Difference between revisions of "deLemus"

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==Summary==
 
==Summary==
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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, 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,''' 213–214 (2022).</ref> From the BA.1 strain of November 2021, to the BQ.1 strain of October 2022,<ref name="Wang" /> each omicron subvariant has successively proliferated and outcompeted its once dominant antecedent.<ref name="Del Rio" /> The emergence of all these variants has assuredly brought along many novel mutations that continues 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).</ref> leading to its persistent global circulation.
+
The dynamic epidemiology of coronavirus disease 2019 (COVID-19) since its outbreak has been a result of the continuous evolution of its etiological agent, 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,''' 213–214 (2022).</ref> From the BA.1 strain of November 2021, to the BQ.1 strain of October 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 assuredly brought along many novel mutations that continues 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).</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, making up of more than 40% of its sequence coverage in early January 2023.<ref name="CNBC XBB.1.5" /> The identified leading mutations are listed as follows:
 
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, making up of more than 40% of its sequence coverage in early January 2023.<ref name="CNBC XBB.1.5" /> The identified leading mutations are listed as follows:
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==References==
 
==References==
 
<references>
 
<references>
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1. Please arrange according to alphabetical order of name tag
 
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<ref name=":0">Harvey, W. T. ''et al.'' SARS-CoV-2 variants, Spike mutations and immune escape. ''Nat Rev Microbiol'' '''19,''' 409–424 (2021).</ref>
 
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<ref name=":2">Li, B. et al. Identification of Potential Binding Sites of Sialic Acids on the RBD Domain of SARS-CoV-2 Spike Protein. ''Front Chem.'' '''9''', 659764 (2021)</ref>
 
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<ref name=":3">McCallum, M. ''et al''. N-Terminal Domain Antigenic Mapping Reveals a Site of Vulnerability for SARS-CoV-2. ''Cell'' '''184''', 2332-2347 (2021).</ref>
 
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<ref name=":4">Zhou, L, ''et al''. Predicting Spike Protein NTD Mutations of SARS-CoV-2 Causing Immune Evasion by Molecular Dynamics Simulations. ''Phys Chem Chem Phys '''''24''', 3410–3419 (2022).</ref>
 
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<ref name="Bugembe">Bugembe, D. L. ''et al.'' Emergence and spread of a SARS-COV-2 lineage a variant (A.23.1) with altered Spike Protein in Uganda. ''Nat Microbiol'' '''6,''' 1094–1101 (2021).</ref>
 
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<ref name="Buchanan">Buchanan, C. J. ''et al.'' Pathogen-sugar interactions revealed by Universal Saturation Transfer Analysis. ''Science'' '''377,''' (2022).</ref>
 
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<ref name="Cong_CellHM2021">Cong, Z. ''et al.'' Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. ''Cell Host & Microbe'' '''29,''' 1931-3128 (2021).</ref>
 
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<ref name="CellRep20220517">Westendorf, K. ''et al.'' LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. ''Cell Rep'' '''39,''' 110812 (2022).</ref>
 
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<ref name="COVID Data Tracker">COVID Data Tracker: Variant Proportion https://covid.cdc.gov/covid-data-tracker/#variant-proportions (2023).</ref>
 
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<ref name="Donzelli">Donzelli, S. ''et al.'' Evidence of a SARS-CoV-2 double spike mutation D614G/S939F potentially affecting immune response of infected subjects. ''Comput Struct Biotechnol J'' '''20,''' 733–744 (2022).</ref>
 
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<ref name="Gaebler">Gaebler, C. ''et al.'' Evolution of antibody immunity to SARS-CoV-2. ''Nature'' '''591,''' 639–644 (2021).</ref>
 
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<ref name="Greaney"> Greaney, A. ''et al.'' Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. ''Cell Host Microbe'' '''29,''' 463-476 (2021).</ref>
 
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<ref name="Henrich">Henrich, S. ''et al.'' The crystal structure of the proprotein processing proteinase furin explains its stringent specificity. ''Nat Struct Mol Biol'' '''10,''' 520–526 (2003).</ref>
 
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<ref name="KempCIP">Kemp, S. A. ''et al''. SARS-CoV-2 evolution during treatment of chronic infection. ''Nature'' '''592''', 277–282 (2021).</ref>
 
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<ref name="LiImpactCell">Li, Q. ''et al''. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. ''Cell'' '''182''', 1284-1294.e9 (2020).</ref>
 
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<ref name="Olivie">Oliva, R., Shaikh, A. R., Petta, A., Vangone, A. & Cavallo, L. D936Y and other mutations in the fusion core of the SARS-CoV-2 spike protein heptad repeat 1: Frequency, geographical distribution, and structural effect. ''Molecules'' '''26''', 1–13 (2021).</ref>
 
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<ref name="Sun_Glycobio2021">Sun, X.-L. The role of cell surface sialic acids for SARS-CoV-2 infection. ''Glycobiology'' '''31,''' 1245–1253 (2021).</ref>
 
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<ref name="Tian_2009">Tian, S. A 20 residues motif delineates the furin cleavage site and its physical properties may influence viral fusion. ''Biochem Insights'' '''2,''' (2009).</ref>
 
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<ref name="VanBlargan2022">VanBlargan, L. A. ''et al.'' An infectious SARS-CoV-2 B.1.1.529 omicron virus escapes neutralization by therapeutic monoclonal antibodies. ''Nat Med'' '''28,''' 490–495 (2022).</ref>
 
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<ref name="Wang_JMedVirol2022">Wang, Q. ''et al''. Key Mutations on Spike Protein Altering ACE2 Receptor Utilization and Potentially Expanding Host Range of Emerging SARS‐CoV‐2 Variants. ''J Med Virol.'' '''95''', 1-11 (2022).</ref>
 
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<ref name="WangQ_LancetID2022">Wang, Q. ''et al.'' Resistance of SARS-CoV-2 omicron subvariant BA.4.6 to antibody neutralisation. ''Lancet Infect Dis'' '''22,''' 1666–1668 (2022).</ref>
 
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<ref name="Weisblum_eLife">Weisblum, Y. ''et al.'' Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. ''eLife'' '''9,''' (2020).</ref>
 
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<ref name="Zhou_CellHM2020">Zhou, T. ''et al.'' Cryo-EM structures of SARS-CoV-2 spike without and with ACE2 reveal a pH-dependent switch to mediate endosomal positioning of receptor-binding domains. ''Cell Host Microbe'' '''28,''' (2020).</ref>
 
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<ref name="Choi">Choi, Bina and Choudhary, Manish C. and Regan, James and Sparks, Jeffrey A. and Padera, Robert F. and Qiu, Xueting and Solomon, Isaac H. and Kuo, Hsiao-Hsuan and Boucau, Julie and Bowman, Kathryn and Adhikari, U. Das and Winkler, Marisa L. and Mueller, Al, J. Z. Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. new engl J. Med. February, 2008–2009 (2020).</ref>
 
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<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>
 
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<ref name="Guo_JVirol2022">Guo, H. ''et al''. The Glycan-Binding Trait of the Sarbecovirus Spike N-Terminal Domain Reveals an Evolutionary Footprint. ''J Virol.'' '''96''', e00958-22 (2022)</ref>
 
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<ref name="Hoffmann_MolCell2020">Hoffmann, M., Kleine-Weber, H. & Pöhlmann, S. A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells. ''Mol Cell'' '''78,''' (2020).</ref>
 
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<ref name="Jaimes">Jaimes, J. A., Millet, J. K. & Whittaker, G. R. Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 Site. ''iScience'' '''23,''' 101212 (2020).</ref>
 
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<ref name="Tegally">Tegally, H. ''et al.'' Emergence of SARS-CoV-2 omicron lineages BA.4 and BA.5 in South Africa. ''Nat Med'' '''28,''' 1785–1790 (2022).</ref>
 
 
<ref name="Del Rio">Del Rio, C. & Malani, P. N. COVID-19 in 2022 - The Beginning of the End or the End of the Beginning? ''JAMA'' '''327''', 2389–2390 (2022).</ref>
 
<ref name="Del Rio">Del Rio, C. & Malani, P. N. COVID-19 in 2022 - The Beginning of the End or the End of the Beginning? ''JAMA'' '''327''', 2389–2390 (2022).</ref>
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<ref name="Aggarwal">Aggarwal, A. ''et al''. Mechanistic Insights into the Effects of Key Mutations on SARS-CoV-2 RBD–ACE2 Binding. ''Phys Chem Chem Phys'' '''23''',  26451–26458 (2021)</ref>
 
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<ref name="Callaway">Callaway, E. What Omicron’s BA.4 and BA.5 variants mean for the pandemic. ''Nature'' '''606''', 848–849 (2022).</ref>
 
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<ref name="CaoY_CellHM2022">Cao, Y. ''et al.'' Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. ''Cell Host Microbe'' '''30,''' (2022).</ref>
 
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<ref name="CaoY_Nature2022">Cao, Y. ''et al.'' BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron Infection. ''Nature'' '''608,''' 593–602 (2022).</ref>
 
 
<ref name="CNBC XBB.1.5">Highly immune evasive omicron XBB.1.5 variant is quickly becoming dominant in U.S. as it doubles weekly https://www.cnbc.com/2022/12/30/covid-news-omicron-xbbpoint1point5-is-highly-immune-evasive-and-binds-better-to-cells.html (2023).</ref>
 
<ref name="CNBC XBB.1.5">Highly immune evasive omicron XBB.1.5 variant is quickly becoming dominant in U.S. as it doubles weekly https://www.cnbc.com/2022/12/30/covid-news-omicron-xbbpoint1point5-is-highly-immune-evasive-and-binds-better-to-cells.html (2023).</ref>
 
<ref name="European Centre">European Centre for Disease Prevention and Control: Spread of the SARS-CoV-2 Omicron variant sub-lineage BQ.1 in the EU/EEA https://www.ecdc.europa.eu/sites/default/files/documents/Epi-update-BQ1.pdf (2022).</ref>
 
<ref name="European Centre">European Centre for Disease Prevention and Control: Spread of the SARS-CoV-2 Omicron variant sub-lineage BQ.1 in the EU/EEA https://www.ecdc.europa.eu/sites/default/files/documents/Epi-update-BQ1.pdf (2022).</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,''' 3–20 (2021).</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,''' 3–20 (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,''' 2126–2128 (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,''' 2126–2128 (2021).</ref>
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<ref name="Shaheen">Shaheen, N. ''et al.'' Could the New BA.2.75 Sub-Variant Cause the Emergence of a Global Epidemic of COVID-19? A Scoping Review. ''Infect Drug Resist'' '''15,''' 6317–6330 (2022).</ref>
 
 
<ref name="Wang">Wang, Q. ''et al.'' Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. ''Cell'' '''186,''' (2023).</ref>
 
<ref name="Wang">Wang, Q. ''et al.'' Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. ''Cell'' '''186,''' (2023).</ref>
−
<ref name="WangQ_Nature2022">Wang, Q. ''et al.'' Antibody evasion by SARS-CoV-2 omicron subvariants BA.2.12.1, BA.4 and BA.5. ''Nature'' '''608,''' 603–608 (2022).</ref>
 
−
<ref name="Yamasoba">Yamasoba, D. et al. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. ''Cell'' '''185''', 2103-2115.e19 (2022).</ref>
 
 
</references>
 
</references>
  

Revision as of 04:14, 8 February 2023

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

Spike Glycoprotein

The spike glycoprotein of the severe acute respiratory syndrome coronavirus 2 (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.[1] 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 ~ 1 – 325), a receptor-binding domain (RBD ~ 326 – 525), and 2 C-terminal subdomains (CTD1 and CTD2 ~ 526 – 688), while the downstream S2 region is responsible for mediating virus-host cell membrane fusion.

Update (03/02/2023)

The recently confirmed leading mutations are listed as follows.

2023.01.31

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

2023.01.17 - 2023.01.25

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


Summary

The dynamic epidemiology of coronavirus disease 2019 (COVID-19) since its outbreak has been a result of the continuous evolution of its etiological agent, 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),[2] from which a diverse variant soup is generated.[3] From the BA.1 strain of November 2021, to the BQ.1 strain of October 2022,[4][5] each omicron subvariant has successively proliferated and outcompeted its once dominant antecedent.[6] The emergence of all these variants has assuredly brought along many novel mutations that continues to fine-tune the fitness of the virus,[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, making up of more than 40% of its sequence coverage in early January 2023.[8] The identified leading mutations are listed as follows:

References

  1. ↑ Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat Rev Mol Cell Biol 23, 3–20 (2021).
  2. ↑ Karim, S. S. A. & Karim, Q. A. Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic. Lancet 398, 2126–2128 (2021).
  3. ↑ Callaway, E. COVID ‘variant soup’ is making winter surges hard to predict. Nature 611, 213–214 (2022).
  4. ↑ Wang, Q. et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 186, (2023).
  5. ↑ European Centre for Disease Prevention and Control: Spread of the SARS-CoV-2 Omicron variant sub-lineage BQ.1 in the EU/EEA https://www.ecdc.europa.eu/sites/default/files/documents/Epi-update-BQ1.pdf (2022).
  6. ↑ Del Rio, C. & Malani, P. N. COVID-19 in 2022 - The Beginning of the End or the End of the Beginning? JAMA 327, 2389–2390 (2022).
  7. ↑ Carabelli, A. M. et al. SARS-CoV-2 variant biology: Immune escape, transmission and fitness. Nat Rev Microbiol (2023).
  8. ↑ Highly immune evasive omicron XBB.1.5 variant is quickly becoming dominant in U.S. as it doubles weekly https://www.cnbc.com/2022/12/30/covid-news-omicron-xbbpoint1point5-is-highly-immune-evasive-and-binds-better-to-cells.html (2023).


Map

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