Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage

Zhang, Jiahao; Fan, Linqian; Xu, Haolin; Fu, Yuan-Hui; Xu, Peng; Zheng, Yan-Peng; Yu, Jie-mei; He, Jinsheng

doi:10.3390/v14102296

Cited by 6 publications

(10 citation statements)

References 52 publications

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“…The C to U bias was also found in other variants of SARS-CoV-2 [ 16 , 26 ]. It was revealed that the proportion of the C to U transition for the Delta variant in different regions was about 36% [ 16 ]. However, we found that its proportion for Omicron in Oceania and Asia was also approximately 36%, but in North America, South America, and Europe, the proportions exceeded 41%, and in Africa it was only 32%.…”

Section: Discussionmentioning

confidence: 73%

“…The tendency of mutation biases and context preferences suggested the contribution of the APOBEC, as APOBEC cytosine deaminase enzyme could cause transition of C to U [25]. The C to U bias was also found in other variants of SARS-CoV-2 [16,26]. It was revealed that the proportion of the C to U transition for the Delta variant in different regions was about 36% [16].…”

Section: Discussionmentioning

confidence: 92%

“…SNP calling is important for understanding the genetic variations of the virus. Our previous studies have shown that the Delta variant had a much greater genetic diversity at early stage than at later stage [ 16 , 22 ]. The present study revealed that the Omicron genome harbored fewer SNPs than Delta, it was less diversified, and the number of SNPs varied little among continents, indicating that the virus had a good fitness to humans since its emergence.…”

Section: Discussionmentioning

confidence: 99%

“…It is important to detect co-occurring mutations to study the cooperative manner of different genes at the genetic level [ 31 , 32 ]. Our previous study had shown that a linkage involving 10 SNPs existed on the genome of the Delta variant [ 16 ]. In this study, four linkages were detected on the Omicron variant, among which linkage I occurred at a sharply increasing frequency over time and contained a much higher number of SNPs, which was 38, than that of the Delta variant.…”

Section: Discussionmentioning

confidence: 99%

“…For the whole SARS-CoV-2 Omicron genomes, the single nucleotide polymorphisms (SNPs) calling and SNP-linkage analysis were developed, and the compiled R codes were deposited in Github as previously described [ 16 ]. Data was analyzed with GraphPad Prism (version 8.0.2).…”

Section: Methodsmentioning

confidence: 99%

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Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found

Zheng

Zhang

Liu

et al. 2023

Viruses

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The Omicron variant is currently ravaging the world, raising serious concern globally. Monitoring genomic variations and determining their influence on biological features are critical for tracing its ongoing transmission and facilitating effective measures. Based on large-scale sequences from different continents, this study found that: (i) The genetic diversity of Omicron is much lower than that of the Delta variant. Still, eight deletions (Del 1–8) and 1 insertion, as well as 130 SNPs, were detected on the Omicron genomes, with two deletions (Del 3 and 4) and 38 SNPs commonly detected on all continents and exhibiting high-occurring frequencies. (ii) Four groups of tightly linked SNPs (linkage I–IV) were detected, among which linkage I, containing 38 SNPs, with 6 located in the RBD, increased its occurring frequency remarkably over time. (iii) The third codons of the Omicron shouldered the most mutation pressures, while the second codons presented the least flexibility. (iv) Four major mutants with amino acid substitutions in the RBD were detected, and further structural analysis suggested that the substitutions did not alter the viral receptor binding ability greatly. It was inferred that though the Omicron genome harbored great changes in antigenicity and remarkable ability to evade immunity, it was immune-pressure selected. This study tracked mutational signatures of Omicron variant and the potential biological significance of the SNPs, and the linkages await further functional verification.

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Section: Discussionmentioning

confidence: 73%

Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found

Zheng

Zhang

Liu

et al. 2023

Viruses

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Bridging Computational Predictions and Empirical Data: Insights into SARS-CoV-2 Mutational Impacts and Evolution

Shaukat,

Nguyen,

Hsu

et al. 2024

Preprint

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The emergence of SARS-CoV-2 has unleashed a global health crisis, demanding advanced research into its genomic mutations and their consequences. Our study combines computational models and empirical validation to predict the effects of these mutations, aiming to understand their impact on the virus's behaviour, including its transmissibility and immune escape mechanisms. Utilising advanced prediction tools, we analysed mutations across the virus's genome, focusing on changes to both structural and non-structural proteins. This approach identified key mutations likely to influence protein functionality and the virus's evolution. Our findings, integrating computational predictions with real-world data, offer insights into SARS-CoV-2's evolutionary path and its implications for developing vaccines and therapies. We highlight the necessity of ongoing genomic surveillance and the combined use of computational and empirical methods to stay ahead of viral mutations. This study not only deepens our understanding of SARS-CoV-2 but also lays groundwork for future research on viral evolution and pandemic response strategies, emphasizing our approach's potential to inform public health decisions and research priorities.

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Global lineage evolution pattern of sars-cov-2 in Africa, America, Europe, and Asia: A comparative analysis of variant clusters and their relevance across continents

Hyug Choi,

Sook Jun,

Yong Jeon

et al. 2023

Journal of Translational Internal Medicine

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Objective The objective of this study is to provide a comparative analysis of variant clusters and their relevance across Africa, America, Europe, and Asia, in order to understand the evolutionary patterns of the virus across different regions and to inform the development of targeted interventions and genomic surveillance eforts. Methods The study analyzed the global lineage evolution pattern of 74, 075 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 32 countries across four continents, focusing on variant clusters and their relevance across regions. Variants were weighted according to their hierarchical level. The correlation between variants was visualized through Dimensionality reduction analysis and Pairwise Pearson's correlation. We presented a reconstructed phylogenetic tree based on correlation analysis and variant weights. Results The analysis revealed that each continent had distinct variant clusters and different evolutionary patterns. The Americas had two clustered variants before lineage divergence and a downstream confluence lineage, Europe had bifurcation into two global lineages with an early occurrence of certain cluster while Asia had a downstream confluence of two large lineages diverging by two distinct clusters. Based on the cluster patterns of shared variants of the SARS-CoV-2 virus, Africa demonstrated a relatively clear distinction among three distinct regions. Conclusions The study provides insights into the evolutionary patterns of SARS-CoV-2 and highlights the importance of international collaboration in tracking and responding to emerging variants. The study found that the global pandemic was driven by Omicron variants that evolved with significant differences between countries and regions, and with different patterns across continents.

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Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage

Cited by 6 publications

References 52 publications

Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found

Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found

Bridging Computational Predictions and Empirical Data: Insights into SARS-CoV-2 Mutational Impacts and Evolution

Global lineage evolution pattern of sars-cov-2 in Africa, America, Europe, and Asia: A comparative analysis of variant clusters and their relevance across continents

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