Difference between revisions of "deLemus"

Latest revision as of 10:25, 15 December 2023

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

The dynamic epidemiology of coronavirus disease 2019 (COVID-19) since its outbreak has been a result of the continuous evolution of its etiological agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Within the first 2 years of this pandemic, the World Health Organization (WHO) has already announced 4 variants of concern (VOC), namely alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2), together with numerous variants of interest (VOI). The latest lineage to be designated a VOC would be omicron (B.1.1.529),^[1] from which a diverse variant soup is generated.^[2] From the original BA.1 strain of November 2021 to the most recent XBB and BQ.1 strains of late 2022,^[3]^[4] each omicron subvariant has successively proliferated and outcompeted its once dominant antecedent.^[5] The emergence of all these variants has brought along many novel mutations that continue to fine-tune the fitness of the virus,^[6]^[7] leading to its persistent global circulation. Recent emerging variant (EV) data retrieved from GISAID, as of 17 January 2023, has revealed that the top 4 most rapidly spreading lineages are the BA.1.1.22, CH.1.1, XBB.1.5, and BQ.1.1 variants, among which XBB.1.5 has been found to be especially prevalent in the US,^[8] making up of more than 40% of its sequence coverage in early January 2023.

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.^[9] 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 ^[10]:

2023.122023.112023.102023.092023.082023.072023.062023.052023.042023.032023.022023.01

2023.12.01-2023.12.17

Outlined Mutations	Confirmed in VOC/Emerging Variants
L455F	EG.5.1.1
A475V	EG.5.1.1
E654K	HK.3

2023.11.01-2023.11.17

Outlined Mutations	Confirmed in VOC/Emerging Variants
N185D	HK.3.2
L455F	EG.5.1.1
A475V	JF.1
T572I	FY.2
Q613H	XBB.1.16
D1153Y	HK.3

2023.10.06

Outlined Mutations	Confirmed in VOC/Emerging Variants
L455F	EG.5.1.1
A475V	GK.1

2023.09.08-2023.09.28

Outlined Mutations	Confirmed in VOC/Emerging Variants
R403K	BA.2.86 (Pirola)
L455F	EG.5.1.1
S494P	EG.5.1.1
P521S	XBB.1.16.15
E554K	BA.2.86 (Pirola) & FE.1
Q613H	BA.2.86 (Pirola)
P621S	BA.2.86 (Pirola)
T732I	XBB.2.3 x XBB.1.5
S939F	BA.2.86 (Pirola)
V1264L	CK.1.1

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^[11]

RBD Mutation Profile of Latest VOIs.

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^[12]

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

↑ Karim, S. S. A. & Karim, Q. A. Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic. Lancet 398, 2126 (2021).
↑ Callaway, E. COVID ‘variant soup’ is making winter surges hard to predict. Nature 611, 213 (2022).
↑ Wang, Q. et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 186, 279 (2023).
↑ Qu, P. et al. Enhanced Neutralization Resistance of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe 31, 9 (2023)
↑ Rössler, A. et al. BA.2 and BA.5 Omicron Differ Immunologically from Both BA.1 Omicron and Pre-Omicron Variants. Nat Commun 13, 7701 (2022)
↑ Carabelli, A. M. et al. SARS-CoV-2 variant biology: Immune escape, transmission and fitness. Nat Rev Microbiol (2023). DOI: https://doi.org/10.1038/s41579-022-00841-7.
↑ Witte, L. et al. Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape. Nat Commun 14, 302 (2023).
↑ Callaway, E. Coronavirus variant XBB.1.5 rises in the United States — is it a global threat? Nature 613, 222 (2023).
↑ Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat Rev Mol Cell Biol 23, 3 (2021).
↑ deLemus team, Analysis of Leading Mutations in SARS-CoV-2 Spike Glycoproteins (in preparation, 2023).
↑ Cov-Lineages https://cov-lineages.org/
↑ GISAID https://gisaid.org/

[Karim-1] Karim, S. S. A. & Karim, Q. A. Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic. Lancet 398, 2126 (2021).

[2] Callaway, E. COVID ‘variant soup’ is making winter surges hard to predict. Nature 611, 213 (2022).

[Wang-3] Wang, Q. et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 186, 279 (2023).

[European_Centre-4] Qu, P. et al. Enhanced Neutralization Resistance of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe 31, 9 (2023)

[Del_Rio-5] Rössler, A. et al. BA.2 and BA.5 Omicron Differ Immunologically from Both BA.1 Omicron and Pre-Omicron Variants. Nat Commun 13, 7701 (2022)

[6] Carabelli, A. M. et al. SARS-CoV-2 variant biology: Immune escape, transmission and fitness. Nat Rev Microbiol (2023). DOI: https://doi.org/10.1038/s41579-022-00841-7.

[7] Witte, L. et al. Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape. Nat Commun 14, 302 (2023).

[8] Callaway, E. Coronavirus variant XBB.1.5 rises in the United States — is it a global threat? Nature 613, 222 (2023).

[Jackson2021-9] Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat Rev Mol Cell Biol 23, 3 (2021).

[deLemus-10] Lemus team, Analysis of Leading Mutations in SARS-CoV-2 Spike Glycoproteins (in preparation, 2023).

[Cov-Lineages-11] Cov-Lineages https://cov-lineages.org/

[GISAID-12] GISAID https://gisaid.org/

[1]

[2]

[3]

[4]

[5]

[6]

[7]

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Difference between revisions of "deLemus"

Latest revision as of 10:25, 15 December 2023

Spike Glycoprotein

Update

2023.12.01-2023.12.17

2023.11.01-2023.11.17

2023.10.06

2023.09.08-2023.09.28

2023.08.04 - 2023.08.22

RBD Mutation Profile of Latest VOIs.

2023.06.30 - 2023.07.05

2023.06.01 - 2023.06.13

2023.05.01 - 2023.05.12

2023.04.01 - 2023.04.21

2023.03.01 - 2023.03.21

2023.02.03 - 2023.02.20

2023.01.31

2023.01.17 - 2023.01.25

References

Navigation menu

Search

@@ Line 1: / Line 1: @@
-== '''<big>Current Analysis of SARS-CoV-2 from GISAID Database</big>''' ==
+__NOTOC__
+''Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins''
-The data can be accessed on https://gohkust-my.sharepoint.com/:x:/r/personal/haibinsu_ust_hk/Documents/Group%20Repository/deLemus%20project/All-Unique_GISAID-Update-0301.xlsx?d=w3175ab57e27f4f27aaf2419ffbd62a92&csf=1&web=1&e=UQIcjL
+</br>
+The dynamic epidemiology of coronavirus disease 2019 (COVID-19) since its outbreak has been a result of the continuous evolution of its etiological agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Within the first 2 years of this pandemic, the World Health Organization (WHO) has already announced 4 variants of concern (VOC), namely alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2), together with numerous variants of interest (VOI). The latest lineage to be designated a VOC would be omicron (B.1.1.529),<ref name="Karim" /> from which a diverse variant soup is generated.<ref>Callaway, E. COVID ‘variant soup’ is making winter surges hard to predict. ''Nature'' '''611,''' 213 (2022).</ref> From the original BA.1 strain of November 2021 to the most recent XBB and BQ.1 strains of late 2022,<ref name="Wang" /><ref name="European Centre" /> each omicron subvariant has successively proliferated and outcompeted its once dominant antecedent.<ref name="Del Rio" /> The emergence of all these variants has brought along many novel mutations that continue to fine-tune the fitness of the virus,<ref>Carabelli, A. M. ''et al.'' SARS-CoV-2 variant biology: Immune escape, transmission and fitness. ''Nat Rev Microbiol'' (2023). DOI: https://doi.org/10.1038/s41579-022-00841-7.</ref><ref>Witte, L. ''et al.'' Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape. ''Nat Commun'' '''14,''' 302 (2023).</ref> leading to its persistent global circulation. Recent emerging variant (EV) data retrieved from GISAID, as of 17 January 2023, has revealed that the top 4 most rapidly spreading lineages are the BA.1.1.22, CH.1.1, XBB.1.5, and BQ.1.1 variants, among which XBB.1.5 has been found to be especially prevalent in the US,<ref>Callaway, E. Coronavirus variant XBB.1.5 rises in the United States — is it a global threat? ''Nature'' '''613,''' 222 (2023).</ref> making up of more than 40% of its sequence coverage in early January 2023.
+<!--
+-->
+==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.<ref name="Jackson2021"/> 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.
-<html><iframe width="1200" height="1000" src="https://docs.google.com/spreadsheets/d/e/2PACX-1vQStZdAA6OWKgu0lNpyyqMbX_Uevr6WHX5oD38358hmrIxnF60-jrtuhwA-dkk3L30TMHWsXPoNfXsW/pubhtml?gid=0&single=true"></iframe></html>
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/Domains.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag>
+=='''Update'''==
+The identified leading mutations in 2023 are listed as follows <ref name="deLemus" />:
-== '''<big>SARS-CoV-2 Articles Collection</big>''' ==
+<tabs>
-{| class="wikitable sortable"
+<tab name="2023.12">
-|+
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-12.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
-!No
-!Name
+===2023.12.01-2023.12.17===
-!Link
+{| class="wikitable"
-!Code
 |-
-|1
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|The GISAID Database
-|https://www.gisaid.org/
-|0
 |-
-|4
+| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
-|Nexstrain SARS-CoV-2 resources
-|https://nextstrain.org/sars-cov-2/
-|0
 |-
-|14
+| <span style="color:burlywood;">'''A475V'''</span> || EG.5.1.1
-|A novel  phosphorylation site in SARS-CoV-2 nucleocapsid regulates its RNA-binding  capacity and phase separation in host cells
-|https://academic.oup.com/jmcb/advance-article/doi/10.1093/jmcb/mjac003/6510820?login=false#/
-|0
 |-
-|34
+| <span style="color:hotpink;">'''E654K'''</span> || HK.3
-|Airborne transmission of  respiratory viruses
+|}
-|https://www.science.org/doi/10.1126/science.abd9149/
-|0
+</tab>
+<tab name="2023.11">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-11.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+===2023.11.01-2023.11.17===
+{| class="wikitable"
 |-
-|36
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|SARS-CoV-2 infection in  free-ranging white-tailed deer
-|https://www.nature.com/articles/s41586-021-04353-x?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
 |-
-|41
+| <span style="color:yellowgreen;">'''N185D'''</span> || HK.3.2
-|Do childhood colds help the  body respond to COVID?
-|https://www.nature.com/articles/d41586-021-03087-0?utm_source=twt_nat&utm_medium=social&utm_campaign=nature/
-|0
 |-
-|42
+| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
-|Identification of driver genes  for critical forms of COVID-19 in a deeply phenotyped young patient cohort
-|https://www.science.org/doi/10.1126/scitranslmed.abj7521?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|0
 |-
-|43
+| <span style="color:burlywood;">'''A475V'''</span> || JF.1
-|Immune memory from SARS-CoV-2  infection in hamsters provides variant-independent protection but still  allows virus transmission
-|https://www.science.org/doi/10.1126/sciimmunol.abm3131?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|0
 |-
-|47
+| <span style="color:hotpink;">'''T572I'''</span> || FY.2
-|Naive human B cells engage the  receptor binding domain of SARS-CoV-2, variants of concern, and related  sarbecoviruses
-|https://www.science.org/doi/10.1126/sciimmunol.abl5842?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|0
 |-
-|59
+| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.16
-|Correlates of protection  against symptomatic and asymptomatic SARS-CoV-2 infection
-|https://www.nature.com/articles/s41591-021-01540-1?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|0
 |-
-|65
+| <span style="color:cornflowerblue;">'''D1153Y'''</span> || HK.3
-|Immune correlates of  protection by mRNA-1273 vaccine against SARS-CoV-2 in nonhuman primates
+|}
-|https://www.science.org/doi/full/10.1126/science.abj0299?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|0
+</tab>
+<tab name="2023.10">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-10.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+===2023.10.06===
+{| class="wikitable"
 |-
-|66
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|How do vaccinated people  spread Delta? What the science says
-|https://www.nature.com/articles/d41586-021-02187-1?utm_source=twt_nat&utm_medium=social&utm_campaign=nature/
-|0
 |-
-|72
+| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
-|Boosting stem cell immunity to  viruses
-|https://www.science.org/doi/10.1126/science.abj5673/
-|0
 |-
-|73
+| <span style="color:burlywood;">'''A475V'''</span> || GK.1
-|Targeting aging cells improves  survival
+|}
-|https://www.science.org/doi/10.1126/science.abi4474/
-|0
+</tab>
+<tab name="2023.09">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-09.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+===2023.09.08-2023.09.28===
+{| class="wikitable"
 |-
-|74
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|After the pandemic:  perspectives on the future trajectory of COVID-19
-|https://www.nature.com/articles/s41586-021-03792-w?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|2
 |-
-|87
+| <span style="color:burlywood;">'''R403K'''</span> || BA.2.86 (Pirola)
-|Hybrid immunity
-|https://www.science.org/doi/10.1126/science.abj2258/
-|0
 |-
-|93
+| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
-|How your DNA may affect  whether you get COVID-19 or become gravely ill
-|https://www.sciencenews.org/article/coronavirus-covid-how-dna-genetic-risk-infection-severe-illness/
-|0
 |-
-|95
+| <span style="color:burlywood;">'''S494P'''</span> || EG.5.1.1
-|Naturally enhanced  neutralizing breadth against SARS-CoV-2 one year after infection
-|https://www.nature.com/articles/s41586-021-03696-9?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
 |-
-|96
+| <span style="color:burlywood;">'''P521S'''</span> || XBB.1.16.15
-|How were the first treatments  for COVID identified?
-|https://www.compoundchem.com/2021/06/16/recovery-trial//
-|0
 |-
-|100
+| <span style="color:hotpink;">'''E554K'''</span> || BA.2.86 (Pirola) & FE.1
-|Antibody sugars are  bittersweet
-|https://www.science.org/doi/10.1126/science.abj0435/
-|0
 |-
-|101
+| <span style="color:hotpink;">'''Q613H'''</span> || BA.2.86 (Pirola)
-|CRISPR diagnostics
-|https://www.science.org/doi/10.1126/science.abi9335/
-|0
 |-
-|104
+| <span style="color:hotpink;">'''P621S'''</span> || BA.2.86 (Pirola)
-|Complement control for  COVID-19
-|https://www.science.org/doi/10.1126/sciimmunol.abj1014/
-|0
 |-
-|109
+| <span style="color:cornflowerblue;">'''T732I'''</span> || XBB.2.3 x XBB.1.5
-|Estimating infectiousness  throughout SARS-CoV-2 infection course
-|https://www.science.org/doi/10.1126/science.abi5273/
-|0
 |-
-|115
+| <span style="color:cornflowerblue;">'''S939F'''</span> || BA.2.86 (Pirola)
-|Face masks effectively limit  the probability of SARS-CoV-2 transmission
-|https://www.science.org/doi/10.1126/science.abg6296/
-|0
 |-
-|126
+| <span style="color:cornflowerblue;">'''V1264L'''</span> || CK.1.1
-|How COVID broke the evidence  pipeline
+|}
-|https://www.nature.com/articles/d41586-021-01246-x?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
+</tab>
+<tab name="2023.08">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-08.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.08.04 - 2023.08.22===
+{| class="wikitable"
 |-
-|131
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|It’s time to consider a patent  reprieve for COVID vaccines
-|https://www.nature.com/articles/d41586-021-00863-w?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
 |-
-|132
+| <span style="color:yellowgreen;">'''N185D'''</span> || XBB.1.5
-|SARS-CoV-2 transmission  without symptoms
-|https://www.science.org/doi/10.1126/science.abf9569/
-|0
 |-
-|135
+| <span style="color:yellowgreen;">'''L212S'''</span> || FY.4.2
-|Five reasons why COVID herd  immunity is probably impossible
-|https://www.nature.com/articles/d41586-021-00728-2?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
 |-
-|137
+| <span style="color:burlywood;">'''V445A'''</span> || XBC.1.6
-|Rare COVID reactions might  hold key to variant-proof vaccines
-|https://www.nature.com/articles/d41586-021-00722-8?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
 |-
-|138
+| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
-|Increased mortality in  community-tested cases of SARS-CoV-2 lineage B.1.1.7
-|https://www.nature.com/articles/s41586-021-03426-1?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|0
 |-
-|139
+| <span style="color:burlywood;">'''F456L'''</span> || EG.5.1 (Eris)
-|Cell Press Coronavirus  Resource Hub
-|https://www.cell.com/COVID-19/
-|0
 |-
-|140
+| <span style="color:hotpink;">'''E554Q'''</span> || XBB.1.5.18
-|Nexstrain SARS-CoV-2 resources
-|https://nextstrain.org/sars-cov-2//
-|0
 |-
-|141
+| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.16
-|CoVariants
-|https://covariants.org//
-|0
 |-
-|142
+| <span style="color:cornflowerblue;">'''T883I'''</span> || XBB.1.16
-|The GISAID Database
+|}
-|https://www.gisaid.org//
+''*The reported mutations of detected variants are from Cov-Lineages<ref name="Cov-Lineages" />''
-|0
+</br>
+===<big>RBD Mutation Profile of Latest VOIs.</big>===
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-08_VarRBD.png" alt="test for htmltag img" class="wikimg" style="display: block;width:65%;margin-left: auto;margin-right: auto;"></htmltag>
+</tab>
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+<html>
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+        });
+    </script>
+</html>
+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.06.30 - 2023.07.05===
+{| class="wikitable"
 |-
-|143
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|UniProt (Data Retrieving)
-|https://www.uniprot.org/uploadlists//
-|0
 |-
-|161
+| <span style="color:yellowgreen;">'''H146K'''</span> || FL.2.3 (XBB.1.9.1.2.3)
-|Multiple Sequence Alignment
-|https://www.ebi.ac.uk/Tools/msa/clustalo//
-|0
 |-
-|6
+| <span style="color:burlywood;">'''S446N'''</span> || FL.19
-|InterPro (List of Protein  Family)
-|https://www.ebi.ac.uk/interpro//
-|0
 |-
-|7
+| <span style="color:burlywood;">'''F456L'''</span> || XBF
-|More evidence suggests  COVID-19 was in the US by Christmas 2019
+|}
-|https://apnews.com/article/more-evidence-covid-in-US-by-Christmas-2019-11346afc5e18eee81ebcf35d9e6caee2/
-|0
+</tab>
+<tab name="2023.06">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-06.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+<html>
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+</html>
+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.06.01 - 2023.06.13===
+{| class="wikitable"
 |-
-|9
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|A COVID Vaccine for All
-|https://www.scientificamerican.com/article/a-covid-vaccine-for-all//
-|1
 |-
-|10
+| <span style="color:burlywood;">'''F490P'''</span> || XBB.1.9.1
-|Single-cell immunology of  SARS-CoV-2 infection
-|https://www.nature.com/articles/s41587-021-01131-y?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|1
 |-
-|11
+| <span style="color:hotpink;">'''E554K'''</span> || XBB.1.9.1 (sublineage)
-|Innate immunological pathways  in COVID-19 pathogenesis
-|https://www.science.org/doi/10.1126/sciimmunol.abm5505?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|15
+| <span style="color:hotpink;">'''Q675K'''</span> || XBB.1.22.1
-|Early non-neutralizing,  afucosylated antibody responses are associated with COVID-19 severity
-|https://www.science.org/doi/10.1126/scitranslmed.abm7853?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|22
+| <span style="color:cornflowerblue;">'''L858I'''</span> || CH.1.1.1
-|COVID-19 vaccine side effects:  The positives about feeling bad
+|}
-|https://www.science.org/doi/10.1126/sciimmunol.abj9256?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
+</tab>
+<tab name="2023.05">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-05.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+<html>
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+    </script>
+</html>
+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.05.01 - 2023.05.12===
+{| class="wikitable"
 |-
-|24
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|COVID-19 vaccine breakthrough  infections
-|https://www.science.org/doi/10.1126/science.abl8487?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|25
+| <span style="color:burlywood;">'''F456L'''</span> || FD.1.1 & EG.5.1 (2023.08)
-|B.1.1.529 escapes the majority  of SARS-CoV-2 neutralizing antibodies of diverse epitopes
-|https://www.biorxiv.org/content/10.1101/2021.12.07.470392v1/
-|1
 |-
-|26
+| <span style="color:burlywood;">'''S494P'''</span> || XBB.2.3 & XBB.1.1
-|Immune dysregulation and  immunopathology induced by SARS-CoV-2 and related coronaviruses — are we our  own worst enemy?
-|https://www.nature.com/articles/s41577-021-00656-2?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|1
 |-
-|32
+| <span style="color:hotpink;">'''T572I'''</span> || FY.1 ( XBB.1.22.1.1 )
-|Robust immune responses are  observed after one dose of BNT162b2 mRNA vaccine dose in SARS-CoV-2  experienced individuals
+|}
-|https://www.science.org/doi/10.1126/scitranslmed.abi8961?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
+''*The reported mutations of detected variants are from GISAID''
-|1
+</tab>
+<tab name="2023.04">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-04.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+<html>
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+    </script>
+</html>
+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.04.01 - 2023.04.21===
+{| class="wikitable"
 |-
-|33
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|mRNA vaccines induce durable  immune memory to SARS-CoV-2 and variants of concern
-|https://www.science.org/doi/10.1126/science.abm0829?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|39
+| <span style="color:yellowgreen;">'''H146K'''</span> || XBB.1.5 & XBB.1.16
-|Amilorides inhibit SARS-CoV-2  replication in vitro by targeting RNA structures
-|https://www.science.org/doi/10.1126/sciadv.abl6096/
-|1
 |-
-|44
+| <span style="color:yellowgreen;">'''M153I'''</span> || XBB.2.3.3
-|Allelic variation in class I  HLA determines CD8+ T cell repertoire shape and cross-reactive memory  responses to SARS-CoV-2
-|https://www.science.org/doi/10.1126/sciimmunol.abk3070?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|48
+| <span style="color:yellowgreen;">'''E180V'''</span> || XBB.1.16
-|A broadly cross-reactive  antibody neutralizes and protects against sarbecovirus challenge in mice
-|https://www.science.org/doi/10.1126/scitranslmed.abj7125?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|50
+| <span style="color:burlywood;">'''K444R'''</span> || XBB.1.5
-|Scent of a vaccine
-|https://www.science.org/doi/10.1126/science.abg9857?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|52
+| <span style="color:burlywood;">'''T478R'''</span> || XBB.1.16, XBB.1.5, CH.1.1.2 & XBB.2.3
-|A potent SARS-CoV-2  neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster  model of COVID-19
-|https://www.nature.com/articles/s41467-021-25480-z/
-|1
 |-
-|53
+| <span style="color:burlywood;">'''F490P'''</span> || XBB.2.6
-|High genetic barrier to  SARS-CoV-2 polyclonal neutralizing antibody escape
-|https://www.nature.com/articles/s41586-021-04005-0?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|1
 |-
-|54
+| <span style="color:burlywood;">'''S494P'''</span> || XBB.1.5
-|Bispecific antibodies  targeting distinct regions of the spike protein potently neutralize  SARS-CoV-2 variants of concern
-|https://www.science.org/doi/10.1126/scitranslmed.abj5413?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|58
+| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.16
-|Broad betacoronavirus  neutralization by a stem helix–specific human antibody
-|https://www.science.org/doi/10.1126/science.abj3321?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|61
+| <span style="color:hotpink;">'''P621S'''</span> || XBB.2.3
-|Chimeric spike mRNA vaccines  protect against Sarbecovirus challenge in mice
-|https://www.science.org/doi/10.1126/science.abi4506?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|1
 |-
-|62
+| <span style="color:hotpink;">'''A688V'''</span> || XAY.1.1.1
-|Ultrapotent antibodies against  diverse and highly transmissible SARS-CoV-2 variants
+|}
-|https://www.science.org/doi/10.1126/science.abh1766/
-|1
+</tab>
+<tab name="2023.03">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-03.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+<html>
+    <style>
+        .molstar {
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+</html>
+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.03.01 - 2023.03.21===
+{| class="wikitable"
 |-
-|63
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|Cross-reactive antibodies  against human coronaviruses and the animal coronavirome suggest diagnostics  for future zoonotic spillovers
-|https://www.science.org/doi/10.1126/sciimmunol.abe9950/
-|1
 |-
-|64
+| <span style="color:yellowgreen;">'''Y248S'''</span> || BQ.1
-|Neutralizing activity of  Sputnik V vaccine sera against SARS-CoV-2 variants
-|https://www.nature.com/articles/s41467-021-24909-9?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|1
 |-
-|67
+| <span style="color:burlywood;">'''F490P'''</span> || XBB.1 & XBB.1.5
-|Broad sarbecovirus  neutralization by a human monoclonal antibody
-|https://www.nature.com/articles/s41586-021-03817-4?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|1
 |-
-|69
+| <span style="color:hotpink;">'''T547I'''</span> || XBB.1.16
-|Rapid and stable mobilization  of CD8+ T cells by SARS-CoV-2 mRNA vaccine
-|https://www.nature.com/articles/s41586-021-03841-4?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|1
 |-
-|70
+| <span style="color:hotpink;">'''Q613H'''</span> || DV.1, CH.1.1.1 & CH.1.1.17
-|Immune responses against  SARS-CoV-2 variants after heterologous and homologous ChAdOx1  nCoV-19/BNT162b2 vaccination
-|https://www.nature.com/articles/s41591-021-01449-9?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|1
 |-
-|71
+| <span style="color:hotpink;">'''I666V'''</span> || XBB.1.5
-|Systems vaccinology of the  BNT162b2 mRNA vaccine in humans
-|https://www.nature.com/articles/s41586-021-03791-x?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|1
 |-
-|75
+| <span style="color:cornflowerblue;">'''V1264L'''</span> || CH.1.1
-|A recombinant spike protein  subunit vaccine confers protective immunity against SARS-CoV-2 infection and  transmission in hamsters
+|}
-|https://www.science.org/doi/10.1126/scitranslmed.abg1143/
-|1
+</tab>
+<tab name="2023.02">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-02.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
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+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.02.03 - 2023.02.20===
+{| class="wikitable"
 |-
-|76
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|Masitinib is a broad  coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2
-|https://www.science.org/doi/full/10.1126/science.abg5827/
-|1
 |-
-|83
+| <span style="color:yellowgreen;">'''K147I'''</span> || XBB.1.5.2.1
-|Engineered single-domain  antibodies tackle COVID variants
-|https://www.nature.com/articles/d41586-021-01721-5?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|1
 |-
-|84
+| <span style="color:yellowgreen;">'''Y248S'''</span> || BQ.1.1.43
-|CD8+ T cells specific for  conserved coronavirus epitopes correlate with milder disease in patients with  COVID-19
-|https://www.science.org/doi/10.1126/sciimmunol.abg5669/
-|1
 |-
-|89
+| <span style="color:burlywood;">'''S494P'''</span> || XBB.1.5
-|Evidence for increased  breakthrough rates of SARS-CoV-2 variants of concern in  BNT162b2-mRNA-vaccinated individuals
-|https://www.nature.com/articles/s41591-021-01413-7?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|1
 |-
-|92
+| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.9.2 & XBB.2.4
-|Artificial Proteins Never Seen  in the Natural World Are Becoming New COVID Vaccines and Medicines
-|https://www.scientificamerican.com/article/artificial-proteins-never-seen-in-the-natural-world-are-becoming-new-covid-vaccines-and-medicines//
-|1
 |-
-|94
+| <span style="color:hotpink;">'''P612S'''</span> || XBF
-|Drug-induced phospholipidosis  confounds drug repurposing for SARS-CoV-2
-|https://www.science.org/doi/full/10.1126/science.abi4708/
-|1
 |-
-|98
+| <span style="color:hotpink;">'''T678I'''</span> || BA.2.75 x BA.5
-|Impact of vaccination on new  SARS-CoV-2 infections in the United Kingdom
-|https://www.nature.com/articles/s41591-021-01410-w?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|1
 |-
-|103
+| <span style="color:hotpink;">'''N679R'''</span> || CH.1.1
-|Immunogenicity of Ad26.COV2.S  vaccine against SARS-CoV-2 variants in humans
-|https://www.nature.com/articles/s41586-021-03681-2?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|1
 |-
-|106
+| <span style="color:cornflowerblue;">'''P1162S'''</span> || XBK.1
-|BNT162b2 vaccine induces  neutralizing antibodies and poly-specific T cells in humans
+|}
-|https://www.nature.com/articles/s41586-021-03653-6?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
+''*The reported mutations of detected variants are from GISAID<ref name="GISAID" />''
-|1
+</tab>
+<tab name="2023.01">
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-01.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+<html>
+    <style>
+        .molstar {
+            position: relative;
+            width: 80%;
+            padding-bottom: 56.25%;
+        }
+    </style>
+    <link rel="stylesheet" type="text/css" href="https://molstar.org/viewer/molstar.css" />
+    <script type="text/javascript" src="https://molstar.org/viewer/molstar.js"></script>
+    <div id="viewer-1" class="molstar" style="display: block; margin-left:auto; margin-right:auto; padding-bottom: 40%;"></div>
+    <script type="text/javascript">
+        molstar.Viewer.create('viewer-1', {
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+            layoutShowControls: false,
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+            viewer.loadSnapshotFromUrl('https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/pdb/LM_latest.molx', 'molx');
+        });
+    </script>
+</html>
+* Generated 3D structure of spike protein with highlighted leading mutations (AlphaFold2, colab version 2022).
+<big>Here are the recently confirmed leading mutations.</big>
+===2023.01.31===
+{| class="wikitable"
 |-
-|108
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|SARS-CoV-2 variants of concern  partially escape humoral but not T cell responses in COVID-19 convalescent  donors and vaccine recipients
-|https://www.science.org/doi/10.1126/sciimmunol.abj1750/
-|1
 |-
-|112
+| <span style="color:burlywood;">'''V445A'''</span> || BQ.1.1
-|Shared B cell memory to  coronaviruses and other pathogens varies in human age groups and tissues
-|https://www.science.org/doi/10.1126/science.abf6648/
-|1
 |-
-|114
+| <span style="color:cornflowerblue;">'''T883I'''</span> || BQ.1.1
-|A network analysis of COVID-19  mRNA vaccine patents
+|}
-|https://www.nature.com/articles/s41587-021-00912-9?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
+===2023.01.17 - 2023.01.25===
-|1
+{| class="wikitable"
 |-
-|117
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants
-|High titers and low  fucosylation of early human anti–SARS-CoV-2 IgG promote inflammation by  alveolar macrophages
-|https://www.science.org/doi/10.1126/scitranslmed.abf8654/
-|1
 |-
-|119
+| <span style="color:yellowgreen;">'''H146- / H146K'''</span> || BQ.1.1 / XBB.1.5
-|COVID-19–related anosmia is  associated with viral persistence and inflammation in human olfactory  epithelium and brain infection in hamsters
-|https://www.science.org/doi/10.1126/scitranslmed.abf8396/
-|1
 |-
-|121
+| <span style="color:burlywood;">'''F486A'''</span> || BQ.1.1
-|How Pfizer Makes Its Covid-19  Vaccine
-|https://www.nytimes.com/interactive/2021/health/pfizer-coronavirus-vaccine.html?smid=tw-share/
-|1
 |-
-|123
+| <span style="color:hotpink;">'''E583D'''</span> || BQ.1.1
-|A broadly neutralizing  antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2  variants in mice
-|https://www.biorxiv.org/content/10.1101/2021.04.27.441655v1/
-|1
 |-
-|124
+| <span style="color:hotpink;">'''Q613H'''</span> ||  BQ.1.1
-|Adjuvanting a subunit COVID-19  vaccine to induce protective immunity
-|https://www.nature.com/articles/s41586-021-03530-2/
-|1
 |-
-|129
+| <span style="color:cornflowerblue;">'''S939F'''</span> || BQ.1.1
-|The SARS-CoV-2 mRNA-1273  vaccine elicits more RBD-focused neutralization, but with broader antibody  binding within the RBD
+|}
-|https://www.biorxiv.org/content/10.1101/2021.04.14.439844v1/
-|1
+</tab>
+</tabs>
+<!--
+===2023.01.31===
+{| class="wikitable"
 |-
-|136
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants !! Conformation
-|The neutralizing antibody,  LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates
-|https://www.science.org/doi/10.1126/scitranslmed.abf1906/
-|1
 |-
-|145
+| V445A || BQ.1.1 || Amino acid site located at an RBD epitope<ref name="Weisblum_eLife"/> ; Mutation reduces neutralization by antibody <ref name="CellRep20220517"/>
-|Immunity to SARS-CoV-2  variants of concern
+|}
-|https://www.science.org/doi/10.1126/science.abg7404/
+===2023.01.17 - 2023.01.25===
-|1
+{| class="wikitable"
 |-
-|146
+! Outlined Mutations !! Confirmed in VOC/Emerging Variants !! Conformation
-|Lilly COVID-19 Antibody  Combination Shows 87% Risk Reduction in Phase III Trial
-|https://www.genengnews.com/news/lilly-covid-19-antibody-combination-shows-87-risk-reduction-in-phase-iii-trial//
-|1
 |-
-|148
+| H146-/K || BQ.1.1, XBB.1.5 || Amino acid site recognized by mAbs targeting NTD<ref name=":3"/>
-|Perspectives on therapeutic  neutralizing antibodies against the Novel Coronavirus SARS-CoV-2
-|https://www.ijbs.com/v16p1718.htm/
-|1
 |-
-|149
+| E583D || BQ.1.1 || Viral functions to be confirmed by further investigation
-|Targeting the SARS-CoV-2-spike  protein: from antibodies to miniproteins and peptides
-|https://pubs.rsc.org/en/content/articlelanding/2021/md/d0md00385a#!divAbstract/
-|1
 |-
-|151
+| Q613H ||  BQ.1.1 || Speculate to enhance replicative fitness and transmissibility due to close proximity to D614G ; Potential functions to be elucidated<ref name=":0"/><ref name="Bugembe"/>
-|SARS-CoV-2 501Y.V2 escapes  neutralization by South African COVID-19 donor plasma
-|https://www.nature.com/articles/s41591-021-01285-x/
-|1
 |-
-|153
+| S939F || BQ.1.1 || Destabilize both pre-fusion and post-fusion S2 conformation<ref name="Olivie"/> ; Capable to enhance infectivity and modulate T-cell immune response when combined with D614G<ref name="LiImpactCell"/><ref name="Donzelli"/>
-|A therapeutic neutralizing  antibody targeting receptor binding domain of SARS-CoV-2 spike protein
+|}
-|https://www.nature.com/articles/s41467-020-20602-5/
-|1
+<big>The following leading mutations call for special attention with respect to the upcoming variants.</big>
+==NTD==
+{| class="wikitable"
 |-
-|2
+! Outlined Mutations !! Conformation
-|Antibody responses to the  BNT162b2 mRNA vaccine in individuals previously infected with SARS-CoV-2
-|https://www.nature.com/articles/s41591-021-01325-6/
-|1
 |-
-|12
+| A27P || An antigenic site targeted by the group 3 antibody C1717<ref name=":2" />
-|The neutralizing antibody,  LY-CoV555, protects against SARS-CoV-2 infection in non-human primates
-|https://stm.sciencemag.org/content/early/2021/04/05/scitranslmed.abf1906.full/
-|1
 |-
-|35
+| K147- || Involved in interacting with multiple monoclonal antibodies<ref name=":4" /> ; Mutation to threonine (K147T) at this site promotes immune evasion<ref name=":3" />
-|Evolutionary trajectory of  SARS-CoV-2 and emerging variants
-|https://virologyj.biomedcentral.com/articles/10.1186/s12985-021-01633-w/
-|2
 |-
-|45
+| N164K || Functional impact to be confirmed in future investigation.
-|Dynamic Expedition of Leading  Mutations in SARS-CoV-2 Spike Glycoproteins
-|https://www.biorxiv.org/content/10.1101/2021.12.29.474427v1/
-|2
 |-
-|46
+| Q183G || Interactions with surface glycoconjugates mediate the viral attachment<ref name="Sun_Glycobio2021" /> ; Caused a loss of an amide group; May abrogate the hydrogen bond between the amino acid and the carboxylic group of surface sialosides<ref name="Buchanan" />
-|Mapping the proteo-genomic  convergence of human diseases
-|https://www.science.org/doi/10.1126/science.abj1541?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|2
 |-
-|49
+| N185D || Functional impact to be confirmed in future investigation.
-|From Alpha to Epsilon:  Consortium study illuminates surfaces of Spike most resistant to antibody  escape
-|https://www.lji.org/news-events/news/post/from-alpha-to-epsilon-consortium-study-illuminates-surfaces-of-spike-most-resistant-to-antibody-escape//
-|2
 |-
-|91
+|H245N
-|Defining variant-resistant  epitopes targeted by SARS-CoV-2 antibodies: A global consortium study
+|Located in the supersite loop of the NTD antigenic supersite for antibodies SLS28 and S2X333<ref name=":4" /><ref name=":3" /> ; Caused a loss of a positive charge ; Introduces an NXS sequon (<sub>245</sub>NRS<sub>247</sub>) for ''N''-glycosylation
-|https://www.science.org/doi/10.1126/science.abh2315#.YVFR4Ob9en8.twitter/
-|2
 |-
-|99
+|G252V
-|The biological and clinical  significance of emerging SARS-CoV-2 variants
+|Site is critical for the binding of human antibody COV2-3439<ref>Suryadevara N. ''et al.'' An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer. ''J Clin Invest'' '''132,''' 159062 (2022).</ref>
-|https://www.nature.com/articles/s41576-021-00408-x?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|2
 |-
-|152
+|G257D
-|Evolution of a virus-like  architecture and packaging mechanism in a repurposed bacterial protein
+|Located in the supersite loop of the NTD antigenic supersite for antibodies SLS28 and S2X333<ref name=":4" /><ref name=":3" /> ; Caused a gain of negative charge
-|https://www.science.org/doi/10.1126/science.abg2822/
-|2
 |-
-|156
+|A262S
-|Spike mutation T403R allows  bat coronavirus RaTG13 to use human ACE2
+|Enhance the utilization of ACE2 in numerous mammals<ref name="Wang_JMedVirol2022" /> ; May increase interspecies and intraspecies transmissibility
-|https://www.biorxiv.org/content/10.1101/2021.05.31.446386v1/
+|}
-|2
+==RBD==
+{| class="wikitable"
 |-
-|16
+! Outlined Mutations !! Conformation
-|Evolution of antibody immunity  to SARS-CoV-2
-|https://www.nature.com/articles/s41586-021-03207-w/
-|2
 |-
-|17
+| R346I/S || Possibly lead to immune evasion due to the disruption of class 3 antibodies binding site<ref name="Gaebler"/> <ref name="WangQ_LancetID2022"/>
-|Evolution of antibody immunity  to SARS-CoV2
-|https://www.nature.com/articles/s41586-021-03207-w/
-|2
 |-
-|19
+| K444N/R || Escape mutations for covalescent plasma<ref name="Weisblum_eLife"/>
-|Innovative X-ray imaging shows  COVID-19 can cause vascular damage to the heart
-|https://medicalxpress.com/news/2021-12-x-ray-imaging-covid-vascular-heart.html/
-|3
 |-
-|21
+| G446V || Substantially decreases the neutralization titers of plasma<ref name="Greaney"/>
-|Bacteriophage self-counting in  the presence of viral replication
-|https://www.pnas.org/content/118/51/e2104163118/
-|3
 |-
-|37
+| N450D || Results in antibody resistance<ref name="Cong_CellHM2021"/>
-|Structural analysis of  receptor binding domain mutations in SARS-CoV-2 variants of concern that  modulate ACE2 and antibody binding
-|https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01652-1#.YbBFgwgnRMI.twitter/
-|3
 |-
-|40
+| E484R/S || A site of mutation being reported in multiple variants, mutation at this site could harbor escape mutations that impede the binding and neutralization ability of antibodies<ref name=":0"/> <ref name="Greaney"/>
-|Structural basis for continued  antibody evasion by the SARS-CoV-2 receptor binding domain
-|https://www.science.org/doi/10.1126/science.abl6251?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|3
 |-
-|51
+| F490P || Mutation at this site enables antibody escape over mAb COV2-2479, COV2-2050, COV2-2096 based on DMS study.<ref name="Greaney"/>
-|Ensemble cryo-electron  microscopy reveals conformational states of the nsp13 helicase in the  SARS-CoV-2 helicase replication-transcription complex
-|https://www.biorxiv.org/content/10.1101/2021.11.10.468168v1/
-|3
 |-
-|56
+| S494P || This mutation persistently shows up in an immunocompromised patient of COVID-19, which was treated various drugs and antibodies e.g. remdesivir, intravenous immunoglobulin, etc.<ref name="Choi"/>
-|Membrane fusion and immune  evasion by the spike protein of SARS-CoV-2 Delta variant
+|}
-|https://www.science.org/doi/10.1126/science.abl9463?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|3
+==CTDs==
+{| class="wikitable"
 |-
-|57
+! Outlined Mutations !! Conformation
-|Structural basis of mismatch  recognition by a SARS-CoV-2 proofreading enzyme
-|https://www.science.org/doi/full/10.1126/science.abi9310?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|3
 |-
-|78
+| T547I || Functional impact to be confirmed in future investigation.
-|Water-Triggered, Irreversible  Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid  State to Aqueous Solution
-|https://pubs.acs.org/doi/10.1021/jacs.1c05301/
-|3
 |-
-|79
+| T572I || Functional impact to be confirmed in future investigation.
-|A glycan gate controls opening  of the SARS-CoV-2 spike protein
-|https://www.nature.com/articles/s41557-021-00758-3?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|3
 |-
-|80
+| D574V || Located at the CTD1 region, substitution to an electrically neutral valine residue permits the endosomal entry efficiency and immune evasion ability of SARS-CoV-2.<ref name="Zhou_CellHM2020"/>
-|The antiandrogen enzalutamide  downregulates TMPRSS2 and reduces cellular entry of SARS-CoV-2 in human lung  cells
-|https://www.nature.com/articles/s41467-021-24342-y?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|3
 |-
-|81
+| E619Q || Functional impact to be confirmed in future investigation.
-|Identification of  SARS-CoV-2–induced pathways reveals drug repurposing strategies
-|https://www.science.org/doi/10.1126/sciadv.abh3032/
-|3
 |-
-|82
+| E658S || Functional impact to be confirmed in future investigation.
-|Mn2+ coordinates  Cap-0-RNA to align substrates for efficient 2′-O-methyl transfer by  SARS-CoV-2 nsp16
-|https://www.science.org/doi/10.1126/scisignal.abh2071/
-|3
 |-
-|85
+| I666V || Functional impact to be confirmed in future investigation.
-|A potential interaction  between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors
-|https://www.cell.com/biophysj/fulltext/S0006-3495(21)00146-6/
-|3
 |-
-|86
+| S673G || Functional impact to be confirmed in future investigation.
-|Structural basis of ribosomal  frameshifting during translation of the SARS-CoV-2 RNA genome
-|https://www.science.org/doi/10.1126/science.abf3546/
-|3
 |-
-|88
+| P681Y || Located at the C-terminal of the CTD2, this substitution can diminish the cleavage efficiency of the S1/S2 interface because the bulky nature of tyrosine hinders the binding of furin to the cleavage loop.<ref name="Henrich"/><ref name="Tian_2009"/></big>
-|Protective efficacy of  Ad26.COV2.S against SARS-CoV-2 B.1.351 in macaques
-|https://www.nature.com/articles/s41586-021-03732-8?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|3
 |-
-|90
+| I688V || Functional impact to be confirmed in future investigation.
-|Cryo-EM structure of  SARS-CoV-2 ORF3a in lipid nanodiscs
+|}
-|https://www.nature.com/articles/s41594-021-00619-0?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
+==S2==
-|3
+{| class="wikitable"
 |-
-|102
+! Outlined Mutations !! Conformation
-|A multi-omics investigation of  the composition and function of extracellular vesicles along the temporal  trajectory of COVID-19
-|https://www.nature.com/articles/s42255-021-00425-4?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
-|3
 |-
-|105
+| D796H || Located in S2 region, the single aspartic acid-to-histidine substitution was found to enhance the neutralization resistance of the spike glycoprotein in a chronical infection patient.<ref name="KempCIP" /></big>
-|Improving SARS-CoV-2  structures: Peer review by early coordinate release
+|}
-|https://www.cell.com/biophysj/fulltext/S0006-3495(21)00046-1/
-|3
+== References ==
+<references>
+<ref name="XBB.1.5">Yue, C. ''et al''. Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion. Preprint at https://www.biorxiv.org/content/10.1101/2023.01.03.522427v2 (2023).</ref>
+<ref name=":4">Cao, Y. ''et al.'' Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. ''Nature'' (2022). DOI:10.1038/s41586-022-05644-7</ref>
+<ref name="Zahradník">Zahradník, J. ''et al.'' SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. ''Nat Microbiol'' '''6,''' 1188 (2021).</ref>
+<ref name="Makowski">Makowski, E. K., Schardt, J. S., Smith, M. D. & Tessier, P. M. Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape. ''PLOS Comput Biol'' '''18,''' (2022).</ref>
+<ref name=":0">Qu, P. ''et al.'' Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant. ''Cell Host Microbe'' '''30,''' 1518 (2022).</ref>
+<ref name=":2">Tamura, T. ''et al.'' Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two omicron subvariants. Preprint at https://www.biorxiv.org/content/10.1101/2022.12.27.521986v1 (2022).</ref>
+<ref name=":3">Wang, Q. ''et al.'' Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. ''Cell'' '''186,''' 279 (2023).</ref>
+<ref name=":1">Qu, P. ''et al.'' Enhanced neutralization resistance of SARS-CoV-2 omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. ''Cell Host Microbe'' '''31,''' 9 (2023).</ref>
+<ref name="Tuekprakhon">Tuekprakhon, A. ''et al.'' Antibody escape of SARS-CoV-2 omicron BA.4 and BA.5 from Vaccine and BA.1 Serum. ''Cell'' '''185,''' 2422 (2022).</ref>
+<ref name="Wang">Wang, Q. ''et al.'' Antibody evasion by SARS-CoV-2 omicron subvariants BA.2.12.1, BA.4 and BA.5. ''Nature'' '''608,''' 603 (2022).</ref>
+</references>
+==Summary==
+<tabs>
+<tab name="NTD"><htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/NTD.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag></tab>
+<tab name="RBD"><htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/RBD.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag></tab>
+<tab name="CTDs"><htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/CTDs.png" alt="test for htmltag img" class="wikimg" style="display:block;width:70%;margin-left: auto;margin-right: auto;"></htmltag></tab>
+<tab name="S2"><htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/S2.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag></tab>
+</tabs>
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/NTD.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag>
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/RBD.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag>
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/CTDs.png" alt="test for htmltag img" class="wikimg" style="display:block;width:70%;margin-left: auto;margin-right: auto;"></htmltag>
+<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/S2.png" alt="test for htmltag img" class="wikimg" style="display: block;width:70%;margin-left: auto;margin-right: auto;"></htmltag>
+== '''Deep Mutational Scanning Data''' ==
+<big>The RBD-ACE2 binding data</big><ref>Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE Jr, Bloom JD. Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host Microbe. 2021 Jan 13;29(1):44-57.e9. doi: 10.1016/j.chom.2020.11.007. Epub 2020 Nov 19. PMID: 33259788; PMCID: PMC7676316.</ref> <big>showed that R346S, N354S, E484R and S494P are the mutations lead to increased binding affinity in all the 5 background sequence.</big>
+{| class="wikitable"
+|+
+RBD-ACE2 binding affinity
+|'''Unique  Mutations'''
+|'''Date'''
+|'''Wuhan'''
+|'''Alpha'''
+|'''Beta'''
+|'''Eta'''
+|'''Delta'''
 |-
-|107
+|'''R346S'''
-|Cooperative multivalent  receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core
+|2023.01
-|https://www.biorxiv.org/content/10.1101/2021.05.24.445443v2/
+|0.12
-|3
+|0.14
+|0.07
+|0.03
+|0.11
 |-
-|110
+|'''N354S'''
-|Revealing the spike's real  shape
+|2023.05
-|https://www.science.org/content/blog-post/revealing-spike-s-real-shape/
+|0.03
-|3
+|0.01
+|0.04
+|0.32
+|0.02
 |-
-|113
+|'''E484R'''
-|SARS-CoV-2 gene content and  COVID-19 mutation impact by comparing 44 Sarbecovirus genomes
+|2023.01
-|https://www.nature.com/articles/s41467-021-22905-7?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_NRJournals/
+|0.06
-|3
+|0.04
+|  -
+|  -
+|0.11
 |-
-|116
+|'''S494P'''
-|X-ray screening identifies  active site and allosteric inhibitors of SARS-CoV-2 main protease
+|2023.01
-|https://www.science.org/doi/10.1126/science.abf7945/
+|0.33
-|3
+|0.18
-|-
+|0.13
-|118
+|0.14
-|Viral genomes reveal patterns  of the SARS-CoV-2 outbreak in Washington State
+|0.06
-|https://www.science.org/doi/10.1126/scitranslmed.abf0202/
+|}
-|3
+<big>Immune escape data</big><ref>Tyler N. Starr., et al., Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution.''Science''377,420-424(2022).DOI:10.1126/science.abo7896</ref> <big>shows that the escape ability of R346S, V445A, G446I, and E484R against certain antibodies exceeds 90% mutations.</big>
-|-
+{| class="wikitable"
-|120
+|+
-|COVID-19 tissue atlases reveal  SARS-CoV-2 pathology and cellular targets
+Immune Escaping
-|https://www.nature.com/articles/s41586-021-03570-8?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
+|'''Unique  Mutations'''
-|3
+|'''Date'''
-|-
+|'''Antybody1'''
-|125
+|'''Antybody2'''
-|Structural biology in the time  of COVID-19: perspectives on methods and milestones
+|'''Antybody3'''
-|https://journals.iucr.org/m/issues/2021/03/00/mf5052/index.html/
+|'''Antybody4'''
-|3
+|'''Antybody5'''
-|-
-|127
-|Massively Multiplexed Affinity  Characterization of Therapeutic Antibodies Against SARS-CoV-2 Variants
-|https://www.biorxiv.org/content/10.1101/2021.04.27.440939v1/
-|3
 |-
-|128
+|'''R346S'''
-|Fine-tuning the Spike: Role of  the nature and topology of the glycan shield in the structure and dynamics of  the SARS-CoV-2 S
+|2023.01
-|https://www.biorxiv.org/content/10.1101/2021.04.01.438036v2/
+|COV2-2082
-|3
+|COV2-2096
-|-
+|COV2-2479
-|133
+|COV2-2832
-|Identification of lectin  receptors for conserved SARS-CoV-2 glycosylation sites
-|https://www.biorxiv.org/content/10.1101/2021.04.01.438087v1/
-|3
-|-
-|134
-|Electrostatic interactions  between the SARS-CoV-2 virus and a charged electret fibre
-|https://pubs.rsc.org/en/content/articlelanding/2021/sm/d1sm00232e/
-|3
-|-
-|144
-|How SARS-CoV-2’s Sugar-Coated  Shield Helps Activate the Virus
-|https://www.biophysics.org/news-room/how-sars-cov-2s-sugar-coated-shield-helps-activate-the-virus/
-|3
-|-
-|147
-|Structural basis for  backtracking by the SARS-CoV-2 replication-transcription complex
-|https://www.biorxiv.org/content/10.1101/2021.03.13.435256v1/
-|3
-|-
-|155
-|The emerging plasticity of  SARS-CoV-2
-|https://science.sciencemag.org/content/371/6536/1306.full/
-|3
-|-
-|157
-|Prospective mapping of viral  mutations that escape antibodies used to treat COVID-19
-|https://science.sciencemag.org/content/371/6531/850/
-|3
-|-
-|3
-|Identification of lection  receptor for conserved SARS-C0V-2 glycosilation
-|https://www.biorxiv.org/content/10.1101/2021.04.01.438087v1/
-|3
-|-
-|5
-|Computational epitope map of  SARS-CoV-2 spike protein
-|https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008790/
-|3
-|-
-|8
-|Activity of convalescent and  vaccine serum against SARS-CoV-2 Omicron
-|https://www.nature.com/articles/s41586-022-04399-5#Echobox=1641674359/
-|4
-|-
-|13
-|Structural basis of Omicron  neutralization by affinity-matured public antibodies
-|https://www.biorxiv.org/content/10.1101/2022.01.03.474825v1/
-|4
-|-
-|18
-|The hyper-transmissible  SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine  escape and a switch in cell entry mechanism
-|https://www.gla.ac.uk/media/Media_829360_smxx.pdf/
-|4
-|-
-|20
-|Exponential growth, high  prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta  variant
-|https://www.science.org/doi/10.1126/science.abl9551?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|4
-|-
-|23
-|CryoEM structure of Omicron  (B.1.1.529) variant spike protein in complex with human ACE2 reveals new salt  bridges formed by mutated residues R498 and R493 in the RBD and residues D38  and E35, respectively, in ACE2.
-|https://twitter.com/cryoem_UBC/status/1471390036851511299/
-|4
-|-
-|27
-|SARS-CoV-2 B.1.1.529 variant  (Omicron) evades neutralization by sera from vaccinated and convalescent  individuals
-|https://www.medrxiv.org/content/10.1101/2021.12.08.21267491v1/
-|4
-|-
-|28
-|Modelling the potential  consequences of the Omicron SARS-CoV-2 variant in England
-|https://cmmid.github.io/topics/covid19/omicron-england.html/
-|4
-|-
-|29
-|Omicron and Delta Variant of  SARS-CoV-2: A Comparative Computational Study of Spike protein
-|https://www.biorxiv.org/content/10.1101/2021.12.02.470946v1/
-|4
-|-
-|30
-|Where did ‘weird’ Omicron come  from?
-|https://www.science.org/content/article/where-did-weird-omicron-come?utm_campaign=NewsfromScience&utm_source=Social&utm_medium=Twitter/
-|4
-|-
-|31
-|The Omicron SARSCoV2  mutations in each gene and the drugs, candidates, & vaccines that target  them. The 3CL protease and RNA polymerase have only 1 mutation each (unlike  spike, which has >30); the drug candidates targeting them might be more  likely to retain efficacy.
-|https://twitter.com/davidrliu/status/1464714206150807559/photo/1/
-|4
-|-
-|38
-|The mutation map of the 5  Variants of Concern
-|https://covariants.org/shared-mutations/
-|4
-|-
-|55
-|Classification of Omicron  (B.1.1.529): SARS-CoV-2 Variant of Concern
-|https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern/
-|4
-|-
-|60
-|Molecular basis of immune  evasion by the Delta and Kappa SARS-CoV-2 variants
-|https://www.science.org/doi/10.1126/science.abl8506?utm_campaign=SciMag&utm_source=Social&utm_medium=Twitter/
-|4
-|-
-|68
-|The mutation that helps Delta  spread like wildfire
-|https://www.nature.com/articles/d41586-021-02275-2?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|4
-|-
-|77
-|SARS-CoV-2 immune evasion by  the B.1.427/B.1.429 variant of concern
-|https://www.science.org/doi/10.1126/science.abi7994/
-|4
-|-
-|97
-|Spatiotemporal invasion  dynamics of SARS-CoV-2 lineage B.1.1.7 emergence
-|https://www.science.org/doi/full/10.1126/science.abj0113/
-|4
-|-
-|111
-|Reduced sensitivity of  SARS-CoV-2 variant Delta to antibody neutralization
-|https://www.nature.com/articles/s41586-021-03777-9?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|4
-|-
-|122
-|Fe-S cofactors in the  SARS-CoV-2 RNA-dependent RNA polymerase are potential antiviral targets
-|https://www.science.org/doi/10.1126/science.abi5224/
-|4
-|-
-|130
-|Coronavirus variants are  spreading in India — what scientists know so far
-|https://www.nature.com/articles/d41586-021-01274-7?utm_source=twitter&utm_medium=social&utm_content=organic&utm_campaign=NGMT_USG_JC01_GL_Nature/
-|4
-|-
-|150
-|Genomics and epidemiology of  the P.1 SARS-CoV-2 lineage in Manaus, Brazil
-|https://www.science.org/doi/10.1126/science.abh2644/
-|4
-|-
-|154
-|A novel variant of interest of  SARS-CoV-2 with multiple spike mutations detected through travel surveillance  in Africa
-|https://www.krisp.org.za/publications.php?pubid=330/
-|4
-|-
-|158
-|Antibody resistance of  SARS-CoV-2 variants B.1.351 and B.1.1.7
-|https://www.nature.com/articles/s41586-021-03398-2/
-|4
-|-
-|159
-|Development of potency,  breadth and resilience to viral escape mutation in SARS-CoV-2 neutralizing  anitbodies
-|https://www.biorxiv.org/content/10.1101/2021.03.07.434227v1/
-|4
-|-
-|160
-|SARS-CoV-2 Variants | UK+  South African + Brazil Variants/
-|https://www.youtube.com/watch?v=OYgVmOLF2mY/
-|4
-|-
-|162
-|Summary of Clinical Data on  New Coronavirus Variant, Suggests Humans can still win the Long war
-|https://m.weibo.cn/status/4647414625212687?sourceType=weixin&from=10AC195010&wm=4260_0001&featurecode=newtitle/
-|4
-|-
-|163
-|Delta Variant US confirmed rate doubles in 7 days!
-|https://mp.weixin.qq.com/s/8lRnwUUz_3dV7QMtfg2s4w/
-|4
-|-
-|164
-|Delta variant isn’t over,  Delta+ variant strikes again
-|https://m.weibo.cn/status/4650675290506335?sourceType=weixin&from=10B6195010&wm=2468_1001&featurecode=newtitle/
-|4
-|-
-|165
-|Delta coronavirus variant:  scientists brace for impact
-|https://www.nature.com/articles/d41586-021-01696-3?utm_source=twt_nat&utm_medium=social&utm_campaign=nature/
-|4
-|-
-|166
-|Menacing: What is the new crown Delta mutant, and how can we respond?
-|https://mp.weixin.qq.com/s/g9gPLEN6R02F49eRGGSuAA/
-|4
-|-
-|167
-|Race to understand Sars-CoV-2  variants amid fears virus might evade vaccines
-|https://www.chemistryworld.com/news/race-to-understand-sars-cov-2-variants-amid-fears-virus-might-evade-vaccines/4013891.article/
-|4
-|-
-|168
-|New versions of Omicron are masters of immune evasion
-|https://www.science.org/content/article/new-versions-omicron-are-masters-immune-evasion
-|
-|-
-|169
-|Twitt from Jon Cohen
-|https://twitter.com/sciencecohen/status/1524852142476959744
-|
-|-
-|170
-|Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop
-|https://www.sciencedirect.com/science/article/pii/S0022283620302874
 |
 |-
-|171
+|'''V445A'''
-|Comparative phylogenetic analysis of SARS-CoV-2 spike protein—possibility effect on virus spillover
+|2023.01
-|https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8083239/
+|COV2-2050
-|
+|COV2-2094
+|COV2-2479
+|COV2-2499
+|COV2-2677
 |-
-|172
+|'''G446I'''
-|Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum
+|2023.05
-|https://www.cell.com/cell/fulltext/S0092-8674(22)00710-3
+|COV2-2096
+|COV2-2479
+|COV2-2499
 |
-|-
-|173
-|Mutational effects on ACE2-binding affinity and expression in SARS-CoV-2 variant RBDs
-|https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS_Omicron/RBD-heatmaps/
 |
 |-
-|174
+|'''E484R'''
-|Omicron RBD DMS
+|2023.01
-|https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS_Omicron/
+|COV2-2050
-|
+|COV2-2096
-|-
+|COV2-2479
-|175
+|COV2-2832
-|Principles of SARS-CoV-2 glycosylation
-|https://www.sciencedirect.com/science/article/pii/S0959440X22000811
-|
-|-
-|176
-|BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
-|https://www.nature.com/articles/s41586-022-04980-y
-|
-|-
-|177
-|Nature：谢晓亮/曹云龙等揭示Omicron感染极难实现群体免疫
-|https://mp.weixin.qq.com/s/j2RTj0Jmvt1A_PpEpmtfLw
-|
-|-
-|178
-|Worldometer COVID-19 CORONAVIRUS PANDEMIC
-|https://www.worldometers.info/coronavirus/
-|
-|-
-|179
-|Twitt from Mrigank Shail, MD
-|https://twitter.com/mrigankshail/status/1536811673117511680
-|
-|-
-|180
-|Neutralization Escape by SARS-CoV-2 Omicron Subvariants BA.2.12.1, BA.4, and BA.5
-|https://www.nejm.org/doi/full/10.1056/NEJMc2206576
-|
-|-
-|181
-|Drivers of adaptive evolution during chronic SARS-CoV-2 infections
-|https://www.nature.com/articles/s41591-022-01882-4.pdf
-|
-|-
-|182
-|CHRONIC COVID: THE EVOLVING STORY
-|https://media.nature.com/original/magazine-assets/d41586-022-01613-2/d41586-022-01613-2.pdf
-|
-|-
-|183
-|What Omicron’s BA.4 and BA.5 variants mean for the pandemic
-|https://www.nature.com/articles/d41586-022-01730-y?utm_term=Autofeed&utm_campaign=nature&utm_medium=Social&utm_source=Twitter#Echobox=1656123519
-|
-|-
-|184
-|Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
-|https://www.science.org/doi/10.1126/science.abm1208
-|
-|-
-|185
-|The BA.5 story: The takeover by this Omicron sub-variant is not pretty
-|https://erictopol.substack.com/p/the-ba5-story
-|
-|-
-|186
-|Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution
-|https://www.science.org/doi/10.1126/science.abo7896
-|
-|-
-|187
-|Supplementary Appendix Supplement to: Zhao X, Zhang R, Qiao S, et al. Omicron SARS-CoV-2 neutralization from inactivated and ZF2001 vaccines
-|https://www.nejm.org/doi/suppl/10.1056/NEJMc2206900/suppl_file/nejmc2206900_appendix.pdf
-|
-|-
-|188
-|Genetic drift, selection and the evolution of the mutation rate
-|https://doi.org/10.1038/nrg.2016.104
-|
-|-
-|189
-|The worst virus variant just arrived. The pandemic is not over.
-|https://www.washingtonpost.com/opinions/2022/07/07/worst-virus-variant-just-arrived-pandemic-is-not-over/
-|
-|-
-|190
-|The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
-|https://www.science.org/doi/10.1126/science.abp8337
-|
-|-
-|191
-|Mendelian randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics
-|https://doi.org/10.1073/pnas.2106858119
-|
-|-
-|192
-|Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design
-|https://doi.org/10.1093/molbev/msaa188
-|
-|-
-|193
-|Causes and Consequences of Purifying Selection on SARS-CoV-2
-|https://doi.org/10.1093/gbe/evab196
-|
-|-
-|194
-|The imminent BA.5 vaccine booster
-|https://erictopol.substack.com/p/the-imminent-ba5-vaccine-booster
-|
-|-
-|195
-|Nonsynonymous to Synonymous Substitution Ratio ka/ks: Measurement for Rate of Evolution in Evolutionary Computation
-|http://dx.doi.org/10.1007/978-3-540-87700-4_45
-|
-|-
-|196
-|Continuous genomic diversification of long polynucleotide fragments drives the emergence of new SARS-CoV-2 variants of concern
-|<nowiki>https://doi.org/10.1093/pnasnexus/pgac018</nowiki>
-|
-|-
-|197
-|The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2
-|<nowiki>https://doi.org/10.1016/j.molcel.2020.11.004</nowiki>
 |
 |}
+<big>Overall, by the first half of this year, '''R346S''' and '''E484R''' are the most potential dangerous mutations we captured.</big>
+-->
+==References==
+<references>
+<ref name="Del Rio">Rössler, A. ''et al''. BA.2 and BA.5 Omicron Differ Immunologically from Both BA.1 Omicron and Pre-Omicron Variants. ''Nat Commun'' '''13''', 7701 (2022)</ref>
+<ref name="European Centre">Qu, P. ''et al''. Enhanced Neutralization Resistance of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. ''Cell Host Microbe'' '''31''', 9 (2023)</ref>
+<ref name="Jackson2021">Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. ''Nat Rev Mol Cell Biol'' '''23,''' 3 (2021).</ref>
+<ref name="Karim">Karim, S. S. A. & Karim, Q. A. Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic. ''Lancet'' '''398,''' 2126 (2021).</ref>
+<ref name="Wang">Wang, Q. ''et al.'' Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. ''Cell'' '''186,''' 279 (2023).</ref>
+<ref name="deLemus">deLemus team, Analysis of Leading Mutations in SARS-CoV-2 Spike Glycoproteins (in preparation, 2023).</ref>
+<ref name="GISAID">GISAID https://gisaid.org/</ref>
+<ref name="Cov-Lineages">Cov-Lineages https://cov-lineages.org/</ref>
+</references>
+<html><a href="https://www.revolvermaps.com/livestats/locations/57gzazn1dbb/"><img src="//rf.revolvermaps.com/h/m/a/0/ff0000/128/0/57gzazn1dbb.png" width="180" height="120" alt="Map" style="border:0;"></a></html>
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