Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2

Fang, Zhenhao; Peng, Lei; Lin, Qianqian; Zhou, Liqun; Yang, Luojia; Feng, Yanzhi; Ren, Ping; Renauer, Paul; Park, Jonathan J.; Zhou, Xiaoyu; Wilen, Craig B.; Chen, Sidi

doi:10.1101/2022.03.22.485418

Cited by 4 publications

(2 citation statements)

References 10 publications

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“…NSP13 has also shown strong evidence of positive selection which may be justified due to its role in inhibiting antiviral immunity by hijacking host deubiquitinase USP13 and suppresses type I IFN response through contact with TBK1 ( 64 , 79 ). S has shown continuous strong positive selection in our study in all the three phases as supported by other studies ( 64 , 80 ). NSP1 showed a large jump in the d N /d S ratio with a drastic increase in the number of d N after vaccination.…”

Section: Resultssupporting

confidence: 92%

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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Section: Resultssupporting

confidence: 92%

Analysis of SARS-CoV-2 genome evolutionary patterns

Gupta,

Bhatnagar

2024

Microbiol Spectr

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“…Mutations within E are associated with a reduction in virulence (92,93). S has shown continuous strong positive selection in our study in all the three phases as supported by other studies (48,94).…”

Section: Increase In Selection Pressure On E S and Nsp1 Post-vaccinationsupporting

confidence: 90%

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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