1 )

*The reported mutations of detected variants are from GISAID

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.04.01 - 2023.04.21

Outlined Mutations	Confirmed in VOC/Emerging Variants
H146K	XBB.1.5 & XBB.1.16
M153I	XBB.2.3.3
E180V	XBB.1.16
K444R	XBB.1.5
T478R	XBB.1.16, XBB.1.5, CH.1.1.2 & XBB.2.3
F490P	XBB.2.6
S494P	XBB.1.5
Q613H	XBB.1.16
P621S	XBB.2.3
A688V	XAY.1.1.1

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.03.01 - 2023.03.21

Outlined Mutations	Confirmed in VOC/Emerging Variants
Y248S	BQ.1
F490P	XBB.1 & XBB.1.5
T547I	XBB.1.16
Q613H	DV.1, CH.1.1.1 & CH.1.1.17
I666V	XBB.1.5
V1264L	CH.1.1

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.02.03 - 2023.02.20

Outlined Mutations	Confirmed in VOC/Emerging Variants
K147I	XBB.1.5.2.1
Y248S	BQ.1.1.43
S494P	XBB.1.5
Q613H	XBB.1.9.2 & XBB.2.4
P612S	XBF
T678I	BA.2.75 x BA.5
N679R	CH.1.1
P1162S	XBK.1

*The reported mutations of detected variants are from GISAID

• Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).

Here are the recently confirmed leading mutations.

2023.01.31

Outlined Mutations	Confirmed in VOC/Emerging Variants
V445A	BQ.1.1
T883I	BQ.1.1

2023.01.17 - 2023.01.25

Outlined Mutations	Confirmed in VOC/Emerging Variants
H146- / H146K	BQ.1.1 / XBB.1.5
F486A	BQ.1.1
E583D	BQ.1.1
Q613H	BQ.1.1
S939F	BQ.1.1

References