Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2

Sathipati, Srinivasulu Yerukala; Shukla, Sanjay Kumar; Ho, Shinn-Ying

doi:10.1016/j.isci.2021.103560

Cited by 8 publications

(1 citation statement)

References 82 publications

(71 reference statements)

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“…2 Alterations of the amino acid in the Spike protein influenced the binding affinity and the viral fusion process. 47 Our results showed that D614G mutation occurred in all (100%) Delta and Omicron variants identified in this study, indicating that it was fixed in the viral population. Indeed, all VOCs were generated from the G614 variant lineage.…”

Section: Discussionsupporting

confidence: 52%

Sequence analysis of the Spike, nsp12 (RNA-dependent RNA polymerase), nsp3 (PLpro), and nsp5 (3CLpro) genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

Hakim,

Gunadi,

Rahayu

et al. 2023

Preprint

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During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.

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Section: Discussionsupporting

confidence: 52%

Sequence analysis of the Spike, nsp12 (RNA-dependent RNA polymerase), nsp3 (PLpro), and nsp5 (3CLpro) genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

Hakim,

Gunadi,

Rahayu

et al. 2023

Preprint

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Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV

Shekhawat

Chowdhury

2022

J Biol Phys

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The hydrophobic force is one of the most dominant factors in protein folding. A protein becomes functional only when it achieves its three-dimensional structure and stability upon folding. For a better understanding of the hydrophobic effects and their function in protein folding, quantitative measurement of the hydrophobicity of amino acid side chains is crucial. Spike protein is the primary structural protein in SARS-CoV-2 and SARS-CoV. This study explores how protein sequences in SARS-CoV-2 and SARS-CoV spike proteins encode hydrophobic interactions. Computational tools/techniques have been utilized to investigate the protein sequences of the spike proteins of SARS-CoV-2 and SARS-CoV. Investigations provided an estimate of hydrophobic distribution and its relative strength, indicating a hydrophobic pattern. Analysis of the spike protein's hydrophobic profile may help identify and treat the virus-caused disease; additionally, it can give an insight into the transmissibility and pathogenicity of the virus. Supplementary Information The online version contains supplementary material available at 10.1007/s10867-022-09615-x.

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Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

Hakim,

Gunadi,

Rahayu

et al. 2024

Virus Genes

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Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2

Cited by 8 publications

References 82 publications

Sequence analysis of the Spike, nsp12 (RNA-dependent RNA polymerase), nsp3 (PLpro), and nsp5 (3CLpro) genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

Sequence analysis of the Spike, nsp12 (RNA-dependent RNA polymerase), nsp3 (PLpro), and nsp5 (3CLpro) genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV

Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia

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