Genomic surveillance unfolds the SARS-CoV-2 transmission and divergence dynamics in Bangladesh

Shishir, Tushar Ahmed; Jannat, Taslimun; Naser, Iftekhar Bin

doi:10.3389/fgene.2022.966939

Cited by 3 publications

(3 citation statements)

References 47 publications

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“…The global d N /d S ratio in the SARS-CoV-2 genome during the pre-vaccination period was calculated as 0.48 ± 0.06, thus indicating a purifying selection pressure. The observed value is similar to previous studies showing that SARS-CoV-2 genome depicts overall purifying selection pressure ( 61 – 63 ) amd study reporting overall SARS-CoV-2 genome dN/dS of around 0.55 ( 61 ). The d N /d S ratio increased to 0.99 ± 0.11 in the post-vaccination period in various demographic regions, suggesting SARS-CoV-2 genomes showing overall neutral selection.…”

Section: Resultssupporting

confidence: 90%

“…A continuous trend of positive selection was identified in S in all the three phases. Previous studies during the year 2020 have identified ORF10 to be under strong positive selection, along with ORF3a, ORF8 and N also depicting much higher number of d N ( 62 , 67 , 68 ). ORF8 is involved in host-pathogen interactions through its nine encoded proteins ( 69 ), ORF3a is involved in interference with host ion channels by encoding viroporin ( 70 ), while overexpression of ORF10 is known to downregulate IFN-1 expression, leading to suppression of the antiviral innate immune response ( 71 ).…”

Section: Resultsmentioning

confidence: 92%

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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: 90%

Section: Resultsmentioning

confidence: 92%

Analysis of SARS-CoV-2 genome evolutionary patterns

Gupta,

Bhatnagar

2024

Microbiol Spectr

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“… 40 Our results corroborates with the findings of the one of the earlier studies from Bangladesh which reported that the AY.122 lineage increased significantly from September 2021 while B.1.617.2 was declining. 41 The 20J clade of Gamma variant and 21D clade of the Eta variant were found to be circulating in Bangladesh for only 2–3 months (March to June, 2021) with relatively lower prevalence (<5.0%) than other clades. The Gamma variant is associated with a higher degree of transmissibility.…”

Section: Discussionmentioning

confidence: 94%

Temporal dynamics and fatality of SARS‐CoV‐2 variants in Bangladesh

Rahman¹,

Hoque

Chowdhury³

et al. 2023

Health Science Reports

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Background and Aims: Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods: We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases.Results: SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in

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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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Genomic surveillance unfolds the SARS-CoV-2 transmission and divergence dynamics in Bangladesh

Cited by 3 publications

References 47 publications

Analysis of SARS-CoV-2 genome evolutionary patterns

Analysis of SARS-CoV-2 genome evolutionary patterns

Temporal dynamics and fatality of SARS‐CoV‐2 variants in Bangladesh

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

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