ArticleVirulence2021
Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis.
Article in Virulence, 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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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- A novel Dual-guide CRISPR-Cas13 strategy improves specificity for single-nucleotide variant detection.Nucleic acids research · 2026Article
- Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples.BMC infectious diseases · 2025Article
- Development of a general anti-viral therapeutic using cholestosome technology to exploit inhibition of intracellular viral production.Biochemistry and biophysics reports · 2025Article
- SARS-CoV-2 Omicron subvariant genomic variation associations with immune evasion in Northern California: A retrospective cohort study.PloS one · 2025Article
- Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis.Virology journal · 2024Article
- Time Reveals the Truth! What Treatments for COVID-19 Were Quickly Abandoned, and Which Methods, Contrary to Popular Belief, Are Still Flourishing?Journal of biomedical physics & engineering · 2024Article
- Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins.Computational and structural biotechnology journal · 2024Article
- Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of theMicrobiology spectrum · 2024Article
- Secondary attack rate following on-site isolation of patients with suspected COVID-19 in multiple-bed rooms.Antimicrobial resistance and infection control · 2024Observational
- Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.Nature communications · 2024Article
- Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Genomic Variation Associated With Breakthrough Infection in Northern California: A Retrospective Cohort Study.The Journal of infectious diseases · 2023Article
- Intra- vs. Interhost Evolution of SARS-CoV-2 Driven by Uncorrelated Selection-The Evolution Thwarted.Molecular biology and evolution · 2023Article
- A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center.Antimicrobial resistance and infection control · 2023Article
- Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture.Viruses · 2023Article
- SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.PloS one · 2023Article
- Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences.International journal of molecular sciences · 2022Article
- Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin.International journal of biological macromolecules · 2022Article
- SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic.Microorganisms · 2022Article
- Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia.Frontiers in medicine · 2022Article
- Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data.Briefings in bioinformatics · 2021Article
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Authors and funding
17 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies' composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual's respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a.
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