SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Konings, Frank; Perkins, Mark D.; Kuhn, Jens H.; Pallen, Mark J.; Alm, Erik; Archer, Brett N.; Barakat, Amal; Bedford, Trevor; Bhiman, Jinal N.; Caly, Leon; Carter, Lisa L.; Cullinane, Anne; Oliveira, Túlio de; Druce, Julian; Masry, Ihab El; Evans, Roger; Gao, George F.; Gorbalenya, Alexander E.; Hamblion, Esther; Herring, Belinda L.; Hodcroft, Emma B.; Holmes, Edward C.; Kakkar, Manish; Khare, Shagun; Koopmans, Marion; Korber, Bette; Leite, Juliana Almeida; MacCannell, Duncan; Marklewitz, Marco; Maurer‐Stroh, Sebastian; Rico, Jairo Andrés Méndez; Munster, Vincent J.; Neher, Richard A.; Munnink, Bas B. Oude; Pavlin, Boris I; Peiris, Malik; Poon, L.C.; Pybus, Oliver G.; Rambaut, Andrew; Resende, Paola Cristina; Subissi, Lorenzo; Thiel, Volker; Tong, Suxiang; Werf, Sylvie van der; Gottberg, Anne von; Ziebuhr, John; Kerkhove, Maria D. Van

doi:10.1038/s41564-021-00932-w

Cited by 240 publications

(203 citation statements)

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“…To disassociate variants and country names, a new naming system was recently devised by the World Health Organization (WHO). Under this naming convention, the B.1.1.7 variant, originally identified in the UK, was called alpha, the B.1.351 variant was named beta, and the P.1 variant as gamma [10]. Like other viruses, SARS-CoV-2 mutates and evolves as it replicates.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant

Antony

Vijayan

2021

Biomolecules

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The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has had a significant impact on people’s daily lives. The rapidly spreading B.1.617 lineage harbors two key mutations—L452R and E484Q—in the receptor binding domain (RBD) of its spike (S) protein. To understand the impact and structural dynamics of the variations in the interface of S protein and its host factor, the human angiotensin-converting enzyme 2 (hACE2), triplicate 500 ns molecular dynamics simulations were performed using single (E484Q or L452R) and double (E484Q + L452R) mutant structures and compared to wild type simulations. Our results indicate that the E484Q mutation disrupts the conserved salt bridge formed between Lys31 of hACE2 and Glu484 of S protein. Additionally, E484Q, which could favor the up conformation of the RBD, may help in enhanced hACE2 binding and immune escape. L452R introduces a charged patch near the binding surface that permits increased electrostatic attraction between the proteins. An improved network of intramolecular interactions observed is likely to increase the stability of the S protein and conformational changes may prevent the binding of neutralizing antibodies. The results obtained from the molecular dynamics simulations suggest that structural and dynamic changes introduced by these variations enhance the affinity of the viral S protein to hACE2 and could form the basis for further studies.

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Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant

Antony

Vijayan

2021

Biomolecules

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“…Despite vaccines being in development and in clinical use, social practices will be relevant in the next few years and a clinical exploration to develop novel treatments should be continued for multiple new variants of SARS-CoV-19 that have emerged or emerging, such as the variant identified in the UK, called B.1.1.7 (Alpha), the variant identified in South Africa called B.1.351 (Beta), which emerged independently from B.1.1.7 in Brazil, which is a variant called P.1 (Gamma), the variant B.1.617.2 lineage, first identified in India, which is now called Delta, Delta plus (some places in USA) and the Midwest variant (S Q677H) [169][170][171][172]. In the beginning of 2021, new cases have dropped significantly in the entire nation as people started to get vaccines.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2: Understanding the Transcriptional Regulation of ACE2 and TMPRSS2 and the Role of Single Nucleotide Polymorphism (SNP) at Codon 72 of p53 in the Innate Immune Response against Virus Infection

Lodhi

Singh

Rajput

et al. 2021

IJMS

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Human ACE2 and the serine protease TMPRSS2 of novel SARS-CoV-2 are primary entry receptors in host cells. Expression of these genes at the transcriptional level has not been much discussed in detail. The ISRE elements of the ACE2 promoter are a binding site for the ISGF3 complex of the JAK/STAT signaling pathway. TMPRSS2, including IFNβ, STAT1, and STAT2, has the PARP1 binding site near to TSS either up or downstream promoter region. It is well documented that PARP1 regulates gene expression at the transcription level. Therefore, to curb virus infection, both promoting type I IFN signaling to boost innate immunity and prevention of virus entry by inhibiting PARP1, ACE2 or TMPRSS2 are safe options. Most importantly, our aim is to attract the attention of the global scientific community towards the codon 72 Single Nucleotide Polymorphism (SNP) of p53 and its underneath role in the innate immune response against SARS-CoV-2. Here, we discuss codon 72 SNP of human p53′s role in the different innate immune response to restrict virus-mediated mortality rate only in specific parts of the world. In addition, we discuss potential targets and emerging therapies using bioengineered bacteriophage, anti-sense, or CRISPR strategies.

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“…Over the course of the global pandemic, several SARS-CoV-2 variants have emerged with mutations changing the amino acid sequence of the receptor-binding domain of the spike protein [29]. Three variants of concern; Alpha, Beta, and Gamma [30] were effectively inactivated within 30 seconds by both 0.07% CPC mouthwashes, with a reduction in viral titre below the LOD and equivalent to the 70% ethanol control. As the CPC molecule disrupts the viral lipid envelope and the membrane is unchanged by mutations, our data supports the likely efficacy of CPC mouthwash in reducing viral load irrespective of the SARS-CoV-2 variant.…”

Section: Discussionmentioning

confidence: 99%

Virucidal activity of CPC-containing oral rinses against SARS-CoV-2 variants and are active in the presence of human saliva

Anderson

Patterson

Richards

et al. 2021

Preprint

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The role of human saliva in aerosol-based transmission of SARS-CoV-2 has highlighted the need to understand the potential of oral hygiene products to inactivate the virus. Here we examined the efficacy of mouthwashes containing cetylpyridinium chloride (CPC) or chlorhexidine (CHX) in inactivating SARS-CoV-2. After 30 seconds contact under standard aqueous conditions CPC mouthwashes achieved a ≥4.0log10 PFU/mLreduction in SARS-CoV-2 (USA-WA1/2020) titres whereas comparable products containing CHX achieved <2.0log10 PFU/mL reduction. Further testing with CPC mouthwashes demonstrated efficacy against multiple SARS-CoV-2 variants, with inactivation below the limit of detection observed against the Alpha (B.1.1.7), Beta (B.1.35.1) and Gamma (P.1) variants. Virucidal efficacy of CPC mouthwash was also observed in the presence of human saliva with the product delivering ≥4.0log10 PFU/mL reduction in SARS-CoV-2 titres after 30 seconds providing additional evidence for the virucidal efficacy of CPC mouthwashes under simulated physiological conditions. Together these data suggest CPC-based mouthwashes are effective at inactivating SARS-CoV-2 and further supports the use of mouthwash to mitigate the risk of transmission during dentistry procedures.

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SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

Cited by 240 publications

References 1 publication

Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant

Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant

SARS-CoV-2: Understanding the Transcriptional Regulation of ACE2 and TMPRSS2 and the Role of Single Nucleotide Polymorphism (SNP) at Codon 72 of p53 in the Innate Immune Response against Virus Infection

Virucidal activity of CPC-containing oral rinses against SARS-CoV-2 variants and are active in the presence of human saliva

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