ArticleNucleic acids research2022
Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- SARS-CoV-2 intra-host viral diversity associated with host innate and vaccine-induced immunity in an obese mouse model.BMC infectious diseases · 2026Article
- Intra-host variation and transmission dynamics of SARS-CoV-2 Omicron outbreaks in Shandong, China.mSphere · 2025Article
- Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.Journal of virology · 2025Article
- SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues.Journal of virology · 2025Article
- Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines.Nature communications · 2024Article
- Molecular Characterization and Genomic Surveillance of SARS-CoV-2 Lineages in Central India.Viruses · 2024Article
- Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing.Virologica Sinica · 2024Article
- An elusive debate on the evidence for RNA editing in SARS-CoV-2.RNA biology · 2024Article
- Puzzles, challenges, and information reservoir of SARS-CoV-2 quasispecies.Journal of virology · 2023Review
- SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion.mBio · 2023Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.Nature communications · 2023Article
- The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions.Immunoinformatics (Amsterdam, Netherlands) · 2023Review
- 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
- Within-host diversity of SARS-CoV-2 lineages and effect of vaccination.Research square · 2022Article
- Commentary on "Poor evidence for host-dependent regular RNA editing in the transcriptome of SARS-CoV-2".Journal of applied genetics · 2022Article
- Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data.Nature communications · 2022Article
- Heterologous immunity induced by 1Frontiers in immunology · 2022Review
Corrections and comments
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Authors and funding
27 authors at 5 institutions in 1 country.
Funding
Abstract
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.