Difference between revisions of "Time Course"

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__NOTOC__
 
__NOTOC__
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TBA
 
  
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==Previously Confirmed Mutations ==
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<big>Within the first 2 years of this pandemic, the World Health Organization (WHO) has already announced 4 variants of concern (VOC), which are the previously circulating α (B.1.1.7), β (B.1.351), γ (P.1), and δ (B.1.617.2) strains, and many other variants of interest (VOI).<ref name="WHO" /> The successive emergence of new SARS-CoV-2 variants has brought along many novel mutations. Between July and October 2022, 3 new members of the omicron (B.1.1.529) lineage have emerged, and subsequently been recognized as variants of interest (VOI) by the World Health Organization (WHO), which are the BA.2.75, XBB, and BQ.1 subvariants.<ref name="Covariants" /> Each of these VOIs has brought along an array of novel mutations in the constantly evolution of SARS-CoV-2. The time course analysis of identified leading mutations are presented here.<br /></big>
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<big>In the last 6 months, 3 new members of the omicron (B.1.1.529) lineage have emerged, and subsequently been recognized as variants of interest (VOI) by the World Health Organization (WHO), which are the BA.2.75, XBB, and BQ.1 subvariants that rose to prominence in July, August and October 2022 respectively. Each of these VOIs has brought along an array of novel mutable sites crucial for refining the viral fitness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Leading mutations identified by our deLemus analysis that emerged within the aforementioned timeframe are listed as follows:<br /></big>
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<tabs>
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<tab name="2023.07">
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{{#tag:tab| <htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-07a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"> </htmltag> |collapsed=true| name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-07b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-07c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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<tab name="2023.06">
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{{#tag:tab| <htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-06a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"> </htmltag> |collapsed=true| name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-06b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-06c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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<tab name="2023.05">
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{{#tag:tab| <htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-05a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"> </htmltag> |collapsed=true| name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-05b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-05c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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<tab name="2023.04">
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{{#tag:tab| <htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-04a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"> </htmltag> |collapsed=true| name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-04b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-04c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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</tab>
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<tab name="2023.03">
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{{#tag:tab| <htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-03a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"> </htmltag> |collapsed=true| name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-03b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-03c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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<tab name="2023.02">
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{{#tag:tab| <htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-02a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"> </htmltag> |collapsed=true| name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-02b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-02c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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</tab>
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<tab name="2023.01">
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-01a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-01b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/2023-01c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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</tab>
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<tab name="2022.08">
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/32a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/32b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/32c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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</tab>
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<tab name="2022.06">
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/30a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/30b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/30c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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</tab>
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<tab name="2021.08">
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/20a.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="NTD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/20b.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="RBD"}}
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{{#tag:tab|<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/20c.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>|collapsed=true|name="Other Domains"}}
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''Click the button to show figure.''
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</tab>
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<tab name="2021.03">
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<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/15.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
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</tab>
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<tab name="2020.12">
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<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/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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</tab>
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<tab name="2020.11">
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<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/11.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
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</tab>
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<tab name="2020.10">
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<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/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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</tab>
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</tabs>
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==References==
 +
<references>
 +
<ref name="WHO">WHO https://www.who.int/activities/tracking-SARS-CoV-2-variants</ref>
 +
<ref name="Covariants">Covariants https://covariants.org/</ref>
 +
</references>
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<!--
 +
<big>Within the first 2 years of this pandemic, the World Health Organization (WHO) has already announced 4 variants of concern (VOC), which are the previously circulating α (B.1.1.7), β (B.1.351), γ (P.1), and δ (B.1.617.2) strains, and many other variants of interest (VOI). The successive emergence of new SARS-CoV-2 variants has brought along many novel mutations, most of which continually refine and improve the fitness of the virus. The identified leading mutations before the outbreak of those VOCs are listed as follows:<br /></big>
 +
 
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 +
</tabs>
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 +
==2022.08.31==
 +
<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/32.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
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{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| R346T || XBB
 +
|-
 +
| F486S || XBB
 +
|-
 +
| F490S || XBB
 +
|}
 +
==2022.06.30==
 +
<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/30.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| F157L || BA.2.75
 +
|-
 +
| G257S || BA.2.75
 +
|-
 +
| G339H || BA.2.75
 +
|-
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| N460K || BA.2.75
 +
|}
 +
 
 +
==2021.03.31==
 +
<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/15.png" alt="test for htmltag img" class="wikimg" style="display: block;width:100%;margin-left: auto;margin-right: auto;"></htmltag>
 +
{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| T19R || δ (B.1.617.2)
 +
|-
 +
| E156- || δ (B.1.617.2)
 +
|-
 +
| F157- || δ (B.1.617.2)
 +
|-
 +
| R158G || δ (B.1.617.2)
 +
|-
 +
| L452R || δ (B.1.617.2)
 +
|-
 +
| T478K || δ (B.1.617.2)
 +
|-
 +
| P681R || δ (B.1.617.2)
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|-
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| D950N || δ (B.1.617.2)
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|}
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==2020.10.31==
 +
<htmltag tagname="img" src="https://wiki.laviebay.hkust.edu.hk/deLemus/RESEARCH_TEAMS/images/PublishedPlot/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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{| class="wikitable"
 +
|-
 +
! Outlined Mutations !! Confirmed in VOC/Emerging Variants
 +
|-
 +
| H69- || α (B.1.1.7)
 +
|-
 +
| V70- || α (B.1.1.7)
 +
|-
 +
| Y144- || α (B.1.1.7)
 +
|-
 +
| N501Y || α (B.1.1.7)
 +
|-
 +
| D614G || α (B.1.1.7)
 +
|-
 +
| P681H || α (B.1.1.7)
 +
|-
 +
| S982A || α (B.1.1.7)
 +
|-
 +
| D1118H || α (B.1.1.7)
 +
|}
  
 
===F486P/I ===
 
===F486P/I ===
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<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="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=":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="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="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=":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=":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=":3">Wang, Q. ''et al.'' Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. ''Cell'' '''186,''' 279 (2023).</ref>
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<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>
 
<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>
 
</references>
 +
-->
 +
[[Category:deLemus]]

Latest revision as of 15:28, 4 August 2023


Within the first 2 years of this pandemic, the World Health Organization (WHO) has already announced 4 variants of concern (VOC), which are the previously circulating α (B.1.1.7), β (B.1.351), γ (P.1), and δ (B.1.617.2) strains, and many other variants of interest (VOI).[1] The successive emergence of new SARS-CoV-2 variants has brought along many novel mutations. Between July and October 2022, 3 new members of the omicron (B.1.1.529) lineage have emerged, and subsequently been recognized as variants of interest (VOI) by the World Health Organization (WHO), which are the BA.2.75, XBB, and BQ.1 subvariants.[2] Each of these VOIs has brought along an array of novel mutations in the constantly evolution of SARS-CoV-2. The time course analysis of identified leading mutations are presented here.

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References

  1. ↑ WHO https://www.who.int/activities/tracking-SARS-CoV-2-variants
  2. ↑ Covariants https://covariants.org/
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