Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world

Weber, Stefanie; Ramirez, Christina M.; Doerfler, Walter

doi:10.1016/j.virusres.2020.198170

Cited by 39 publications

(53 citation statements)

References 16 publications

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“…We have summarised the polymorphism along with respective allele frequencies and amino acid consequences in Figure 1. Weber et al (2020) have interrogated 572 SARS-CoV-2 genomes isolated worldwide and characterised 10 distinct mutation hotspots that have been found in up to 80% of the viral genomes they examined [61]. While our reported variant positions are not 100 % in concordant with these hotspots, some of them display changes on or adjacent to our reported positions.…”

Section: Discussionmentioning

confidence: 49%

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations

Dimonaco

Salavati

Shih

2020

Viruses

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In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international “CoronaHack” in April 2020, we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2; n = 163), bat (bat-CoV; n = 215) and pangolin (pangolin-CoV; n = 7) available in public repositories. We have also noted the pangolin-CoV isolate MP789 to bare stronger resemblance to SARS-CoV-2 than other pangolin-CoV. Following de novo gene annotation prediction, analyses of gene–gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Last, we have characterised several high impact variants (in-frame insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance.

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Section: Discussionmentioning

confidence: 49%

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations

Dimonaco

Salavati

Shih

2020

Viruses

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“…Divergence of immune response might be a repercussion of viral mutations. Namely, several reports result showed that, due to SARS-CoV-2 rapidly spreading across countries, new mutation hotspots are emerging in different parts of the genome, indicating a presence of different viral strains in Europe and Asia, with European strains being more virulent [35][36][37][38]. Also, sex differences in monocyte subsets redistribution are described [39].…”

Section: Plos Onementioning

confidence: 99%

SARS-CoV-2 infection induces mixed M1/M2 phenotype in circulating monocytes and alterations in both dendritic cell and monocyte subsets

et al. 2020

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Clinical manifestations of SARS-CoV-2 infection range from mild to critically severe. The aim of the study was to highlight the immunological events associated with the severity of SARS-CoV-2 infection, with an emphasis on cells of innate immunity. Thirty COVID-19 patients with mild/moderate symptoms and 27 patients with severe/critically severe symptoms were recruited from the Clinical Center of Kragujevac during April 2020. Flow cytometric analysis was performed to reveal phenotypic and functional alterations of peripheral blood cells and to correlate them with the severity of the disease. In severe cases, the number of T and B lymphocytes, dendritic cells, NK cells, and HLA-DR-expressing cells was drastically decreased. In the monocyte population proportion between certain subsets was disturbed and cells coexpressing markers of M1 and M2 monocytes were found in intermediate and non-classical subsets. In mild cases decline in lymphocyte number was less pronounced and innate immunity was preserved as indicated by an increased number of myeloid and activated dendritic cells, NK cells that expressed activation marker at the same level as in control and by low expression of M2 marker in monocyte population. In patients with severe disease, both innate and adoptive immunity are devastated, while in patients with mild symptoms decline in lymphocyte number is lesser, and the innate immunity is preserved.

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“…Researchers aimed too to analyse SARS-CoV-2 proteins modulating host immune response like type I interferon pathways ( Li et al, 2020b ). People have tried to uncover the relation between hotspot mutations and viral pathogenicity ( Weber et al, 2020 ). Some research papers focused on characterizing B and T cell epitopes of certain proteins of SARS-CoV-2 which can help in vaccine development ( Li et al, 2020c ).…”

Section: Introductionmentioning

confidence: 99%

Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs

Sengupta

Hassan²,

Choudhury

2021

Infection, Genetics and Evolution

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Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world

Cited by 39 publications

References 16 publications

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations

SARS-CoV-2 infection induces mixed M1/M2 phenotype in circulating monocytes and alterations in both dendritic cell and monocyte subsets

Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs

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