Comparative study: nonsynonymous and synonymous substitution of SARS-CoV-2, SARS-CoV, and MERS-CoV genome

Sohpal, Vipan Kumar

doi:10.5808/gi.20058

Cited by 8 publications

(9 citation statements)

References 19 publications

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“…d) Ti/Tv ratio analysis: Lambda variant was found to have the lowest dN/dS ratio but the highest Ti/Tv ratio. A negative correlation has previously been observed between Ti/Tv ratio and dN/dS ratio under positive selection in the comparative analysis of SARS-CoV, SARS-CoV-2 and MERS-CoV for all the nucleotide substitution models (25). The reason for this could be explained by the fact that Tv substitutions favour dN.…”

Section: Omicron Genome Had Largest Number Of Mutations But Dn/ds Was...mentioning

confidence: 77%

“…The ratio of dN/dS >1 indicates positive selection and has been reported in the S glycoprotein (22,23). Comparative analysis of SARS-CoV, SARS-CoV-2 and MERS-CoV substitution models showed a positive evolution model along with higher dN/dS, due to the dominance of dN (24,25). Studies of mutations in the diagnostic targets in COVID-19 have suggested that the N gene has the highest number of mutations (26,27).…”

Section: Introductionmentioning

confidence: 78%

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Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns

Gupta¹,

Gupta

Bhatnagar

2023

Preprint

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The spread of SARS-CoV-2 virus accompanied by abundance of sequence data available publicly provides a window for determining the spatio-temporal patterns of viral evolution in response to vaccination. In this study, SARS-CoV-2 genome sequences were collected from seven different countries in the period January 2020 to December 2022. The sequences were classified into three categories, namely: pre-vaccination phase, post-vaccination phase and recent period data. Comparison between the three categories was performed based on parameters like mutation rates, selection pressure (dN/dS ratio) and transition to transversion ratios (Ti/Tv). Similar comparisons were also performed amongst SARS-CoV-2 variants. The comparative analysis showed increase in the percent genomic mutation rates after vaccination and in recent period across different countries from the pre-vaccination phase. The dN/dS ratios showed positive selection that increased after vaccination. The Ti/Tv ratios decreased after vaccination, with C→U and G→U being the most frequent transition and transversion in all the countries. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates while Delta showed the highest dN/dS ratio. Mutation rates were highest in NSP3, S, N and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. N, ORF8, ORF3a and ORF10 were under highest positive selection before vaccination. They were overtaken by E, S and NSP1 in the after vaccination as well as recent sequences, with the largest change observed in NSP1. Protein-wise dN/dS ratio was also seen to vary across the different variants.

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Section: Omicron Genome Had Largest Number Of Mutations But Dn/ds Was...mentioning

confidence: 77%

Section: Introductionmentioning

confidence: 78%

Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns

Gupta¹,

Gupta

Bhatnagar

2023

Preprint

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“…Natural selection for immune evasion impedes the functionality of genes: SARS-CoV-2 has accumulated far more nonsynonymous mutations than synonymous mutations, indicating positive selection [65][66][67]. Amino acid substitutions presumably led to rapid diversification early in the pandemic as a result of the virus adapting to the new host species, and immune evasion has been a driving force since 2020 [68].…”

Section: Darwinian Mechanisms That Drive Degeneration Of Genetic Info...mentioning

confidence: 99%

Attenuation and Degeneration of SARS-CoV-2 Despite Adaptive Evolution

Liu¹

2023

Cureus

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The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has followed similar trends as other RNA viruses, such as human immunodeficiency virus type 1 and the influenza A virus. Rapid initial diversification was followed by strong competition and a rapid succession of dominant variants. Hostinitiated RNA editing has been the primary mechanism for introducing mutations. A significant number of mutations detrimental to viral replication have been quickly purged. Fixed mutations are mostly diversifying mutations selected for host adaptation and immune evasion, with the latter accounting for the majority of the mutations. However, immune evasion often comes at the cost of functionality, and thus, optimal functionality is still far from being accomplished. Instead, selection for antibody-escaping variants and accumulation of near-neutral mutations have led to suboptimal codon usage and reduced replicative capacity, as demonstrated in non-respiratory cell lines. Beneficial adaptation of the virus includes reduced infectivity in lung tissues and increased tropism for the upper airway, resulting in shorter incubation periods, milder diseases, and more efficient transmission between people.

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“…The ratio of d N /d S > 1 indicates positive selection and has been reported in the S glycoprotein ( 22 , 23 ). Comparative analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV showed a positive evolution model along with higher d N -d S due to the dominance of d N ( 24 ). Studies of mutations in the diagnostic targets in COVID-19 have suggested that the N gene has the highest number of mutations ( 25 , 26 ).…”

Section: Introductionmentioning

confidence: 97%

Analysis of SARS-CoV-2 genome evolutionary patterns

Gupta,

Bhatnagar

2024

Microbiol Spectr

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The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020–December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (d N /d S ratio), and transition to transversion ratios (T i /T v ). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t -test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The d N /d S ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest d N /d S change was observed in E, NSP1, and NSP13. The T i /T v ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest d N /d S ratio. Protein-wise d N /d S ratio was also seen to vary across the different variants. IMPORTANCE To the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.

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Comparative study: nonsynonymous and synonymous substitution of SARS-CoV-2, SARS-CoV, and MERS-CoV genome

Cited by 8 publications

References 19 publications

Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns

Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns

Attenuation and Degeneration of SARS-CoV-2 Despite Adaptive Evolution

Analysis of SARS-CoV-2 genome evolutionary patterns

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