ArticlePloS one2021
Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- From Energy Deprivation Stress to Catalytic Adaptation of Reductive Dehalogenase TmrA for 1,1-DCA Dechlorination: An Experimental and in Silico Study.Microbial biotechnology · 2026Article
- Evidence of rapid rise in population immunity from SARS-CoV-2 subclinical infections through pre-vaccination serial serosurveys in Pakistan.Journal of global health · 2025Article
- Disparities in age and gender-specific SARS-CoV-2 diagnostic testing trends: a retrospective study from Pakistan.BMC public health · 2024Article
- Risk factors for mortality in hospitalized COVID-19 patients across five waves in Pakistan.Scientific reports · 2024Article
- Shift in SARS-CoV-2 variants of concern from Delta to Omicron was associated with reduced hospitalizations, increased risk of breakthrough infections but lesser disease severity.Journal of infection and public health · 2024Article
- Secondary attack rates and determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) household transmission in Pakistan: A case-ascertained prospective, longitudinal study.Journal of infection and public health · 2024Article
- Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels.Viruses · 2024Article
- Building Research Capacity in Low- and Middle-Income Countries and Pandemic Preparedness: Lessons Learned and Future Directions.The American journal of tropical medicine and hygiene · 2024Article
- Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan.Virology journal · 2024Article
- Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.Nature communications · 2024Article
- Optimal entropic properties of SARS-CoV-2 RNA sequences.Royal Society open science · 2024Article
- Exploring the relationship between SARS-CoV-2 variants, illness severity at presentation, in-hospital mortality and COVID-19 vaccination in a low middle-income country: A retrospective cross-sectional study.Health science reports · 2023Article
- Humoral and T cell responses to SARS-CoV-2 reveal insights into immunity during the early pandemic period in Pakistan.BMC infectious diseases · 2023Article
- Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic.Scientific reports · 2023Article
- Investigating the impact of prior COVID-19 on IgG antibody and interferon γ responses after BBIBP-CorV vaccination in a disease endemic population: A prospective observational study.Health science reports · 2023Article
- Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective.ACS omega · 2023Review
- L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on "neutralist-selectionist" debate.Computers in biology and medicine · 2023Article
- Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study.JMIR bioinformatics and biotechnology · 2022Article
- VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern.Bioinformatics (Oxford, England) · 2022Article
- A fractal scaling analysis of the SARS-CoV-2 genome sequence.Biomedical signal processing and control · 2022Article
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17 authors.
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Abstract
backgroundWe investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. MATERIALS AND
methodsWe studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.
resultsIn March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site.
conclusionsThe higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.
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