First identification of SARS-CoV-2 lambda (C.37) variant in Southern Brazil

Wink, Priscila Lamb; Volpato, Fabiana Caroline Zempulski; Monteiro, Francielle Liz; Willig, Júlia Biz; Zavascki, Alexandre Prehn; Barth, Afonso Luís; Martins, Andreza Francisco

doi:10.1017/ice.2021.390

Cited by 26 publications

(14 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another novel VOI within the lineage B.1.1.1 (also termed as C.37, or Lambda/λ variant) was detected in Peru. It has mutations L452Q and F490S in RBD [13]. The F490S mutation was suspected to be associated with decreased antibody neutralization susceptibility [14].…”

Section: Introductionmentioning

confidence: 99%

Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2

et al. 2022

View full text Add to dashboard Cite

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 continues to mutate. Numerous studies have indicated that this viral mutation, particularly in the receptor-binding domain area, may increase the viral affinity for human angiotensin-converting enzyme 2 (hACE2), the receptor for viral entry into host cells, thereby increasing viral virulence and transmission. In this study, we investigated the binding affinity of SARS-CoV-2 variants (Delta plus, Iota, Kappa, Mu, Lambda, and C.1.2) on hACE2 using computational modeling with a protein-protein docking approach. The simulation results indicated that there were differences in the interactions between the RBD and hACE2, including hydrogen bonding, salt bridge interactions, non-bonded interactions, and binding free energy differences among these variants. Molecular dynamics simulations revealed that mutations in the RBD increase the stability of the hACE2-spike protein complex relative to the wild type, following the global stability trend and increasing the binding affinity. The value of binding-free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) indicated that all mutations in the spike protein increased the contagiousness of SARS-CoV-2 variants. The findings of this study provide a foundation for developing effective interventions against these variants.

show abstract

Section: Introductionmentioning

confidence: 99%

Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Among the Lambda variant mutations, the L452Q mutation was identified, which is similar to the L452R mutation observed in the Delta and Epsilon variants [2]. A new variant of interest in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designated Lambda, has spread in recent months in some South American countries, but its virological and evolutionary features remain unknown.…”

mentioning

confidence: 72%

“…On the basis of genome sequencing, it was estimated that this variant contains 27 mutations (1 in ORF1a — deletion 3675–3677; 7 in the gene encoding protein S — deletion 246–252, G75V, T76I, L452Q, F490S, D614G and T859N as well as 19 other mutations which are observed in various known variants of the SARS-2 coronavirus). Among the Lambda variant mutations, the L452Q mutation was identified, which is similar to the L452R mutation observed in the Delta and Epsilon variants [ 2 ]. A new variant of interest in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designated Lambda, has spread in recent months in some South American countries, but its virological and evolutionary features remain unknown.…”

mentioning

confidence: 88%

Variant lambda of the severe acute respiratory syndrome coronavirus 2: A serious threat or the beginning of further dangerous mutations

et al. 2022

View full text Add to dashboard Cite

show abstract

“…This variant harbors E484K, N501Y, and P681H mutations in the spike protein, while many other new mutations accompany these mutations, including R346K, Y144T, Y145S, and 146N insertion [ 21 ]. Moreover, a novel VOI termed as C.37, or the Lambda/λ variant, reported in Peru with mutations L452Q and F490S in the RBD was suspected to be associated with decreased antibody neutralization susceptibility, particularly due to the F490S mutation in the RBD [ 22 , 23 ]. The Kappa (κ) variant, also known as B.1.617.1, first identified in India, and designated as a VOI, owns a single mutation, that is, L452R, which was suspected to be associated with reduced antibody neutralization by disrupting the respective conformational epitopes [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches

Muhseen

Kadhim

Yahiya

et al. 2021

Biology

View full text Add to dashboard Cite

Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein’s receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2–RBD is affected, we used protein–protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be −122.6 +/− 0.7 kcal/mol, while for B.1.620, the docking score was −124.9 +/− 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of −51.14 kcal/mol, while for B.1.628, the total binding energy was −68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant.

show abstract

First identification of SARS-CoV-2 lambda (C.37) variant in Southern Brazil

Cited by 26 publications

References 3 publications

Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2

Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2

Variant lambda of the severe acute respiratory syndrome coronavirus 2: A serious threat or the beginning of further dangerous mutations

Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches

Contact Info

Product

Resources

About