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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{{#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/2023-04a.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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<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/2023-03c.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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{{#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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<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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<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 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 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 name="2020.11">
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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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==References==
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<references>
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<ref name="WHO">WHO https://www.who.int/activities/tracking-SARS-CoV-2-variants</ref>
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<ref name="Covariants">Covariants https://covariants.org/</ref>
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</references>
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<!--
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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==
 
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<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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<!--
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{| class="wikitable"
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|-
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! Outlined Mutations !! Confirmed in VOC/Emerging Variants
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|-
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| R346T || XBB
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|-
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| F486S || XBB
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|-
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| F490S || XBB
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|}
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==2022.06.30==
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<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>
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{| class="wikitable"
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|-
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! Outlined Mutations !! Confirmed in VOC/Emerging Variants
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|-
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| F157L || BA.2.75
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|-
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| G257S || BA.2.75
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|-
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| G339H || BA.2.75
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|-
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| N460K || BA.2.75
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|}
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==2021.03.31==
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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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{| class="wikitable"
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|-
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! Outlined Mutations !! Confirmed in VOC/Emerging Variants
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|-
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| T19R || δ (B.1.617.2)
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|-
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| E156- || δ (B.1.617.2)
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|-
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| F157- || δ (B.1.617.2)
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|-
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| R158G || δ (B.1.617.2)
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|-
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| L452R || δ (B.1.617.2)
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|-
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| T478K || δ (B.1.617.2)
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|-
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| 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==
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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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{| class="wikitable"
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|-
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! Outlined Mutations !! Confirmed in VOC/Emerging Variants
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|-
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| H69- || α (B.1.1.7)
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|-
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| V70- || α (B.1.1.7)
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|-
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| Y144- || α (B.1.1.7)
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|-
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| N501Y || α (B.1.1.7)
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|-
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| D614G || α (B.1.1.7)
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|-
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| P681H || α (B.1.1.7)
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|-
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| S982A || α (B.1.1.7)
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|-
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| D1118H || α (B.1.1.7)
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|}
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===F486P/I ===
 
===F486P/I ===
 
<big>Amino acid site 486 has been exhibiting a strong mutational signal since November 2022, based on our deLemus analysis. Mutation at this site in the form of F486P is carried by the currently proliferating XBB.1.5 variant, rendering this variant with an enhanced hACE2-binding affinity when compared to its ancestor, XBB.1.<ref name="XBB.1.5"/> It is likely that the tighter receptor attachment confers quicker transmissibility for the XBB.1.5 strain, as demonstrated by its looming dominance in the US. Additionally, we have noticed another leading mutation located at the same site, F486I, which may also alter the viral fitness of SARS-CoV-2.</big>
 
<big>Amino acid site 486 has been exhibiting a strong mutational signal since November 2022, based on our deLemus analysis. Mutation at this site in the form of F486P is carried by the currently proliferating XBB.1.5 variant, rendering this variant with an enhanced hACE2-binding affinity when compared to its ancestor, XBB.1.<ref name="XBB.1.5"/> It is likely that the tighter receptor attachment confers quicker transmissibility for the XBB.1.5 strain, as demonstrated by its looming dominance in the US. Additionally, we have noticed another leading mutation located at the same site, F486I, which may also alter the viral fitness of SARS-CoV-2.</big>
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[[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.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

Click the button to show figure.

References

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