Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using
            <i>in Silico</i>
            Approach

Boon, Siaw Shi; Xia, Chichao; Wang, Maggie Haitian; Yip, Ka Lai; Luk, Ho Yin; Li, Sile; Ng, Ray Kit; Lai, Christopher K C; Chan, Paul K.S.; Chen, Zigui

doi:10.1128/mbio.02687-21

Cited by 3 publications

(1 citation statement)

References 53 publications

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“…Boon S. et al speculated that N439S, T478S, and N501K mutations gave the virus a chance to infect host cells more efficiently and with low antigenicity. They detected that these mutations allow SARS-Cov2 to enter the host cell easily and make it easier to infect the cell [23].…”

Section: Resultsmentioning

confidence: 99%

Homology Modeling of L18F Mutation on SARS-CoV-2 Spike Protein Receptor-Binding-Domain

KÜÇÜK>

Giritlioğlu

2022

International Journal of Life Sciences and Biotechnology

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Proteinler, birçok yapısal ve fizyolojik sürece katılmak için benzersiz özelliklere sahiptir. Proteinlerin üç boyutlu yapısının bilinmesi, proteinlerin fizyolojik süreçlerdeki rollerini ve bu süreçlerin işlevlerini anlamak için önemlidir. Mutasyonlar nedeniyle proteinlerdeki herhangi bir yapısal bozukluk hastalıklara, tedaviye yanıtsızlığa ve ilaç direnci gelişimine neden olabilir. Son zamanlarda bulaşıcılığı etkileyerek virüsün yayılmasını hızlandıran mutasyonlar içeren yeni SARS-CoV-2 varyantlarının ortaya çıkması endişe kaynağı olmuştur. Çalışmada, mutant tip SARS-CoV-2 spike proteininin oluşumundan sorumlu olan L18F mutasyonunun homoloji modelinin görselleştirilmesi ve kimyasal özelliklerinin in silico yaklaşımla araştırılması amaçlanmıştır. Bu çalışmada amino asit sayısı, moleküler ağırlık, teorik pI değeri, amino asitlerin yüzde bileşimi, toplam negatif yüklü kalıntı sayısı, toplam pozitif yüklü kalıntı sayısı, atom bileşimi, formül, toplam atom numarası, molar yok olma katsayısı, alifatik indeks, ve ortalama hidropati ProtParam aracılığıyla hesaplandı. FASTA amino asit dizisi, vahşi tip ve mutant tip sivri proteinlerde UCSF Chimera aracılığıyla homoloji modellerinin görselleştirilmesi için kullanıldı. Temel kimyasal hesaplamalar da BIOVIA Discovery Studio Visualizer'da görüntülendi. ΔΔG değeri ve L18F mutasyonundaki stabilite değişiklikleri I-Mutant Suite yazılımı ile tahmin edildi. Mutant kalıntının konumunun yüksek oranda korunmuş bir konuma yakın olduğunu ve L18F mutasyonunun hasara neden olmayabileceğini tespit ettik.

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Section: Resultsmentioning

confidence: 99%

Homology Modeling of L18F Mutation on SARS-CoV-2 Spike Protein Receptor-Binding-Domain

KÜÇÜK>

Giritlioğlu

2022

International Journal of Life Sciences and Biotechnology

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A simple risk score for mortality including the PCR Ct value upon admission in patients hospitalized due to COVID-19

et al. 2022

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Purpose To develop a simple score for the outcomes from COVID-19 that integrates information obtained at the time of admission including the Ct value (cycle threshold) for SARS-CoV-2. Methods Patients with COVID-19 hospitalized from February 1st to May 31st 2021 in RoMed hospitals, Germany, were included. Clinical and laboratory parameters upon admission were recorded and patients followed until discharge or death. Logistic regression analysis was used to determine predictors of outcomes. Regression coefficients were used to develop a risk score for death. Results Of 289 patients (46% female, median age 66 years), 29% underwent high-flow nasal oxygen (HFNO) therapy, 28% were admitted to the Intensive Care Unit (ICU, 51% put on invasive ventilation, IV), and 15% died. Age > 70 years, oxygen saturation ≤ 90%, oxygen supply upon admission, eGFR ≤ 60 ml/min and Ct value ≤ 26 were significant ( p < 0.05 each) predictors for death, to which 2, 2, 1, 1 and 2 score points, respectively, could be attributed. Sum scores of ≥ 4 or ≥ 5 points were associated with a sensitivity of 95.0% or 82.5%, and a specificity of 72.5% or 81.7% regarding death. The high predictive value of the score was confirmed using data obtained between December 15th 2020 and January 31st 2021 ( n = 215). Conclusion In COVID-19 patients, a simple scoring system based on data available shortly after hospital admission including the Ct value had a high predictive value for death. The score may also be useful to estimate the likelihood for required interventions at an early stage. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-022-01783-1.

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Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant

Hallak

2022

Commun Biol

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We build statistical models to describe the substitution process in the SARS-CoV-2 as a function of explanatory factors describing the sequence, its function, and more. These models serve two different purposes: first, to gain knowledge about the evolutionary biology of the virus; and second, to predict future mutations in the virus, in particular, non-synonymous amino acid substitutions creating new variants. We use tens of thousands of publicly available SARS-CoV-2 sequences and consider tens of thousands of candidate models. Through a careful validation process, we confirm that our chosen models are indeed able to predict new amino acid substitutions: candidates ranked high by our model are eight times more likely to occur than random amino acid changes. We also show that named variants were highly ranked by our models before their appearance, emphasizing the value of our models for identifying likely variants and potentially utilizing this knowledge in vaccine design and other aspects of the ongoing battle against COVID-19.

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Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach

Abstract: Our study showed the global distribution of SARS-CoV-2 S protein variants from January 2020 to the end of April 2021. We highlighted the key amino acids of S protein subjected to positive selection.

Cited by 3 publications

References 53 publications

Homology Modeling of L18F Mutation on SARS-CoV-2 Spike Protein Receptor-Binding-Domain

Homology Modeling of L18F Mutation on SARS-CoV-2 Spike Protein Receptor-Binding-Domain

A simple risk score for mortality including the PCR Ct value upon admission in patients hospitalized due to COVID-19

Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant

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