Difference between revisions of "deLemus"

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__NOTOC__
 
__NOTOC__
 
''Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins''
 
''Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins''
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</br>
 
</br>
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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.  
 
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.  
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==Spike Glycoprotein==
 
==Spike Glycoprotein==
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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.
 
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.
  
 
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=='''Update'''==
 
=='''Update'''==
 
The identified leading mutations in 2023 are listed as follows <ref name="deLemus" />:
 
The identified leading mutations in 2023 are listed as follows <ref name="deLemus" />:
  
 
<tabs>
 
<tabs>
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<tab name="2023.12">
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<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>
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 +
===2023.12.01-2023.12.17===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:burlywood;">'''A475V'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:hotpink;">'''E654K'''</span> || HK.3
 +
|}
 +
 +
</tab>
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<tab name="2023.11">
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<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"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:yellowgreen;">'''N185D'''</span> || HK.3.2
 +
|-
 +
| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:burlywood;">'''A475V'''</span> || JF.1
 +
|-
 +
| <span style="color:hotpink;">'''T572I'''</span> || FY.2
 +
|-
 +
| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.16
 +
|-
 +
| <span style="color:cornflowerblue;">'''D1153Y'''</span> || HK.3
 +
|}
 +
 +
</tab>
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<tab name="2023.10">
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<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>
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 +
===2023.10.06===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:burlywood;">'''A475V'''</span> || GK.1
 +
|}
 +
 +
</tab>
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 +
<tab name="2023.09">
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<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"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:burlywood;">'''R403K'''</span> || BA.2.86 (Pirola)
 +
|-
 +
| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:burlywood;">'''S494P'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:burlywood;">'''P521S'''</span> || XBB.1.16.15
 +
|-
 +
| <span style="color:hotpink;">'''E554K'''</span> || BA.2.86 (Pirola) & FE.1
 +
|-
 +
| <span style="color:hotpink;">'''Q613H'''</span> || BA.2.86 (Pirola)
 +
|-
 +
| <span style="color:hotpink;">'''P621S'''</span> || BA.2.86 (Pirola)
 +
|-
 +
| <span style="color:cornflowerblue;">'''T732I'''</span> || XBB.2.3 x XBB.1.5
 +
|-
 +
| <span style="color:cornflowerblue;">'''S939F'''</span> || BA.2.86 (Pirola)
 +
|-
 +
| <span style="color:cornflowerblue;">'''V1264L'''</span> || CK.1.1
 +
|}
 +
 +
</tab>
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 +
<tab name="2023.08">
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<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"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:yellowgreen;">'''N185D'''</span> || XBB.1.5
 +
|-
 +
| <span style="color:yellowgreen;">'''L212S'''</span> || FY.4.2
 +
|-
 +
| <span style="color:burlywood;">'''V445A'''</span> || XBC.1.6
 +
|-
 +
| <span style="color:burlywood;">'''L455F'''</span> || EG.5.1.1
 +
|-
 +
| <span style="color:burlywood;">'''F456L'''</span> || EG.5.1 (Eris)
 +
|-
 +
| <span style="color:hotpink;">'''E554Q'''</span> || XBB.1.5.18
 +
|-
 +
| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.16
 +
|-
 +
| <span style="color:cornflowerblue;">'''T883I'''</span> || XBB.1.16
 +
|}
 +
''*The reported mutations of detected variants are from Cov-Lineages<ref name="Cov-Lineages" />''
 +
</br>
 +
===<big>RBD Mutation Profile of Latest VOIs.</big>===
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<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>
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</tab>
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<tab name="2023.07">
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<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-07.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>
 +
 +
===2023.06.30 - 2023.07.05===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:yellowgreen;">'''H146K'''</span> || FL.2.3 (XBB.1.9.1.2.3)
 +
|-
 +
| <span style="color:burlywood;">'''S446N'''</span> || FL.19
 +
|-
 +
| <span style="color:burlywood;">'''F456L'''</span> || XBF
 +
|}
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 +
 +
</tab>
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<tab name="2023.06">
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<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>
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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>
 +
 +
===2023.06.01 - 2023.06.13===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:burlywood;">'''F490P'''</span> || XBB.1.9.1
 +
|-
 +
| <span style="color:hotpink;">'''E554K'''</span> || XBB.1.9.1 (sublineage)
 +
|-
 +
| <span style="color:hotpink;">'''Q675K'''</span> || XBB.1.22.1
 +
|-
 +
| <span style="color:cornflowerblue;">'''L858I'''</span> || CH.1.1.1
 +
|}
 +
 +
 +
</tab>
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<tab name="2023.05">
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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>
 +
 +
===2023.05.01 - 2023.05.12===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:burlywood;">'''F456L'''</span> || FD.1.1 & EG.5.1 (2023.08)
 +
|-
 +
| <span style="color:burlywood;">'''S494P'''</span> || XBB.2.3 & XBB.1.1
 +
|-
 +
| <span style="color:hotpink;">'''T572I'''</span> || FY.1 ( XBB.1.22.1.1 )
 +
|}
 +
''*The reported mutations of detected variants are from GISAID''
 +
 +
 +
</tab>
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<tab name="2023.04">
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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>
 +
 +
===2023.04.01 - 2023.04.21===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:yellowgreen;">'''H146K'''</span> || XBB.1.5 & XBB.1.16
 +
|-
 +
| <span style="color:yellowgreen;">'''M153I'''</span> || XBB.2.3.3
 +
|-
 +
| <span style="color:yellowgreen;">'''E180V'''</span> || XBB.1.16
 +
|-
 +
| <span style="color:burlywood;">'''K444R'''</span> || XBB.1.5
 +
|-
 +
| <span style="color:burlywood;">'''T478R'''</span> || XBB.1.16, XBB.1.5, CH.1.1.2 & XBB.2.3
 +
|-
 +
| <span style="color:burlywood;">'''F490P'''</span> || XBB.2.6
 +
|-
 +
| <span style="color:burlywood;">'''S494P'''</span> || XBB.1.5
 +
|-
 +
| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.16
 +
|-
 +
| <span style="color:hotpink;">'''P621S'''</span> || XBB.2.3
 +
|-
 +
| <span style="color:hotpink;">'''A688V'''</span> || XAY.1.1.1
 +
|}
 +
 +
</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 {
 +
            position: relative;
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    <script type="text/javascript">
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 +
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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>
 +
 +
===2023.03.01 - 2023.03.21===
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| <span style="color:yellowgreen;">'''Y248S'''</span> || BQ.1
 +
|-
 +
| <span style="color:burlywood;">'''F490P'''</span> || XBB.1 & XBB.1.5
 +
|-
 +
| <span style="color:hotpink;">'''T547I'''</span> || XBB.1.16
 +
|-
 +
| <span style="color:hotpink;">'''Q613H'''</span> || DV.1, CH.1.1.1 & CH.1.1.17
 +
|-
 +
| <span style="color:hotpink;">'''I666V'''</span> || XBB.1.5
 +
|-
 +
| <span style="color:cornflowerblue;">'''V1264L'''</span> || CH.1.1
 +
|}
 +
 +
</tab>
 +
 
<tab name="2023.02">
 
<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>
 
<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>
−
 
 
<html>
 
<html>
 
     <style>
 
     <style>
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     <script type="text/javascript" src="https://molstar.org/viewer/molstar.js"></script>
 
     <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>
+
     <div id="viewer-2" class="molstar" style="display: block; margin-left:auto; margin-right:auto; padding-bottom: 40%;"></div>
 
     <script type="text/javascript">
 
     <script type="text/javascript">
−
         molstar.Viewer.create('viewer-1', {
+
         molstar.Viewer.create('viewer-2', {
 
             layoutIsExpanded: false,
 
             layoutIsExpanded: false,
 
             layoutShowControls: false,
 
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! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 
|-
 
|-
−
| K147I || XBB.1.5.2.1
+
| <span style="color:yellowgreen;">'''K147I'''</span> || XBB.1.5.2.1
 
|-
 
|-
−
| Y248S || BQ.1.1.43
+
| <span style="color:yellowgreen;">'''Y248S'''</span> || BQ.1.1.43
 
|-
 
|-
−
| S494P || XBB.1.5
+
| <span style="color:burlywood;">'''S494P'''</span> || XBB.1.5
 
|-
 
|-
−
| N679R || XBF
+
| <span style="color:hotpink;">'''Q613H'''</span> || XBB.1.9.2 & XBB.2.4
 
|-
 
|-
−
| T678I || BA.2.75 x BA.5
+
| <span style="color:hotpink;">'''P612S'''</span> || XBF
 
|-
 
|-
−
| N679R || CH.1.1
+
| <span style="color:hotpink;">'''T678I'''</span> || BA.2.75 x BA.5
 
|-
 
|-
−
| P1162S || XBK.1
+
| <span style="color:hotpink;">'''N679R'''</span> || CH.1.1
 +
|-
 +
| <span style="color:cornflowerblue;">'''P1162S'''</span> || XBK.1
 
|}
 
|}
−
''*The reported mutations of detected variants are from Cov-Lineages<ref name="Cov-Lineages" />''
+
''*The reported mutations of detected variants are from GISAID<ref name="GISAID" />''
 
</tab>
 
</tab>
  
 
<tab name="2023.01">
 
<tab name="2023.01">
−
<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/Confirmed.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
+
<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>
 
<html>
Line 116: Line 505:
 
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 
|-
 
|-
−
| V445A || BQ.1.1
+
| <span style="color:burlywood;">'''V445A'''</span> || BQ.1.1
 
|-
 
|-
−
| T883I || BQ.1.1
+
| <span style="color:cornflowerblue;">'''T883I'''</span> || BQ.1.1
 
|}
 
|}
 
===2023.01.17 - 2023.01.25===
 
===2023.01.17 - 2023.01.25===
Line 125: Line 514:
 
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 
|-
 
|-
−
| H146- / H146K || BQ.1.1 / XBB.1.5
+
| <span style="color:yellowgreen;">'''H146- / H146K'''</span> || BQ.1.1 / XBB.1.5
 
|-
 
|-
−
| F486A || BQ.1.1
+
| <span style="color:burlywood;">'''F486A'''</span> || BQ.1.1
 
|-
 
|-
−
| E583D || BQ.1.1
+
| <span style="color:hotpink;">'''E583D'''</span> || BQ.1.1
 
|-
 
|-
−
| Q613H ||  BQ.1.1
+
| <span style="color:hotpink;">'''Q613H'''</span> ||  BQ.1.1
 
|-
 
|-
−
| S939F || BQ.1.1
+
| <span style="color:cornflowerblue;">'''S939F'''</span> || BQ.1.1
 
|}
 
|}
−
''*The reported mutations of detected variants are from GISAID<ref name="GISAID" />''
+
 
 
</tab>
 
</tab>
  
 
</tabs>
 
</tabs>
  
−
<!--2-column table-->
+
 
−
<!-- End of 2-column table-->
 
−
<!-- 3-column table -->
 
 
<!--
 
<!--
−
 
−
<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>
 
 
===2023.01.31===
 
===2023.01.31===
 
{| class="wikitable"
 
{| class="wikitable"
Line 173: Line 552:
 
|}
 
|}
  
−
-->
 
−
<!-- End of 3-column table -->
 
−
<br />
 
−
 
−
<!--
 
 
<big>The following leading mutations call for special attention with respect to the upcoming variants.</big>
 
<big>The following leading mutations call for special attention with respect to the upcoming variants.</big>
 
==NTD==
 
==NTD==
Line 206: Line 580:
 
|Enhance the utilization of ACE2 in numerous mammals<ref name="Wang_JMedVirol2022" /> ; May increase interspecies and intraspecies transmissibility
 
|Enhance the utilization of ACE2 in numerous mammals<ref name="Wang_JMedVirol2022" /> ; May increase interspecies and intraspecies transmissibility
 
|}
 
|}
 +
 
==RBD==
 
==RBD==
 
{| class="wikitable"
 
{| class="wikitable"
Line 225: Line 600:
 
| 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"/>
 
| 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"/>
 
|}
 
|}
 +
 
==CTDs==
 
==CTDs==
 
{| class="wikitable"
 
{| class="wikitable"
Line 255: Line 631:
 
| 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>
 
| 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>
 
|}
 
|}
−
-->
 
  
−
<!--
+
== 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==
 
==Summary==
 
<tabs>
 
<tabs>
Line 265: Line 653:
 
<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>
 
<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>
 
</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'''
 +
|-
 +
|'''R346S'''
 +
|2023.01
 +
|0.12
 +
|0.14
 +
|0.07
 +
|0.03
 +
|0.11
 +
|-
 +
|'''N354S'''
 +
|2023.05
 +
|0.03
 +
|0.01
 +
|0.04
 +
|0.32
 +
|0.02
 +
|-
 +
|'''E484R'''
 +
|2023.01
 +
|0.06
 +
|0.04
 +
|  -
 +
|  -
 +
|0.11
 +
|-
 +
|'''S494P'''
 +
|2023.01
 +
|0.33
 +
|0.18
 +
|0.13
 +
|0.14
 +
|0.06
 +
|}
 +
<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"
 +
|+
 +
Immune Escaping
 +
|'''Unique  Mutations'''
 +
|'''Date'''
 +
|'''Antybody1'''
 +
|'''Antybody2'''
 +
|'''Antybody3'''
 +
|'''Antybody4'''
 +
|'''Antybody5'''
 +
|-
 +
|'''R346S'''
 +
|2023.01
 +
|COV2-2082
 +
|COV2-2096
 +
|COV2-2479
 +
|COV2-2832
 +
|
 +
|-
 +
|'''V445A'''
 +
|2023.01
 +
|COV2-2050
 +
|COV2-2094
 +
|COV2-2479
 +
|COV2-2499
 +
|COV2-2677
 +
|-
 +
|'''G446I'''
 +
|2023.05
 +
|COV2-2096
 +
|COV2-2479
 +
|COV2-2499
 +
|
 +
|
 +
|-
 +
|'''E484R'''
 +
|2023.01
 +
|COV2-2050
 +
|COV2-2096
 +
|COV2-2479
 +
|COV2-2832
 +
|
 +
|}
 +
<big>Overall, by the first half of this year, '''R346S''' and '''E484R''' are the most potential dangerous mutations we captured.</big>
 
-->
 
-->
 +
 
==References==
 
==References==
 
<references>
 
<references>
Line 276: Line 764:
 
<ref name="GISAID">GISAID https://gisaid.org/</ref>
 
<ref name="GISAID">GISAID https://gisaid.org/</ref>
 
<ref name="Cov-Lineages">Cov-Lineages https://cov-lineages.org/</ref>
 
<ref name="Cov-Lineages">Cov-Lineages https://cov-lineages.org/</ref>
−
 
 
</references>
 
</references>
−
 
  
  
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<noscript><a href="https://www.freecounterstat.com" title="free website counter"><img src="https://counter10.optistats.ovh/private/freecounterstat.php?c=9pt5d2hy2d328lsrbbs6nlkm4sax62ug" border="0" title="free website counter" alt="free website counter"></a></noscript>
 
<noscript><a href="https://www.freecounterstat.com" title="free website counter"><img src="https://counter10.optistats.ovh/private/freecounterstat.php?c=9pt5d2hy2d328lsrbbs6nlkm4sax62ug" border="0" title="free website counter" alt="free website counter"></a></noscript>
 
</html>
 
</html>
 +
[[Category: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]:

2023.12.01-2023.12.17

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

  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).
  3. ↑ Wang, Q. et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 186, 279 (2023).
  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)
  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).
  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).
  10. ↑ deLemus team, Analysis of Leading Mutations in SARS-CoV-2 Spike Glycoproteins (in preparation, 2023).
  11. ↑ Cov-Lineages https://cov-lineages.org/
  12. ↑ GISAID https://gisaid.org/


Map

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