ArticleViruses2021
Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples.BMC infectious diseases · 2025Article
- SARS-CoV-2 mutant spectrum complexity is an epidemiologically evolvable trait.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- GENOMICON-Seq enables realistic simulation of amplicon and exome sequencing for low-frequency mutation detection.Scientific reports · 2025Article
- SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues.Journal of virology · 2025Article
- A general and biomedical perspective of viral quasispecies.RNA (New York, N.Y.) · 2025Review
- Impact of Vaccination on Intra-Host Genetic Diversity of Patients Infected with SARS-CoV-2 Gamma Lineage.Viruses · 2024Article
- Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data.NAR genomics and bioinformatics · 2024Article
- Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.Nature communications · 2024Article
- Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak.Virus evolution · 2024Article
- Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater.medRxiv : the preprint server for health sciences · 2023Article
- Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance.Microbial genomics · 2023Article
- Intra- vs. Interhost Evolution of SARS-CoV-2 Driven by Uncorrelated Selection-The Evolution Thwarted.Molecular biology and evolution · 2023Article
- Article
- TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.Virology journal · 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
- Whole-Genome Comparison of Representatives of All Variants of SARS-CoV-2, Including Subvariant BA.2 and the GKA Clade.Advances in virology · 2023Article
- Article
- 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
- Article
- Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.medRxiv : the preprint server for health sciences · 2022Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.
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