Prediction of infectivity of SARS-CoV2: Mathematical model with analysis of docking simulation for spike proteins and angiotensin-converting enzyme 2

Takaoka, Yutaka; Sugano, Aki; Morinaga, Yoshitomo; Ohta, Mika; Miura, Kenji; Kataguchi, Haruyuki; Kumaoka, Minoru; Kimura, Shigemi; Maniwa, Yoshimasa

doi:10.1016/j.mran.2022.100227

Cited by 7 publications

(23 citation statements)

References 41 publications

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“…The docking affinity of the receptor binding domain (RBD) of each spike protein of these variants with ACE2 was analyzed by docking simulation and cluster analysis as in our previous report (Takaoka et al, 2022). The docking affinity is calculated by the following expression: where A is the average score of the most stable cluster and B is the score of the most stable complex in the docking result.…”

Section: Methodsmentioning

confidence: 99%

“…We used docking simulation and cluster analysis to investigate the docking affinity of the receptor binding domain (RBD) of each variant spike protein with ACE2 (Takaoka et al, 2022). We calculated the docking affinity by means of the following expression: where A is the average score of the most stable cluster and B is the score of the most stable complex in the docking result.…”

Section: Methodsmentioning

confidence: 99%

“…We analyzed the evolutionary distance of S gene between the Wuhan variant and Omicron BA.4/5, or BA.2.75 according to our previous method (Takaoka et al, 2022). The sequences of the S gene were obtained by searching EpiCoV database of GISAID for the one with complete sequence in S gene: Accession IDs for Omicron BA.4/5, EPI_ISL_13410397; BA.2.75, EPI_ISL_13438754 respectively (Elbe et al, 2017;Khare et al, 2021).…”

Section: Determination Of the Evolutionary Distance Between Wuhan Var...mentioning

confidence: 99%

“…In addition, Omicron BA.2.75 was discovered and is thought to present a particular risk inasmuch as it may cause a coming epidemic. We previously constructed a mathematical model to predict the infectivity of SARS-CoV-2 variants—Alpha, Beta, Gamma, Delta, Omicron BA.1and BA.2 as ratio per Wuhan variant (Takaoka et al, 2022). In this research here, we report the predicted risks for Omicron BA.4/5, and BA.2.75 which were recently recognized as being causes of epidemic diseases.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, Omicron BA.2.75 is discovered and concerned as the coming epidemic. We have previously constructed a mathematical model to predict the infectivity of SARS-CoV-2—Wuhan, Alpha, Beta, Gamma, Delta, Omicron BA.1and BA.2 variants (Takaoka et al, 2022). In this research, we report the predicted risk of Omicron BA.4/5, and BA.2.75 which are recently being epidemic, by using our methodology in the previous report (Takaoka et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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SARS-CoV-2 Omicron BA.2.75 variant may be much more infective than preexisting variants

Sugano¹,

Takaoka

Kataguchi

et al. 2022

Preprint

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Objectives: In our previous research, we have reported mathematical model with molecular simulation analysis to predict the infectivity of seven SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 based on our previous research. Methods: We subjected Omicron BA.4/5 or BA.2.75 variant of SARS-CoV-2 to the analysis for the evolutionary distance of the spike protein gene (S gene) to appreciate the changes of the spike protein. We performed the molecular docking simulation analyses of the spike protein with human angiotensin-converting enzyme 2 (ACE2) to understand the docking affinity in these variants. We then compared the evolutionary distance and the docking affinity of these variants with that of the seven variants which were analyzed in our previous research. Results: The evolutionary distance of the S gene in BA.4/5 or BA.2.75 from the Wuhan variant were longer than the other variants. The highest docking affinity of the spike protein with ACE2 (ratio per Wuhan variant) was observed in BA.2.75. Conclusion: It is important to note that BA.2.75 has both the highest docking affinity and the longest evolutionary distance of the S gene. These results suggest that the infection of BA.2.75 can be spread further than preexisting variants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Determination Of the Evolutionary Distance Between Wuhan Var...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

SARS-CoV-2 Omicron BA.2.75 variant may be much more infective than preexisting variants

Sugano¹,

Takaoka

Kataguchi

et al. 2022

Preprint

Self Cite

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Update on the omicron sub‐variants BA.4 and BA.5

Tallei

Alhumaid

AlMusa

et al. 2022

Reviews in Medical Virology

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Several nations have recently begun to relax their public health protocols, particularly regarding the use of face masks when engaging in outdoor activities. This is because there has been a general trend towards fewer cases of coronavirus disease 2019 (COVID‐19). However, new Omicron sub‐variants (designated BA.4 and BA.5) have recently emerged. These two subvariants are thought to be the cause of an increase in COVID‐19 cases in South Africa, the United States, and Europe. They have also begun to spread throughout Asia. They evolved from the Omicron lineage with characteristics that make them even more contagious and which allow them to circumvent immunity from a previous infection or vaccination. This article reviews a number of scientific considerations about these new variants, including their apparently reduced clinical severity.

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Phylogenetic Study of Surface Glycoprotein (S1 Spike Protein) Sequence of SARS-CoV-2 Virus

Upendra,

Nagar,

Preetham

et al. 2024

Lecture Notes in Electrical Engineering

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Prediction of infectivity of SARS-CoV2: Mathematical model with analysis of docking simulation for spike proteins and angiotensin-converting enzyme 2

Cited by 7 publications

References 41 publications

SARS-CoV-2 Omicron BA.2.75 variant may be much more infective than preexisting variants

SARS-CoV-2 Omicron BA.2.75 variant may be much more infective than preexisting variants

Update on the omicron sub‐variants BA.4 and BA.5

Phylogenetic Study of Surface Glycoprotein (S1 Spike Protein) Sequence of SARS-CoV-2 Virus

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