Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus

Roy, Chayan; Mandal, Santi M.; Mondal, Suresh K.; Mukherjee, S.; Mapder, Tarunendu; Ghosh, Wriddhiman; Chakraborty, Ranadhir

doi:10.1016/j.ygeno.2020.11.003

Cited by 35 publications

(50 citation statements)

References 59 publications

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“…We suppose that a mutation with n transversions happens 4 times less than a mutation with n − 1 transversions. This probability ratio, which is a standard value in the literature [36], has been recently shown to be close to the observed value for SARS-CoV-2 [49]. To include that in our model, consider mutating a codon c to c , one of its synonymous codons.…”

Section: Adding Transition-transversion Bias To Smssupporting

confidence: 72%

The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2

Gioacchino

Šulc

Komarova

et al. 2021

Molecular Biology and Evolution

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COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We characterize CpG content by a CpG force that accounts for statistical constraints acting on the genome at the nucleotidic and amino-acid levels. The CpG force, as the CpG content, is overall low compared to other pathogenic betacoronaviruses; however it widely fluctuates along the genome, with a particularly low value, comparable to the circulating seasonal HKU1, in the spike coding region and a greater value, comparable to SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3’UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the Zinc finger Anti-viral Protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias and the pressure to lower CpG content.

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Section: Adding Transition-transversion Bias To Smssupporting

confidence: 72%

The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2

Gioacchino

Šulc

Komarova

et al. 2021

Molecular Biology and Evolution

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“…Yountet.aland others have shown that ORF3a has been co-evolved with Spike (S) protein, suggesting the possibility of direct or indirect interactions between ORF3a and S protein [10,12,13].Studies in SARS-CoV-infected Caco2 cells show that ORF3a can be efficiently released in detergentresistant membrane structures and the diacidic motif, ExD, located within the domain VI, plays importantrole in membrane co-localisation [14].ORF3a has multi-functional roles including activating NLRP3 inflammasome and NFkB pathway, upregulating fibrinogen secretion, downregulating IFN Type Iand inducing ER stress and pro-apoptotic activity [5,[15][16][17].Therefore, mutations in this protein warrant further study to understand its role in the virulence and immune evasive potential of the recent SARS-CoV-2.Several mutations have been reported in the ORF3a gene and have been classified in the form of clades and subclades.The mutation patterns of ORF3a gene have been characterized as largely nonsynonymous(Q57H, H93Y, R126T, L127I, W128L, L129F, W131C, D155Y,S171L, D173Y, G196V, and G251V). G251V and Q57H exhibit severe virulence property [18][19][20][21].Interestingly, the 57 th position in ORF3a of pangolin SARS-CoV is H. D155Y and S171L mutations were detectedin Indian patients in May 2020 [22]. To understand the functional importance of these mutants, their characterization is needed.…”

Section: Introductionmentioning

confidence: 99%

D155Y Substitution of SARS-CoV-2 ORF3a Weakens Binding with Caveolin-1

Gupta

Mallick

Banerjee

et al. 2021

Preprint

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The clinical manifestation of the recent pandemic COVID-19, caused by novel SARS-CoV-2, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on the severity of the disease, the contribution of mutations in each of the viral genes towards the degree of severity needs to be elucidated for designing better therapeutic approach against COVID-19. Here, we studied the effect of two substitutions D155Y and S171L, of ORF3a protein, found in COVID-19 patients. Using computational simulations we discovered that the substitutions at 155th and 171st positions changed the amino acids involved in salt bridge formation, hydrogen-bond occupancy, interactome clusters, and the stability of the protein. Protein-protein docking using HADDOCK analysis revealed that out of the two observed substitutions, only the substitution of D155Y, weakened the binding affinity of ORF3a with caveolin-1. The increased fluctuation in the simulated ORF3a-caveolin-1 complex suggested a change in the virulence property of SARS-CoV-2.

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“…Apart from bacteria, viral strains too undergo mutations rapidly, thus becoming increasingly resistant to biocides and medication. The same virus that caused the epidemic in China in 2019–2020 mutated over 30 times and has now spread to over 200 countries in the world, where their altered genotype has made them more suited to prevail in varied climatic conditions, worsening the consequences of the pandemic (Helmy et al 2020 ; Dawood 2020 ; Roy et al 2020 ; Paul and Mandal 2019 ; Chen et al 2020 ).…”

Section: Consequences Of Using Indiscriminate Biocides: Future Concermentioning

confidence: 99%

Biologia Futura: use of biocides during COVID-19-global reshuffling of the microbiota

2021

Self Cite

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Aim The article reviews the current usage of biocides during this lockdown period for sanitizing our living areas due to the pandemic and discusses the pros and cons. Subject COVID-19 spread like wildfire to over 200 countries of the world across all continents. The causative agent, novel coronavirus (SARS-CoV-2) is being counter attacked by a thorough application of disinfectants and sterilants. However, the virus mutated over 30 times during this global pandemic, creating panic and leading to enhanced pathogenicity and consequently to more stringent sanitation measures for controlling it. However, excessive use of different types of biocides for disinfecting surfaces is highly alarming in several cases. Extensive application of biocides affects the microbial flora, leading to an abrupt decrease in the number and diversity of beneficial microbes that may directly affect the functioning of nutrient cycles. Results The increased concentration of biocides in agricultural land via surface water or pond water indirectly affect the soil and water ecosystem, soil aggregation and fertility. This will also lead to the flourishing of resistant strains due to loss of competition from the other species, which fail to persist after prolonged use of biocides. Conclusion It is necessary to realize the environmental impacts of biocides and sterilants. It is the right time to stop their entry into the agricultural ecosystem by following adequate management strategies and complete neutralization.

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Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus

Cited by 35 publications

References 59 publications

The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2

The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2

D155Y Substitution of SARS-CoV-2 ORF3a Weakens Binding with Caveolin-1

Biologia Futura: use of biocides during COVID-19-global reshuffling of the microbiota

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